Starting phenix.real_space_refine
on Thu Mar  5 06:51:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6u86_20678/03_2026/6u86_20678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6u86_20678/03_2026/6u86_20678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6u86_20678/03_2026/6u86_20678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6u86_20678/03_2026/6u86_20678.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6u86_20678/03_2026/6u86_20678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6u86_20678/03_2026/6u86_20678.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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     116      5.16       5
     C   13180      2.51       5
     N    3384      2.21       5
     O    3460      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 148 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 20140
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 618, 5035
          Classifications: {'peptide': 618}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 594}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 17
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 4.65, per 1000 atoms: 0.23
  Number of scatterers: 20140
  At special positions: 0
  Unit cell: (138.86, 138.86, 111.3, 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     116     16.00
     O    3460      8.00
     N    3384      7.00
     C   13180      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.83
  Conformation dependent library (CDL) restraints added in 878.0 milliseconds
  

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4680

  Finding SS restraints...
    Secondary structure from input PDB file:
      120 helices and 4 sheets defined
      64.2% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 87
    Processing helix  chain 'A' and resid 89 through 93
    Processing helix  chain 'A' and resid 94 through 103
    Processing helix  chain 'A' and resid 119 through 127
      removed outlier: 3.686A  pdb=" N   LYS A 123 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 147
      removed outlier: 3.642A  pdb=" N   LEU A 139 " --> pdb=" O   CYS A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 174
      removed outlier: 3.960A  pdb=" N   ILE A 170 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 185
      removed outlier: 3.581A  pdb=" N   LEU A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 219
    Processing helix  chain 'A' and resid 222 through 231
      removed outlier: 3.509A  pdb=" N   VAL A 226 " --> pdb=" O   GLN A 222 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR A 228 " --> pdb=" O   ASP A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 257
    Processing helix  chain 'A' and resid 260 through 282
    Processing helix  chain 'A' and resid 297 through 306
    Processing helix  chain 'A' and resid 308 through 316
      removed outlier: 3.625A  pdb=" N   HIS A 313 " --> pdb=" O   GLU A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 327
    Processing helix  chain 'A' and resid 355 through 362
    Processing helix  chain 'A' and resid 366 through 368
      No H-bonds generated for 'chain 'A' and resid 366 through 368'
    Processing helix  chain 'A' and resid 369 through 374
      removed outlier: 3.966A  pdb=" N   VAL A 373 " --> pdb=" O   ARG A 369 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL A 374 " --> pdb=" O   HIS A 370 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 369 through 374'
    Processing helix  chain 'A' and resid 377 through 414
      removed outlier: 5.639A  pdb=" N   SER A 391 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   ARG A 392 " --> pdb=" O   ARG A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 459
    Processing helix  chain 'A' and resid 461 through 466
    Processing helix  chain 'A' and resid 470 through 492
      removed outlier: 3.540A  pdb=" N   ILE A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU A 477 " --> pdb=" O   GLU A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 512
      removed outlier: 3.612A  pdb=" N   LEU A 500 " --> pdb=" O   TRP A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 517
      removed outlier: 4.150A  pdb=" N   ARG A 517 " --> pdb=" O   TYR A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 532
      removed outlier: 4.167A  pdb=" N   MET A 528 " --> pdb=" O   ILE A 524 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE A 529 " --> pdb=" O   TYR A 525 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A 532 " --> pdb=" O   MET A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 561
      removed outlier: 4.597A  pdb=" N   LEU A 542 " --> pdb=" O   LEU A 538 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   VAL A 543 " --> pdb=" O   ARG A 539 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE A 551 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   GLU A 561 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 606
    Processing helix  chain 'A' and resid 618 through 646
      removed outlier: 3.658A  pdb=" N   VAL A 622 " --> pdb=" O   PHE A 618 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 651
      removed outlier: 3.613A  pdb=" N   ASN A 650 " --> pdb=" O   GLU A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 673
      removed outlier: 4.194A  pdb=" N   SER A 658 " --> pdb=" O   ASP A 654 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ASN A 673 " --> pdb=" O   LEU A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 719
    Processing helix  chain 'B' and resid 76 through 87
    Processing helix  chain 'B' and resid 89 through 93
    Processing helix  chain 'B' and resid 94 through 103
    Processing helix  chain 'B' and resid 119 through 127
      removed outlier: 3.686A  pdb=" N   LYS B 123 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 147
      removed outlier: 3.642A  pdb=" N   LEU B 139 " --> pdb=" O   CYS B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 174
      removed outlier: 3.960A  pdb=" N   ILE B 170 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 185
      removed outlier: 3.580A  pdb=" N   LEU B 182 " --> pdb=" O   GLN B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 219
    Processing helix  chain 'B' and resid 222 through 231
      removed outlier: 3.509A  pdb=" N   VAL B 226 " --> pdb=" O   GLN B 222 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 257
    Processing helix  chain 'B' and resid 260 through 282
    Processing helix  chain 'B' and resid 297 through 306
    Processing helix  chain 'B' and resid 308 through 316
      removed outlier: 3.625A  pdb=" N   HIS B 313 " --> pdb=" O   GLU B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 327
    Processing helix  chain 'B' and resid 355 through 362
    Processing helix  chain 'B' and resid 366 through 368
      No H-bonds generated for 'chain 'B' and resid 366 through 368'
    Processing helix  chain 'B' and resid 369 through 374
      removed outlier: 3.967A  pdb=" N   VAL B 373 " --> pdb=" O   ARG B 369 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL B 374 " --> pdb=" O   HIS B 370 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 369 through 374'
    Processing helix  chain 'B' and resid 377 through 414
      removed outlier: 5.639A  pdb=" N   SER B 391 " --> pdb=" O   ASP B 387 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   ARG B 392 " --> pdb=" O   ARG B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 459
    Processing helix  chain 'B' and resid 461 through 466
    Processing helix  chain 'B' and resid 470 through 492
      removed outlier: 3.541A  pdb=" N   ILE B 474 " --> pdb=" O   SER B 470 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU B 477 " --> pdb=" O   GLU B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 512
      removed outlier: 3.613A  pdb=" N   LEU B 500 " --> pdb=" O   TRP B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 517
      removed outlier: 4.150A  pdb=" N   ARG B 517 " --> pdb=" O   TYR B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 532
      removed outlier: 4.167A  pdb=" N   MET B 528 " --> pdb=" O   ILE B 524 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ILE B 529 " --> pdb=" O   TYR B 525 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL B 532 " --> pdb=" O   MET B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 561
      removed outlier: 4.597A  pdb=" N   LEU B 542 " --> pdb=" O   LEU B 538 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   VAL B 543 " --> pdb=" O   ARG B 539 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE B 551 " --> pdb=" O   PHE B 547 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   GLU B 561 " --> pdb=" O   SER B 557 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 592 through 606
    Processing helix  chain 'B' and resid 618 through 646
      removed outlier: 3.658A  pdb=" N   VAL B 622 " --> pdb=" O   PHE B 618 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 651
      removed outlier: 3.613A  pdb=" N   ASN B 650 " --> pdb=" O   GLU B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 673
      removed outlier: 4.194A  pdb=" N   SER B 658 " --> pdb=" O   ASP B 654 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ASN B 673 " --> pdb=" O   LEU B 669 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 711 through 719
    Processing helix  chain 'C' and resid 76 through 87
    Processing helix  chain 'C' and resid 89 through 93
    Processing helix  chain 'C' and resid 94 through 103
    Processing helix  chain 'C' and resid 119 through 127
      removed outlier: 3.686A  pdb=" N   LYS C 123 " --> pdb=" O   THR C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 147
      removed outlier: 3.642A  pdb=" N   LEU C 139 " --> pdb=" O   CYS C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 174
      removed outlier: 3.960A  pdb=" N   ILE C 170 " --> pdb=" O   SER C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 185
      removed outlier: 3.581A  pdb=" N   LEU C 182 " --> pdb=" O   GLN C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 219
    Processing helix  chain 'C' and resid 222 through 231
      removed outlier: 3.509A  pdb=" N   VAL C 226 " --> pdb=" O   GLN C 222 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR C 228 " --> pdb=" O   ASP C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 257
    Processing helix  chain 'C' and resid 260 through 282
    Processing helix  chain 'C' and resid 297 through 306
    Processing helix  chain 'C' and resid 308 through 316
      removed outlier: 3.625A  pdb=" N   HIS C 313 " --> pdb=" O   GLU C 309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 327
    Processing helix  chain 'C' and resid 355 through 362
    Processing helix  chain 'C' and resid 366 through 368
      No H-bonds generated for 'chain 'C' and resid 366 through 368'
    Processing helix  chain 'C' and resid 369 through 374
      removed outlier: 3.966A  pdb=" N   VAL C 373 " --> pdb=" O   ARG C 369 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   VAL C 374 " --> pdb=" O   HIS C 370 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 369 through 374'
    Processing helix  chain 'C' and resid 377 through 414
      removed outlier: 5.639A  pdb=" N   SER C 391 " --> pdb=" O   ASP C 387 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   ARG C 392 " --> pdb=" O   ARG C 388 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 430 through 459
    Processing helix  chain 'C' and resid 461 through 466
    Processing helix  chain 'C' and resid 470 through 492
      removed outlier: 3.540A  pdb=" N   ILE C 474 " --> pdb=" O   SER C 470 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU C 477 " --> pdb=" O   GLU C 473 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 512
      removed outlier: 3.612A  pdb=" N   LEU C 500 " --> pdb=" O   TRP C 496 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 513 through 517
      removed outlier: 4.150A  pdb=" N   ARG C 517 " --> pdb=" O   TYR C 514 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 521 through 532
      removed outlier: 4.167A  pdb=" N   MET C 528 " --> pdb=" O   ILE C 524 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE C 529 " --> pdb=" O   TYR C 525 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL C 532 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 534 through 561
      removed outlier: 4.596A  pdb=" N   LEU C 542 " --> pdb=" O   LEU C 538 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   VAL C 543 " --> pdb=" O   ARG C 539 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   PHE C 551 " --> pdb=" O   PHE C 547 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   GLU C 561 " --> pdb=" O   SER C 557 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 592 through 606
    Processing helix  chain 'C' and resid 618 through 646
      removed outlier: 3.658A  pdb=" N   VAL C 622 " --> pdb=" O   PHE C 618 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 647 through 651
      removed outlier: 3.612A  pdb=" N   ASN C 650 " --> pdb=" O   GLU C 647 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 654 through 673
      removed outlier: 4.193A  pdb=" N   SER C 658 " --> pdb=" O   ASP C 654 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ASN C 673 " --> pdb=" O   LEU C 669 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 711 through 719
    Processing helix  chain 'D' and resid 76 through 87
    Processing helix  chain 'D' and resid 89 through 93
    Processing helix  chain 'D' and resid 94 through 103
    Processing helix  chain 'D' and resid 119 through 127
      removed outlier: 3.686A  pdb=" N   LYS D 123 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 147
      removed outlier: 3.642A  pdb=" N   LEU D 139 " --> pdb=" O   CYS D 135 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 174
      removed outlier: 3.960A  pdb=" N   ILE D 170 " --> pdb=" O   SER D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 176 through 185
      removed outlier: 3.582A  pdb=" N   LEU D 182 " --> pdb=" O   GLN D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 212 through 219
    Processing helix  chain 'D' and resid 222 through 231
      removed outlier: 3.510A  pdb=" N   VAL D 226 " --> pdb=" O   GLN D 222 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR D 228 " --> pdb=" O   ASP D 224 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 248 through 257
    Processing helix  chain 'D' and resid 260 through 282
    Processing helix  chain 'D' and resid 297 through 306
    Processing helix  chain 'D' and resid 308 through 316
      removed outlier: 3.624A  pdb=" N   HIS D 313 " --> pdb=" O   GLU D 309 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 323 through 327
    Processing helix  chain 'D' and resid 355 through 362
    Processing helix  chain 'D' and resid 366 through 368
      No H-bonds generated for 'chain 'D' and resid 366 through 368'
    Processing helix  chain 'D' and resid 369 through 374
      removed outlier: 3.967A  pdb=" N   VAL D 373 " --> pdb=" O   ARG D 369 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   VAL D 374 " --> pdb=" O   HIS D 370 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 369 through 374'
    Processing helix  chain 'D' and resid 377 through 414
      removed outlier: 5.639A  pdb=" N   SER D 391 " --> pdb=" O   ASP D 387 " (cutoff:3.500A)
      removed outlier: 5.648A  pdb=" N   ARG D 392 " --> pdb=" O   ARG D 388 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 430 through 459
    Processing helix  chain 'D' and resid 461 through 466
    Processing helix  chain 'D' and resid 470 through 492
      removed outlier: 3.541A  pdb=" N   ILE D 474 " --> pdb=" O   SER D 470 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU D 477 " --> pdb=" O   GLU D 473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 496 through 512
      removed outlier: 3.612A  pdb=" N   LEU D 500 " --> pdb=" O   TRP D 496 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 513 through 517
      removed outlier: 4.150A  pdb=" N   ARG D 517 " --> pdb=" O   TYR D 514 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 532
      removed outlier: 4.167A  pdb=" N   MET D 528 " --> pdb=" O   ILE D 524 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ILE D 529 " --> pdb=" O   TYR D 525 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL D 532 " --> pdb=" O   MET D 528 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 534 through 561
      removed outlier: 4.596A  pdb=" N   LEU D 542 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   VAL D 543 " --> pdb=" O   ARG D 539 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE D 551 " --> pdb=" O   PHE D 547 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   GLU D 561 " --> pdb=" O   SER D 557 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 592 through 606
    Processing helix  chain 'D' and resid 618 through 646
      removed outlier: 3.659A  pdb=" N   VAL D 622 " --> pdb=" O   PHE D 618 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 647 through 651
      removed outlier: 3.614A  pdb=" N   ASN D 650 " --> pdb=" O   GLU D 647 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 654 through 673
      removed outlier: 4.194A  pdb=" N   SER D 658 " --> pdb=" O   ASP D 654 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ASN D 673 " --> pdb=" O   LEU D 669 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 711 through 719
    Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335
      removed outlier: 6.697A  pdb=" N   LYS A 329 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ASP A 344 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   THR A 331 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU A 342 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLU A 709 " --> pdb=" O   ARG A 339 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   SER A 341 " --> pdb=" O   VAL A 707 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL A 707 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG A 702 " --> pdb=" O   LEU A 689 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU A 689 " --> pdb=" O   ARG A 702 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335
      removed outlier: 6.697A  pdb=" N   LYS B 329 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ASP B 344 " --> pdb=" O   LYS B 329 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   THR B 331 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU B 342 " --> pdb=" O   THR B 331 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLU B 709 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   SER B 341 " --> pdb=" O   VAL B 707 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL B 707 " --> pdb=" O   SER B 341 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG B 702 " --> pdb=" O   LEU B 689 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU B 689 " --> pdb=" O   ARG B 702 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335
      removed outlier: 6.697A  pdb=" N   LYS C 329 " --> pdb=" O   ASP C 344 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ASP C 344 " --> pdb=" O   LYS C 329 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   THR C 331 " --> pdb=" O   LEU C 342 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU C 342 " --> pdb=" O   THR C 331 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLU C 709 " --> pdb=" O   ARG C 339 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   SER C 341 " --> pdb=" O   VAL C 707 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL C 707 " --> pdb=" O   SER C 341 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG C 702 " --> pdb=" O   LEU C 689 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU C 689 " --> pdb=" O   ARG C 702 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335
      removed outlier: 6.698A  pdb=" N   LYS D 329 " --> pdb=" O   ASP D 344 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ASP D 344 " --> pdb=" O   LYS D 329 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   THR D 331 " --> pdb=" O   LEU D 342 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU D 342 " --> pdb=" O   THR D 331 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   GLU D 709 " --> pdb=" O   ARG D 339 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   SER D 341 " --> pdb=" O   VAL D 707 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   VAL D 707 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ARG D 702 " --> pdb=" O   LEU D 689 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU D 689 " --> pdb=" O   ARG D 702 " (cutoff:3.500A)

    1060 hydrogen bonds defined for protein.
    3084 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: 3.06

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6304
        1.34 -     1.46: 4308
        1.46 -     1.57: 9860
        1.57 -     1.69: 0
        1.69 -     1.81: 180
  Bond restraints: 20652
  Sorted by residual:
  bond pdb=" CB  PRO B 377 "
       pdb=" CG  PRO B 377 "
    ideal  model  delta    sigma   weight residual
    1.506  1.450  0.056 3.90e-02 6.57e+02 2.05e+00
  bond pdb=" CB  PRO C 377 "
       pdb=" CG  PRO C 377 "
    ideal  model  delta    sigma   weight residual
    1.506  1.450  0.056 3.90e-02 6.57e+02 2.05e+00
  bond pdb=" CB  PRO A 377 "
       pdb=" CG  PRO A 377 "
    ideal  model  delta    sigma   weight residual
    1.506  1.450  0.056 3.90e-02 6.57e+02 2.05e+00
  bond pdb=" CB  PRO D 377 "
       pdb=" CG  PRO D 377 "
    ideal  model  delta    sigma   weight residual
    1.506  1.451  0.055 3.90e-02 6.57e+02 2.00e+00
  bond pdb=" CG  LEU B 253 "
       pdb=" CD2 LEU B 253 "
    ideal  model  delta    sigma   weight residual
    1.521  1.481  0.040 3.30e-02 9.18e+02 1.50e+00
  ... (remaining 20647 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 25829
        1.13 -     2.25: 1840
        2.25 -     3.38: 246
        3.38 -     4.51: 65
        4.51 -     5.63: 28
  Bond angle restraints: 28008
  Sorted by residual:
  angle pdb=" N   LEU C 513 "
        pdb=" CA  LEU C 513 "
        pdb=" C   LEU C 513 "
      ideal   model   delta    sigma   weight residual
     114.64  110.87    3.77 1.52e+00 4.33e-01 6.14e+00
  angle pdb=" N   LEU B 513 "
        pdb=" CA  LEU B 513 "
        pdb=" C   LEU B 513 "
      ideal   model   delta    sigma   weight residual
     114.64  110.88    3.76 1.52e+00 4.33e-01 6.12e+00
  angle pdb=" N   LEU D 513 "
        pdb=" CA  LEU D 513 "
        pdb=" C   LEU D 513 "
      ideal   model   delta    sigma   weight residual
     114.64  110.88    3.76 1.52e+00 4.33e-01 6.12e+00
  angle pdb=" N   LEU A 513 "
        pdb=" CA  LEU A 513 "
        pdb=" C   LEU A 513 "
      ideal   model   delta    sigma   weight residual
     114.64  110.90    3.74 1.52e+00 4.33e-01 6.05e+00
  angle pdb=" CA  LEU D 498 "
        pdb=" C   LEU D 498 "
        pdb=" N   PRO D 499 "
      ideal   model   delta    sigma   weight residual
     120.81  118.94    1.87 8.60e-01 1.35e+00 4.71e+00
  ... (remaining 28003 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 10924
       17.58 -    35.16: 1046
       35.16 -    52.75: 154
       52.75 -    70.33: 12
       70.33 -    87.91: 12
  Dihedral angle restraints: 12148
    sinusoidal: 4916
      harmonic: 7232
  Sorted by residual:
  dihedral pdb=" CA  LEU C 534 "
           pdb=" C   LEU C 534 "
           pdb=" N   ARG C 535 "
           pdb=" CA  ARG C 535 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.78   22.22     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  LEU D 534 "
           pdb=" C   LEU D 534 "
           pdb=" N   ARG D 535 "
           pdb=" CA  ARG D 535 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.79   22.21     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  LEU A 534 "
           pdb=" C   LEU A 534 "
           pdb=" N   ARG A 535 "
           pdb=" CA  ARG A 535 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.80   22.20     0      5.00e+00 4.00e-02 1.97e+01
  ... (remaining 12145 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1801
       0.028 -    0.056: 850
       0.056 -    0.084: 349
       0.084 -    0.112: 123
       0.112 -    0.140: 17
  Chirality restraints: 3140
  Sorted by residual:
  chirality pdb=" CA  GLN C 520 "
            pdb=" N   GLN C 520 "
            pdb=" C   GLN C 520 "
            pdb=" CB  GLN C 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.88e-01
  chirality pdb=" CA  GLN D 520 "
            pdb=" N   GLN D 520 "
            pdb=" C   GLN D 520 "
            pdb=" CB  GLN D 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CA  GLN A 520 "
            pdb=" N   GLN A 520 "
            pdb=" C   GLN A 520 "
            pdb=" CB  GLN A 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 3137 not shown)

  Planarity restraints: 3468
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  99 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.24e+00
        pdb=" C   LEU A  99 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LEU A  99 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A 100 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU D  99 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.19e+00
        pdb=" C   LEU D  99 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   LEU D  99 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG D 100 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  99 "   -0.015 2.00e-02 2.50e+03   3.03e-02 9.17e+00
        pdb=" C   LEU C  99 "    0.052 2.00e-02 2.50e+03
        pdb=" O   LEU C  99 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   ARG C 100 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 3465 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 2293
        2.74 -     3.28: 22154
        3.28 -     3.82: 32317
        3.82 -     4.36: 37178
        4.36 -     4.90: 62184
  Nonbonded interactions: 156126
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 159 "
            pdb=" N   GLU A 160 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" OD1 ASP B 159 "
            pdb=" N   GLU B 160 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OD1 ASP C 159 "
            pdb=" N   GLU C 160 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OD1 ASP D 159 "
            pdb=" N   GLU D 160 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   LEU D 513 "
            pdb=" OG1 THR D 516 "
     model   vdw
     2.237 3.040
  ... (remaining 156121 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             1.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     17.420
  Find NCS groups from input model:        0.160
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
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      :  0.007   0.056  20652  Z= 0.284
  Angle     :  0.664   5.634  28008  Z= 0.375
  Chirality :  0.039   0.140   3140
  Planarity :  0.004   0.035   3468
  Dihedral  : 13.343  87.911   7468
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.30 %
    Favored  : 96.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -3.88 (0.14), residues: 2432
  helix: -2.06 (0.11), residues: 1488
  sheet:  None (None), residues: 0
  loop : -3.30 (0.17), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 684 
 TYR   0.013   0.002   TYR B 514 
 PHE   0.016   0.002   PHE D 705 
 TRP   0.019   0.002   TRP C 715 
 HIS   0.008   0.002   HIS C 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00672 (20652)
  covalent geometry    : angle       0.66371 (28008)
  hydrogen bonds       : bond        0.13174 ( 1060)
  hydrogen bonds       : angle       6.51099 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  514 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 510
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 TYR cc_start: 0.8789 (m-80) cc_final: 0.8483 (m-80)
REVERT: A  487 GLN cc_start: 0.8905 (mm-40) cc_final: 0.8456 (mm-40)
REVERT: A  507 LEU cc_start: 0.8873 (mt) cc_final: 0.8432 (mm)
REVERT: A  511 ASN cc_start: 0.8127 (m-40) cc_final: 0.7781 (m-40)
REVERT: A  591 ARG cc_start: 0.8513 (tpp-160) cc_final: 0.8303 (tpp80)
REVERT: B  162 TYR cc_start: 0.8814 (m-80) cc_final: 0.8503 (m-80)
REVERT: B  487 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8384 (mm-40)
REVERT: B  507 LEU cc_start: 0.8918 (mt) cc_final: 0.8484 (mm)
REVERT: B  511 ASN cc_start: 0.8179 (m-40) cc_final: 0.7847 (m-40)
REVERT: C  162 TYR cc_start: 0.8809 (m-80) cc_final: 0.8495 (m-80)
REVERT: C  487 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8395 (mm-40)
REVERT: C  507 LEU cc_start: 0.8923 (mt) cc_final: 0.8496 (mm)
REVERT: C  511 ASN cc_start: 0.8183 (m-40) cc_final: 0.7859 (m-40)
REVERT: D  162 TYR cc_start: 0.8762 (m-80) cc_final: 0.8493 (m-80)
REVERT: D  487 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8401 (mm-40)
REVERT: D  507 LEU cc_start: 0.8893 (mt) cc_final: 0.8446 (mm)
REVERT: D  511 ASN cc_start: 0.8192 (m-40) cc_final: 0.7846 (m-40)
REVERT: D  591 ARG cc_start: 0.8493 (tpp-160) cc_final: 0.8289 (tpp80)
  outliers start: 4
  outliers final: 4
  residues processed: 514
  average time/residue: 0.1479
  time to fit residues: 113.7215
Evaluate side-chains
  298 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 294
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 ASP
Chi-restraints excluded: chain B residue  258 ASP
Chi-restraints excluded: chain C residue  258 ASP
Chi-restraints excluded: chain D residue  258 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 216 optimal weight:    0.9990
   chunk 98 optimal weight:    0.7980
   chunk 194 optimal weight:    0.7980
   chunk 227 optimal weight:    0.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 235 optimal weight:    2.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 316 GLN
A 413 HIS
A 452 GLN
A 530 GLN
B 154 ASN
B 452 GLN
B 530 GLN
C 154 ASN
C 452 GLN
C 530 GLN
D 154 ASN
D 452 GLN
D 530 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.114569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.100995 restraints weight = 39994.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.103694 restraints weight = 21997.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.105535 restraints weight = 14252.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.106758 restraints weight = 10285.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.107586 restraints weight = 8086.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  20652  Z= 0.136
  Angle     :  0.618   8.521  28008  Z= 0.304
  Chirality :  0.039   0.182   3140
  Planarity :  0.004   0.039   3468
  Dihedral  :  4.195  20.709   2704
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 11.58 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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: -0.80 (0.16), residues: 2432
  helix:  0.36 (0.13), residues: 1500
  sheet:  None (None), residues: 0
  loop : -2.00 (0.18), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 684 
 TYR   0.013   0.001   TYR A 412 
 PHE   0.011   0.001   PHE A 472 
 TRP   0.008   0.001   TRP D 101 
 HIS   0.014   0.001   HIS A 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (20652)
  covalent geometry    : angle       0.61835 (28008)
  hydrogen bonds       : bond        0.04151 ( 1060)
  hydrogen bonds       : angle       4.24305 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  480 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 435
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8364 (mmm) cc_final: 0.8083 (mmm)
REVERT: A  162 TYR cc_start: 0.9010 (m-80) cc_final: 0.8726 (m-80)
REVERT: A  215 SER cc_start: 0.9464 (m) cc_final: 0.9061 (t)
REVERT: A  240 GLU cc_start: 0.8195 (pm20) cc_final: 0.7945 (pp20)
REVERT: A  243 ASP cc_start: 0.7977 (p0) cc_final: 0.7675 (p0)
REVERT: A  299 LEU cc_start: 0.8519 (tp) cc_final: 0.8315 (tp)
REVERT: A  387 ASP cc_start: 0.7793 (m-30) cc_final: 0.7576 (m-30)
REVERT: A  507 LEU cc_start: 0.9097 (mt) cc_final: 0.8744 (mm)
REVERT: A  511 ASN cc_start: 0.8394 (m-40) cc_final: 0.8121 (m110)
REVERT: A  590 TYR cc_start: 0.7823 (m-80) cc_final: 0.7582 (m-80)
REVERT: A  599 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7510 (tp30)
REVERT: A  662 LEU cc_start: 0.9371 (tp) cc_final: 0.9076 (tp)
REVERT: B  108 ASP cc_start: 0.8305 (t70) cc_final: 0.7753 (m-30)
REVERT: B  122 MET cc_start: 0.8341 (mmm) cc_final: 0.8091 (mmm)
REVERT: B  162 TYR cc_start: 0.9026 (m-80) cc_final: 0.8731 (m-80)
REVERT: B  215 SER cc_start: 0.9475 (m) cc_final: 0.9069 (t)
REVERT: B  240 GLU cc_start: 0.8219 (pm20) cc_final: 0.7969 (pp20)
REVERT: B  243 ASP cc_start: 0.8005 (p0) cc_final: 0.7708 (p0)
REVERT: B  264 SER cc_start: 0.9173 (m) cc_final: 0.8950 (p)
REVERT: B  270 MET cc_start: 0.8540 (tpp) cc_final: 0.8302 (tpp)
REVERT: B  387 ASP cc_start: 0.7719 (m-30) cc_final: 0.7503 (m-30)
REVERT: B  434 LEU cc_start: 0.8158 (tt) cc_final: 0.7938 (mm)
REVERT: B  507 LEU cc_start: 0.9140 (mt) cc_final: 0.8752 (mm)
REVERT: B  511 ASN cc_start: 0.8485 (m-40) cc_final: 0.8171 (m110)
REVERT: B  530 GLN cc_start: 0.6170 (mt0) cc_final: 0.5652 (mp10)
REVERT: B  590 TYR cc_start: 0.7817 (m-80) cc_final: 0.7605 (m-80)
REVERT: B  599 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7435 (tp30)
REVERT: B  662 LEU cc_start: 0.9382 (tp) cc_final: 0.9089 (tp)
REVERT: C  108 ASP cc_start: 0.8295 (t70) cc_final: 0.7745 (m-30)
REVERT: C  122 MET cc_start: 0.8343 (mmm) cc_final: 0.8084 (mmm)
REVERT: C  162 TYR cc_start: 0.9015 (m-80) cc_final: 0.8731 (m-80)
REVERT: C  215 SER cc_start: 0.9469 (m) cc_final: 0.9066 (t)
REVERT: C  240 GLU cc_start: 0.8217 (pm20) cc_final: 0.7959 (pp20)
REVERT: C  243 ASP cc_start: 0.7968 (p0) cc_final: 0.7677 (p0)
REVERT: C  264 SER cc_start: 0.9146 (m) cc_final: 0.8934 (p)
REVERT: C  270 MET cc_start: 0.8551 (tpp) cc_final: 0.8326 (tpp)
REVERT: C  387 ASP cc_start: 0.7722 (m-30) cc_final: 0.7473 (m-30)
REVERT: C  434 LEU cc_start: 0.8213 (tt) cc_final: 0.7991 (mm)
REVERT: C  507 LEU cc_start: 0.9143 (mt) cc_final: 0.8757 (mm)
REVERT: C  511 ASN cc_start: 0.8492 (m-40) cc_final: 0.8173 (m110)
REVERT: C  530 GLN cc_start: 0.6172 (mt0) cc_final: 0.5634 (mp10)
REVERT: C  599 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7460 (tp30)
REVERT: C  662 LEU cc_start: 0.9393 (tp) cc_final: 0.9100 (tp)
REVERT: D  122 MET cc_start: 0.8330 (mmm) cc_final: 0.8035 (mmm)
REVERT: D  162 TYR cc_start: 0.9030 (m-80) cc_final: 0.8736 (m-80)
REVERT: D  215 SER cc_start: 0.9466 (m) cc_final: 0.9065 (t)
REVERT: D  240 GLU cc_start: 0.8219 (pm20) cc_final: 0.7946 (pp20)
REVERT: D  243 ASP cc_start: 0.8097 (p0) cc_final: 0.7693 (p0)
REVERT: D  264 SER cc_start: 0.9161 (m) cc_final: 0.8932 (p)
REVERT: D  387 ASP cc_start: 0.7710 (m-30) cc_final: 0.7493 (m-30)
REVERT: D  507 LEU cc_start: 0.9122 (mt) cc_final: 0.8751 (mm)
REVERT: D  511 ASN cc_start: 0.8498 (m-40) cc_final: 0.8142 (m110)
REVERT: D  530 GLN cc_start: 0.6209 (mt0) cc_final: 0.5658 (mp10)
REVERT: D  662 LEU cc_start: 0.9398 (tp) cc_final: 0.9123 (tp)
  outliers start: 45
  outliers final: 25
  residues processed: 448
  average time/residue: 0.1244
  time to fit residues: 89.4242
Evaluate side-chains
  355 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 330
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  538 LEU
Chi-restraints excluded: chain C residue  556 VAL
Chi-restraints excluded: chain C residue  605 ILE
Chi-restraints excluded: chain D residue   75 PHE
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  456 PHE
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  556 VAL
Chi-restraints excluded: chain D residue  605 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 131 optimal weight:    0.9990
   chunk 151 optimal weight:    7.9990
   chunk 195 optimal weight:    1.9990
   chunk 140 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 177 optimal weight:    8.9990
   chunk 63 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 204 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
A 154 ASN
** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 GLN
B 148 ASN
B 154 ASN
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 530 GLN
C 148 ASN
C 154 ASN
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 530 GLN
D 148 ASN
D 154 ASN
** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 413 HIS
D 530 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.106745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.092694 restraints weight = 41581.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.095197 restraints weight = 23901.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.096857 restraints weight = 16035.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.098103 restraints weight = 11994.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.098950 restraints weight = 9569.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  20652  Z= 0.202
  Angle     :  0.653   9.427  28008  Z= 0.318
  Chirality :  0.041   0.130   3140
  Planarity :  0.004   0.037   3468
  Dihedral  :  4.259  18.947   2696
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 17.58 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.15 (0.16), residues: 2432
  helix:  1.14 (0.13), residues: 1504
  sheet:  None (None), residues: 0
  loop : -1.68 (0.18), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 684 
 TYR   0.017   0.002   TYR C 471 
 PHE   0.014   0.002   PHE B 311 
 TRP   0.010   0.001   TRP D 333 
 HIS   0.006   0.001   HIS A 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (20652)
  covalent geometry    : angle       0.65283 (28008)
  hydrogen bonds       : bond        0.03974 ( 1060)
  hydrogen bonds       : angle       4.05911 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  447 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 97
    poor density    : 350
  time to evaluate  : 0.808 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.8461 (t70) cc_final: 0.7809 (m-30)
REVERT: A  122 MET cc_start: 0.8554 (mmm) cc_final: 0.8333 (mmm)
REVERT: A  215 SER cc_start: 0.9555 (m) cc_final: 0.9174 (t)
REVERT: A  240 GLU cc_start: 0.8336 (pm20) cc_final: 0.8044 (pp20)
REVERT: A  243 ASP cc_start: 0.8059 (p0) cc_final: 0.7796 (p0)
REVERT: A  540 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8272 (t80)
REVERT: A  599 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7617 (tp30)
REVERT: A  662 LEU cc_start: 0.9431 (tp) cc_final: 0.9093 (tp)
REVERT: B  108 ASP cc_start: 0.8467 (t70) cc_final: 0.7803 (m-30)
REVERT: B  122 MET cc_start: 0.8597 (mmm) cc_final: 0.8352 (mmm)
REVERT: B  215 SER cc_start: 0.9556 (m) cc_final: 0.9173 (t)
REVERT: B  240 GLU cc_start: 0.8311 (pm20) cc_final: 0.7997 (pp20)
REVERT: B  243 ASP cc_start: 0.8010 (p0) cc_final: 0.7733 (p0)
REVERT: B  270 MET cc_start: 0.8738 (tpp) cc_final: 0.8503 (tpp)
REVERT: B  289 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7054 (tm-30)
REVERT: B  540 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8250 (t80)
REVERT: B  599 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7507 (tp30)
REVERT: B  662 LEU cc_start: 0.9435 (tp) cc_final: 0.9104 (tp)
REVERT: C  108 ASP cc_start: 0.8470 (t70) cc_final: 0.7799 (m-30)
REVERT: C  122 MET cc_start: 0.8599 (mmm) cc_final: 0.8354 (mmm)
REVERT: C  215 SER cc_start: 0.9553 (m) cc_final: 0.9169 (t)
REVERT: C  240 GLU cc_start: 0.8334 (pm20) cc_final: 0.8018 (pp20)
REVERT: C  243 ASP cc_start: 0.8067 (p0) cc_final: 0.7803 (p0)
REVERT: C  264 SER cc_start: 0.9281 (m) cc_final: 0.9054 (p)
REVERT: C  270 MET cc_start: 0.8761 (tpp) cc_final: 0.8525 (tpp)
REVERT: C  289 GLU cc_start: 0.7319 (tm-30) cc_final: 0.7060 (tm-30)
REVERT: C  540 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8254 (t80)
REVERT: C  599 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7578 (tp30)
REVERT: C  662 LEU cc_start: 0.9441 (tp) cc_final: 0.9103 (tp)
REVERT: D  108 ASP cc_start: 0.8448 (t70) cc_final: 0.7847 (m-30)
REVERT: D  122 MET cc_start: 0.8569 (mmm) cc_final: 0.8360 (mmm)
REVERT: D  215 SER cc_start: 0.9557 (m) cc_final: 0.9168 (t)
REVERT: D  240 GLU cc_start: 0.8332 (pm20) cc_final: 0.8025 (pp20)
REVERT: D  243 ASP cc_start: 0.8061 (p0) cc_final: 0.7762 (p0)
REVERT: D  264 SER cc_start: 0.9274 (m) cc_final: 0.9056 (p)
REVERT: D  412 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6924 (t80)
REVERT: D  540 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8275 (t80)
REVERT: D  662 LEU cc_start: 0.9443 (tp) cc_final: 0.9095 (tp)
  outliers start: 97
  outliers final: 59
  residues processed: 410
  average time/residue: 0.1108
  time to fit residues: 77.1264
Evaluate side-chains
  379 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 315
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  234 HIS
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  710 VAL
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  234 HIS
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  438 HIS
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  538 LEU
Chi-restraints excluded: chain C residue  540 PHE
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  556 VAL
Chi-restraints excluded: chain C residue  605 ILE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  710 VAL
Chi-restraints excluded: chain D residue   75 PHE
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  234 HIS
Chi-restraints excluded: chain D residue  242 THR
Chi-restraints excluded: chain D residue  277 MET
Chi-restraints excluded: chain D residue  284 THR
Chi-restraints excluded: chain D residue  412 TYR
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  438 HIS
Chi-restraints excluded: chain D residue  456 PHE
Chi-restraints excluded: chain D residue  474 ILE
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  540 PHE
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  556 VAL
Chi-restraints excluded: chain D residue  605 ILE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain D residue  710 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 217 optimal weight:    3.9990
   chunk 109 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 167 optimal weight:   10.0000
   chunk 124 optimal weight:   10.0000
   chunk 216 optimal weight:    4.9990
   chunk 213 optimal weight:    2.9990
   chunk 126 optimal weight:    7.9990
   chunk 222 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 183 optimal weight:    2.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 154 ASN
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 316 GLN
B 413 HIS
C 154 ASN
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 294 GLN
C 316 GLN
C 413 HIS
D 154 ASN
** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 294 GLN
D 316 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.101951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.088024 restraints weight = 42441.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.090347 restraints weight = 24711.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.092010 restraints weight = 16800.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.093171 restraints weight = 12591.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.093971 restraints weight = 10157.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  20652  Z= 0.256
  Angle     :  0.700   9.623  28008  Z= 0.340
  Chirality :  0.042   0.127   3140
  Planarity :  0.004   0.043   3468
  Dihedral  :  4.479  18.801   2696
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 19.73 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.26 (0.17), residues: 2432
  helix:  1.23 (0.13), residues: 1500
  sheet:  None (None), residues: 0
  loop : -1.61 (0.18), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 684 
 TYR   0.021   0.002   TYR A 412 
 PHE   0.016   0.002   PHE A 311 
 TRP   0.014   0.001   TRP C 333 
 HIS   0.018   0.001   HIS D 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 (20652)
  covalent geometry    : angle       0.70001 (28008)
  hydrogen bonds       : bond        0.04201 ( 1060)
  hydrogen bonds       : angle       4.19086 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  443 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 128
    poor density    : 315
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.8496 (t70) cc_final: 0.7925 (m-30)
REVERT: A  122 MET cc_start: 0.8623 (mmm) cc_final: 0.8369 (mmm)
REVERT: A  215 SER cc_start: 0.9539 (m) cc_final: 0.9187 (t)
REVERT: A  243 ASP cc_start: 0.8015 (p0) cc_final: 0.7667 (p0)
REVERT: A  247 ASN cc_start: 0.8651 (m-40) cc_final: 0.8090 (m110)
REVERT: A  289 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7229 (tm-30)
REVERT: A  540 PHE cc_start: 0.8614 (OUTLIER) cc_final: 0.8339 (t80)
REVERT: A  662 LEU cc_start: 0.9443 (tp) cc_final: 0.9119 (tp)
REVERT: B  108 ASP cc_start: 0.8506 (t70) cc_final: 0.7920 (m-30)
REVERT: B  122 MET cc_start: 0.8634 (mmm) cc_final: 0.8380 (mmm)
REVERT: B  215 SER cc_start: 0.9541 (m) cc_final: 0.9189 (t)
REVERT: B  243 ASP cc_start: 0.8022 (p0) cc_final: 0.7672 (p0)
REVERT: B  247 ASN cc_start: 0.8661 (m-40) cc_final: 0.8100 (m110)
REVERT: B  270 MET cc_start: 0.8859 (tpp) cc_final: 0.8604 (tpp)
REVERT: B  289 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7241 (tm-30)
REVERT: B  412 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.6898 (t80)
REVERT: B  662 LEU cc_start: 0.9460 (tp) cc_final: 0.9134 (tp)
REVERT: C  108 ASP cc_start: 0.8500 (t70) cc_final: 0.7914 (m-30)
REVERT: C  122 MET cc_start: 0.8637 (mmm) cc_final: 0.8383 (mmm)
REVERT: C  215 SER cc_start: 0.9534 (m) cc_final: 0.9186 (t)
REVERT: C  243 ASP cc_start: 0.7948 (p0) cc_final: 0.7634 (p0)
REVERT: C  247 ASN cc_start: 0.8666 (m-40) cc_final: 0.8107 (m110)
REVERT: C  264 SER cc_start: 0.9361 (m) cc_final: 0.9112 (p)
REVERT: C  270 MET cc_start: 0.8870 (tpp) cc_final: 0.8624 (tpp)
REVERT: C  289 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7245 (tm-30)
REVERT: C  412 TYR cc_start: 0.7497 (OUTLIER) cc_final: 0.6959 (t80)
REVERT: C  607 MET cc_start: 0.8141 (tmm) cc_final: 0.7830 (tmm)
REVERT: C  662 LEU cc_start: 0.9469 (tp) cc_final: 0.9138 (tp)
REVERT: D  108 ASP cc_start: 0.8498 (t70) cc_final: 0.7841 (m-30)
REVERT: D  122 MET cc_start: 0.8658 (mmm) cc_final: 0.8408 (mmm)
REVERT: D  162 TYR cc_start: 0.9237 (m-80) cc_final: 0.9008 (m-80)
REVERT: D  215 SER cc_start: 0.9535 (m) cc_final: 0.9169 (t)
REVERT: D  243 ASP cc_start: 0.8035 (p0) cc_final: 0.7703 (p0)
REVERT: D  247 ASN cc_start: 0.8676 (m-40) cc_final: 0.8116 (m110)
REVERT: D  264 SER cc_start: 0.9366 (m) cc_final: 0.9105 (p)
REVERT: D  289 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7304 (tm-30)
REVERT: D  412 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.6775 (t80)
REVERT: D  433 MET cc_start: 0.4979 (ttp) cc_final: 0.4637 (ttt)
REVERT: D  540 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8370 (t80)
REVERT: D  662 LEU cc_start: 0.9465 (tp) cc_final: 0.9130 (tp)
  outliers start: 128
  outliers final: 85
  residues processed: 400
  average time/residue: 0.1060
  time to fit residues: 73.1631
Evaluate side-chains
  379 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 289
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  637 LEU
Chi-restraints excluded: chain A residue  675 TYR
Chi-restraints excluded: chain A residue  710 VAL
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  277 MET
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  412 TYR
Chi-restraints excluded: chain B residue  436 LEU
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  710 VAL
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  256 ILE
Chi-restraints excluded: chain C residue  277 MET
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  412 TYR
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  438 HIS
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  474 ILE
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  538 LEU
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  556 VAL
Chi-restraints excluded: chain C residue  605 ILE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  639 ASN
Chi-restraints excluded: chain C residue  710 VAL
Chi-restraints excluded: chain D residue   75 PHE
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  151 LEU
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  242 THR
Chi-restraints excluded: chain D residue  256 ILE
Chi-restraints excluded: chain D residue  277 MET
Chi-restraints excluded: chain D residue  284 THR
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  412 TYR
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  436 LEU
Chi-restraints excluded: chain D residue  438 HIS
Chi-restraints excluded: chain D residue  450 LEU
Chi-restraints excluded: chain D residue  456 PHE
Chi-restraints excluded: chain D residue  474 ILE
Chi-restraints excluded: chain D residue  479 GLN
Chi-restraints excluded: chain D residue  484 VAL
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  540 PHE
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  556 VAL
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain D residue  637 LEU
Chi-restraints excluded: chain D residue  710 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 112 optimal weight:    0.2980
   chunk 131 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 100 optimal weight:    4.9990
   chunk 204 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 109 optimal weight:    0.6980
   chunk 101 optimal weight:    3.9990
   chunk 176 optimal weight:    0.9980
   chunk 236 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 154 ASN
C 154 ASN
D 154 ASN
** D 165 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 = 0.3307 r_free = 0.3307 target = 0.108280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.094791 restraints weight = 41092.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.097278 restraints weight = 23243.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.098995 restraints weight = 15363.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.100056 restraints weight = 11300.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.101026 restraints weight = 9081.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.4529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  20652  Z= 0.106
  Angle     :  0.593  12.385  28008  Z= 0.274
  Chirality :  0.037   0.121   3140
  Planarity :  0.003   0.036   3468
  Dihedral  :  3.901  16.699   2696
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 22.48 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.17), residues: 2432
  helix:  1.56 (0.14), residues: 1496
  sheet:  None (None), residues: 0
  loop : -1.27 (0.18), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 175 
 TYR   0.016   0.001   TYR A 412 
 PHE   0.008   0.001   PHE D 612 
 TRP   0.008   0.001   TRP A 351 
 HIS   0.008   0.001   HIS D 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (20652)
  covalent geometry    : angle       0.59272 (28008)
  hydrogen bonds       : bond        0.03278 ( 1060)
  hydrogen bonds       : angle       3.70337 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  447 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 359
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.8432 (t70) cc_final: 0.7855 (m-30)
REVERT: A  122 MET cc_start: 0.8593 (mmm) cc_final: 0.8268 (mmm)
REVERT: A  215 SER cc_start: 0.9429 (m) cc_final: 0.9077 (t)
REVERT: A  243 ASP cc_start: 0.7754 (p0) cc_final: 0.7315 (p0)
REVERT: A  289 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7207 (tm-30)
REVERT: A  540 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8200 (t80)
REVERT: A  599 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7526 (tp30)
REVERT: A  662 LEU cc_start: 0.9361 (tp) cc_final: 0.9098 (tp)
REVERT: B  108 ASP cc_start: 0.8446 (t70) cc_final: 0.7848 (m-30)
REVERT: B  122 MET cc_start: 0.8585 (mmm) cc_final: 0.8284 (mmm)
REVERT: B  215 SER cc_start: 0.9447 (m) cc_final: 0.9089 (t)
REVERT: B  243 ASP cc_start: 0.7711 (p0) cc_final: 0.7288 (p0)
REVERT: B  289 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7183 (tm-30)
REVERT: B  331 THR cc_start: 0.9429 (m) cc_final: 0.9215 (p)
REVERT: B  540 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8115 (t80)
REVERT: B  599 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7423 (tp30)
REVERT: B  662 LEU cc_start: 0.9389 (tp) cc_final: 0.9103 (tp)
REVERT: C  108 ASP cc_start: 0.8427 (t70) cc_final: 0.7854 (m-30)
REVERT: C  122 MET cc_start: 0.8575 (mmm) cc_final: 0.8286 (mmm)
REVERT: C  215 SER cc_start: 0.9435 (m) cc_final: 0.9104 (t)
REVERT: C  243 ASP cc_start: 0.7697 (p0) cc_final: 0.7265 (p0)
REVERT: C  264 SER cc_start: 0.9312 (m) cc_final: 0.9030 (p)
REVERT: C  289 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7191 (tm-30)
REVERT: C  331 THR cc_start: 0.9438 (m) cc_final: 0.9220 (p)
REVERT: C  512 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9066 (tt)
REVERT: C  540 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8108 (t80)
REVERT: C  662 LEU cc_start: 0.9406 (tp) cc_final: 0.9109 (tp)
REVERT: D  108 ASP cc_start: 0.8426 (t70) cc_final: 0.7862 (m-30)
REVERT: D  122 MET cc_start: 0.8609 (mmm) cc_final: 0.8291 (mmm)
REVERT: D  162 TYR cc_start: 0.9237 (m-80) cc_final: 0.8874 (m-80)
REVERT: D  215 SER cc_start: 0.9427 (m) cc_final: 0.9059 (t)
REVERT: D  243 ASP cc_start: 0.7730 (p0) cc_final: 0.7279 (p0)
REVERT: D  264 SER cc_start: 0.9341 (m) cc_final: 0.9060 (p)
REVERT: D  289 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7225 (tm-30)
REVERT: D  331 THR cc_start: 0.9437 (m) cc_final: 0.9184 (p)
REVERT: D  540 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.8128 (t80)
REVERT: D  662 LEU cc_start: 0.9405 (tp) cc_final: 0.9115 (tp)
  outliers start: 88
  outliers final: 45
  residues processed: 417
  average time/residue: 0.1040
  time to fit residues: 74.7155
Evaluate side-chains
  374 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 324
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  438 HIS
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  502 VAL
Chi-restraints excluded: chain C residue  512 LEU
Chi-restraints excluded: chain C residue  538 LEU
Chi-restraints excluded: chain C residue  540 PHE
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  605 ILE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain D residue   75 PHE
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  242 THR
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  438 HIS
Chi-restraints excluded: chain D residue  456 PHE
Chi-restraints excluded: chain D residue  502 VAL
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  540 PHE
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  593 ILE
Chi-restraints excluded: chain D residue  605 ILE
Chi-restraints excluded: chain D residue  623 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 243 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 147 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 119 optimal weight:    0.7980
   chunk 13 optimal weight:   10.0000
   chunk 204 optimal weight:    1.9990
   chunk 239 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 154 ASN
C 154 ASN
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN
** D 165 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 = 0.3277 r_free = 0.3277 target = 0.106167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.092440 restraints weight = 42030.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.094932 restraints weight = 24079.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.096670 restraints weight = 16109.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.097810 restraints weight = 11937.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.098627 restraints weight = 9566.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8191
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  20652  Z= 0.121
  Angle     :  0.606  10.842  28008  Z= 0.277
  Chirality :  0.037   0.123   3140
  Planarity :  0.003   0.038   3468
  Dihedral  :  3.771  16.208   2696
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.66 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  0.89 (0.17), residues: 2432
  helix:  1.66 (0.14), residues: 1496
  sheet: -1.84 (0.88), residues: 28
  loop : -1.17 (0.19), residues: 908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 684 
 TYR   0.018   0.001   TYR A 455 
 PHE   0.017   0.001   PHE A 462 
 TRP   0.007   0.001   TRP C 333 
 HIS   0.006   0.001   HIS D 413 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (20652)
  covalent geometry    : angle       0.60585 (28008)
  hydrogen bonds       : bond        0.03338 ( 1060)
  hydrogen bonds       : angle       3.65620 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  421 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 97
    poor density    : 324
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.8447 (t70) cc_final: 0.7776 (m-30)
REVERT: A  122 MET cc_start: 0.8608 (mmm) cc_final: 0.8266 (mmm)
REVERT: A  215 SER cc_start: 0.9446 (m) cc_final: 0.9097 (t)
REVERT: A  243 ASP cc_start: 0.7799 (p0) cc_final: 0.7475 (p0)
REVERT: A  247 ASN cc_start: 0.8295 (m-40) cc_final: 0.7563 (m110)
REVERT: A  289 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7266 (tm-30)
REVERT: A  439 ILE cc_start: 0.8832 (mm) cc_final: 0.8569 (pt)
REVERT: A  522 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7494 (m)
REVERT: A  540 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8169 (t80)
REVERT: A  599 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7578 (tp30)
REVERT: A  662 LEU cc_start: 0.9382 (tp) cc_final: 0.9123 (tp)
REVERT: B  108 ASP cc_start: 0.8480 (t70) cc_final: 0.7804 (m-30)
REVERT: B  122 MET cc_start: 0.8627 (mmm) cc_final: 0.8283 (mmm)
REVERT: B  215 SER cc_start: 0.9473 (m) cc_final: 0.9122 (t)
REVERT: B  243 ASP cc_start: 0.7788 (p0) cc_final: 0.7468 (p0)
REVERT: B  247 ASN cc_start: 0.8315 (m-40) cc_final: 0.7583 (m110)
REVERT: B  522 THR cc_start: 0.7740 (OUTLIER) cc_final: 0.7534 (m)
REVERT: B  537 LEU cc_start: 0.8247 (tt) cc_final: 0.7754 (tp)
REVERT: B  599 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7420 (tp30)
REVERT: B  662 LEU cc_start: 0.9401 (tp) cc_final: 0.9122 (tp)
REVERT: C  108 ASP cc_start: 0.8456 (t70) cc_final: 0.7751 (m-30)
REVERT: C  122 MET cc_start: 0.8624 (mmm) cc_final: 0.8296 (mmm)
REVERT: C  215 SER cc_start: 0.9461 (m) cc_final: 0.9117 (t)
REVERT: C  243 ASP cc_start: 0.7741 (p0) cc_final: 0.7405 (p0)
REVERT: C  247 ASN cc_start: 0.8320 (m-40) cc_final: 0.7581 (m110)
REVERT: C  264 SER cc_start: 0.9335 (m) cc_final: 0.9060 (p)
REVERT: C  331 THR cc_start: 0.9470 (m) cc_final: 0.9264 (p)
REVERT: C  522 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7574 (m)
REVERT: C  537 LEU cc_start: 0.8213 (tt) cc_final: 0.7730 (tp)
REVERT: C  662 LEU cc_start: 0.9416 (tp) cc_final: 0.9125 (tp)
REVERT: D  108 ASP cc_start: 0.8458 (t70) cc_final: 0.7779 (m-30)
REVERT: D  122 MET cc_start: 0.8644 (mmm) cc_final: 0.8284 (mmm)
REVERT: D  162 TYR cc_start: 0.9229 (m-80) cc_final: 0.8908 (m-80)
REVERT: D  215 SER cc_start: 0.9454 (m) cc_final: 0.9092 (t)
REVERT: D  243 ASP cc_start: 0.7808 (p0) cc_final: 0.7335 (p0)
REVERT: D  264 SER cc_start: 0.9343 (m) cc_final: 0.9063 (p)
REVERT: D  289 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7284 (tm-30)
REVERT: D  331 THR cc_start: 0.9467 (m) cc_final: 0.9238 (p)
REVERT: D  479 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8720 (tm-30)
REVERT: D  522 THR cc_start: 0.7743 (OUTLIER) cc_final: 0.7540 (m)
REVERT: D  540 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8106 (t80)
REVERT: D  597 SER cc_start: 0.8883 (m) cc_final: 0.8508 (p)
REVERT: D  662 LEU cc_start: 0.9414 (tp) cc_final: 0.9128 (tp)
  outliers start: 97
  outliers final: 66
  residues processed: 391
  average time/residue: 0.1074
  time to fit residues: 72.1479
Evaluate side-chains
  378 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 306
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  639 ASN
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  593 ILE
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  438 HIS
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  522 THR
Chi-restraints excluded: chain C residue  538 LEU
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  556 VAL
Chi-restraints excluded: chain C residue  593 ILE
Chi-restraints excluded: chain C residue  605 ILE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain D residue   75 PHE
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  242 THR
Chi-restraints excluded: chain D residue  277 MET
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  438 HIS
Chi-restraints excluded: chain D residue  450 LEU
Chi-restraints excluded: chain D residue  456 PHE
Chi-restraints excluded: chain D residue  484 VAL
Chi-restraints excluded: chain D residue  522 THR
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  540 PHE
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  605 ILE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain D residue  718 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 213 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0000
   chunk 146 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 173 optimal weight:    6.9990
   chunk 141 optimal weight:    0.7980
   chunk 88 optimal weight:    4.9990
   chunk 235 optimal weight:    1.9990
   chunk 164 optimal weight:    5.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 154 ASN
C 154 ASN
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN
** D 165 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 = 0.3273 r_free = 0.3273 target = 0.106022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.092289 restraints weight = 42269.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.094769 restraints weight = 24253.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.096517 restraints weight = 16210.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.097721 restraints weight = 12007.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.098557 restraints weight = 9562.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  20652  Z= 0.128
  Angle     :  0.622  10.455  28008  Z= 0.283
  Chirality :  0.037   0.120   3140
  Planarity :  0.003   0.037   3468
  Dihedral  :  3.732  16.305   2696
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 23.76 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.17), residues: 2432
  helix:  1.71 (0.14), residues: 1472
  sheet:  None (None), residues: 0
  loop : -1.08 (0.18), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 684 
 TYR   0.014   0.001   TYR A 412 
 PHE   0.014   0.001   PHE A 462 
 TRP   0.008   0.001   TRP C 333 
 HIS   0.006   0.001   HIS C 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (20652)
  covalent geometry    : angle       0.62198 (28008)
  hydrogen bonds       : bond        0.03287 ( 1060)
  hydrogen bonds       : angle       3.65991 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 316
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.8448 (t70) cc_final: 0.7779 (m-30)
REVERT: A  122 MET cc_start: 0.8627 (mmm) cc_final: 0.8264 (mmm)
REVERT: A  215 SER cc_start: 0.9446 (m) cc_final: 0.9089 (t)
REVERT: A  243 ASP cc_start: 0.7778 (p0) cc_final: 0.7344 (p0)
REVERT: A  439 ILE cc_start: 0.8802 (mm) cc_final: 0.8533 (pt)
REVERT: A  479 GLN cc_start: 0.8968 (tm-30) cc_final: 0.8762 (tm-30)
REVERT: A  540 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8152 (t80)
REVERT: A  599 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7580 (tp30)
REVERT: A  662 LEU cc_start: 0.9386 (tp) cc_final: 0.9126 (tp)
REVERT: B  108 ASP cc_start: 0.8461 (t70) cc_final: 0.7785 (m-30)
REVERT: B  122 MET cc_start: 0.8600 (mmm) cc_final: 0.8244 (mmm)
REVERT: B  215 SER cc_start: 0.9456 (m) cc_final: 0.9095 (t)
REVERT: B  243 ASP cc_start: 0.7756 (p0) cc_final: 0.7329 (p0)
REVERT: B  540 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8107 (t80)
REVERT: B  599 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7513 (tp30)
REVERT: B  662 LEU cc_start: 0.9407 (tp) cc_final: 0.9133 (tp)
REVERT: C  108 ASP cc_start: 0.8451 (t70) cc_final: 0.7769 (m-30)
REVERT: C  122 MET cc_start: 0.8598 (mmm) cc_final: 0.8249 (mmm)
REVERT: C  215 SER cc_start: 0.9447 (m) cc_final: 0.9090 (t)
REVERT: C  243 ASP cc_start: 0.7731 (p0) cc_final: 0.7297 (p0)
REVERT: C  264 SER cc_start: 0.9345 (m) cc_final: 0.9064 (p)
REVERT: C  528 MET cc_start: 0.7100 (mmm) cc_final: 0.6851 (mmm)
REVERT: C  540 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8082 (t80)
REVERT: C  662 LEU cc_start: 0.9424 (tp) cc_final: 0.9135 (tp)
REVERT: D  108 ASP cc_start: 0.8453 (t70) cc_final: 0.7837 (m-30)
REVERT: D  122 MET cc_start: 0.8625 (mmm) cc_final: 0.8261 (mmm)
REVERT: D  162 TYR cc_start: 0.9256 (m-80) cc_final: 0.8928 (m-80)
REVERT: D  215 SER cc_start: 0.9444 (m) cc_final: 0.9080 (t)
REVERT: D  243 ASP cc_start: 0.7787 (p0) cc_final: 0.7320 (p0)
REVERT: D  264 SER cc_start: 0.9342 (m) cc_final: 0.9036 (p)
REVERT: D  289 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7259 (tm-30)
REVERT: D  433 MET cc_start: 0.4864 (ttp) cc_final: 0.4574 (ttt)
REVERT: D  528 MET cc_start: 0.7143 (mmm) cc_final: 0.6882 (mmm)
REVERT: D  540 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8171 (t80)
REVERT: D  597 SER cc_start: 0.8899 (m) cc_final: 0.8654 (p)
REVERT: D  598 LEU cc_start: 0.8746 (tt) cc_final: 0.8331 (tp)
REVERT: D  607 MET cc_start: 0.7674 (ppp) cc_final: 0.7436 (ppp)
REVERT: D  662 LEU cc_start: 0.9425 (tp) cc_final: 0.9129 (tp)
  outliers start: 102
  outliers final: 67
  residues processed: 392
  average time/residue: 0.1028
  time to fit residues: 69.9868
Evaluate side-chains
  375 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 304
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 PHE
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain B residue   75 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  291 SER
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  593 ILE
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain C residue   75 PHE
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  291 SER
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  438 HIS
Chi-restraints excluded: chain C residue  450 LEU
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  538 LEU
Chi-restraints excluded: chain C residue  540 PHE
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  556 VAL
Chi-restraints excluded: chain C residue  605 ILE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain D residue   75 PHE
Chi-restraints excluded: chain D residue   84 VAL
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  242 THR
Chi-restraints excluded: chain D residue  277 MET
Chi-restraints excluded: chain D residue  291 SER
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  438 HIS
Chi-restraints excluded: chain D residue  450 LEU
Chi-restraints excluded: chain D residue  456 PHE
Chi-restraints excluded: chain D residue  484 VAL
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  540 PHE
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  605 ILE
Chi-restraints excluded: chain D residue  718 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 46 optimal weight:    0.8980
   chunk 154 optimal weight:    0.8980
   chunk 223 optimal weight:    0.5980
   chunk 95 optimal weight:    3.9990
   chunk 178 optimal weight:    1.9990
   chunk 81 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9990
   chunk 117 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 181 optimal weight:    7.9990
   chunk 73 optimal weight:    0.0670
   overall best weight:    0.6920

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 316 GLN
B 154 ASN
B 316 GLN
C 154 ASN
C 316 GLN
D 154 ASN
** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.109698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.096091 restraints weight = 42081.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.098670 restraints weight = 24010.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.100423 restraints weight = 15927.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.101631 restraints weight = 11715.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.102545 restraints weight = 9296.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  20652  Z= 0.099
  Angle     :  0.602  10.741  28008  Z= 0.269
  Chirality :  0.036   0.123   3140
  Planarity :  0.003   0.036   3468
  Dihedral  :  3.541  15.278   2696
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 24.86 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.17), residues: 2432
  helix:  1.79 (0.14), residues: 1468
  sheet:  None (None), residues: 0
  loop : -0.93 (0.18), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 175 
 TYR   0.014   0.001   TYR A 412 
 PHE   0.021   0.001   PHE A 462 
 TRP   0.012   0.001   TRP A 509 
 HIS   0.005   0.001   HIS A 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 (20652)
  covalent geometry    : angle       0.60214 (28008)
  hydrogen bonds       : bond        0.03039 ( 1060)
  hydrogen bonds       : angle       3.62111 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  432 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 361
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.8418 (t70) cc_final: 0.7771 (m-30)
REVERT: A  122 MET cc_start: 0.8500 (mmm) cc_final: 0.8110 (mmm)
REVERT: A  215 SER cc_start: 0.9401 (m) cc_final: 0.8951 (t)
REVERT: A  243 ASP cc_start: 0.7653 (p0) cc_final: 0.7178 (p0)
REVERT: A  540 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8067 (t80)
REVERT: A  607 MET cc_start: 0.7997 (ppp) cc_final: 0.7622 (ppp)
REVERT: A  662 LEU cc_start: 0.9360 (tp) cc_final: 0.9124 (tp)
REVERT: B  108 ASP cc_start: 0.8456 (t70) cc_final: 0.7809 (m-30)
REVERT: B  122 MET cc_start: 0.8505 (mmm) cc_final: 0.8123 (mmm)
REVERT: B  215 SER cc_start: 0.9391 (m) cc_final: 0.8965 (t)
REVERT: B  243 ASP cc_start: 0.7633 (p0) cc_final: 0.7180 (p0)
REVERT: B  439 ILE cc_start: 0.8695 (mm) cc_final: 0.8377 (pt)
REVERT: B  540 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8072 (t80)
REVERT: B  607 MET cc_start: 0.7953 (ppp) cc_final: 0.7583 (ppp)
REVERT: B  662 LEU cc_start: 0.9393 (tp) cc_final: 0.9153 (tp)
REVERT: C  108 ASP cc_start: 0.8421 (t70) cc_final: 0.7764 (m-30)
REVERT: C  122 MET cc_start: 0.8504 (mmm) cc_final: 0.8120 (mmm)
REVERT: C  215 SER cc_start: 0.9378 (m) cc_final: 0.8962 (t)
REVERT: C  243 ASP cc_start: 0.7607 (p0) cc_final: 0.7144 (p0)
REVERT: C  264 SER cc_start: 0.9314 (m) cc_final: 0.9027 (p)
REVERT: C  439 ILE cc_start: 0.8727 (mm) cc_final: 0.8397 (pt)
REVERT: C  540 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8044 (t80)
REVERT: C  597 SER cc_start: 0.9259 (m) cc_final: 0.8961 (p)
REVERT: C  599 GLU cc_start: 0.8479 (tp30) cc_final: 0.8262 (tm-30)
REVERT: C  662 LEU cc_start: 0.9412 (tp) cc_final: 0.9155 (tp)
REVERT: D  108 ASP cc_start: 0.8439 (t70) cc_final: 0.7790 (m-30)
REVERT: D  122 MET cc_start: 0.8510 (mmm) cc_final: 0.8129 (mmm)
REVERT: D  162 TYR cc_start: 0.9253 (m-80) cc_final: 0.8894 (m-80)
REVERT: D  215 SER cc_start: 0.9381 (m) cc_final: 0.8928 (t)
REVERT: D  243 ASP cc_start: 0.7661 (p0) cc_final: 0.7158 (p0)
REVERT: D  264 SER cc_start: 0.9294 (m) cc_final: 0.9003 (p)
REVERT: D  433 MET cc_start: 0.4895 (ttp) cc_final: 0.4559 (ttt)
REVERT: D  597 SER cc_start: 0.8857 (m) cc_final: 0.8598 (p)
REVERT: D  598 LEU cc_start: 0.8748 (tt) cc_final: 0.8303 (tp)
REVERT: D  607 MET cc_start: 0.7573 (ppp) cc_final: 0.7209 (ppp)
REVERT: D  662 LEU cc_start: 0.9404 (tp) cc_final: 0.9154 (tp)
  outliers start: 71
  outliers final: 56
  residues processed: 412
  average time/residue: 0.1077
  time to fit residues: 75.7127
Evaluate side-chains
  396 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 337
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  639 ASN
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  154 ASN
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  291 SER
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  484 VAL
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain B residue  639 ASN
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  154 ASN
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  291 SER
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  356 VAL
Chi-restraints excluded: chain C residue  438 HIS
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  484 VAL
Chi-restraints excluded: chain C residue  538 LEU
Chi-restraints excluded: chain C residue  540 PHE
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  605 ILE
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  242 THR
Chi-restraints excluded: chain D residue  277 MET
Chi-restraints excluded: chain D residue  291 SER
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  356 VAL
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 HIS
Chi-restraints excluded: chain D residue  484 VAL
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  605 ILE
Chi-restraints excluded: chain D residue  639 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 231 optimal weight:    0.7980
   chunk 106 optimal weight:    0.6980
   chunk 146 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 134 optimal weight:    0.2980
   chunk 161 optimal weight:    6.9990
   chunk 241 optimal weight:    0.9990
   chunk 220 optimal weight:    5.9990
   chunk 191 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 242 optimal weight:    0.0170
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 154 ASN
C 154 ASN
D 154 ASN
D 316 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.110459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.096962 restraints weight = 41702.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.099527 restraints weight = 23726.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.101297 restraints weight = 15725.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.102562 restraints weight = 11537.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.103318 restraints weight = 9085.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.5153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  20652  Z= 0.098
  Angle     :  0.613  10.499  28008  Z= 0.271
  Chirality :  0.037   0.124   3140
  Planarity :  0.003   0.035   3468
  Dihedral  :  3.439  15.185   2696
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 25.78 %
    Favored  : 71.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.17), residues: 2432
  helix:  1.84 (0.14), residues: 1468
  sheet:  None (None), residues: 0
  loop : -0.83 (0.18), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 684 
 TYR   0.013   0.001   TYR A 412 
 PHE   0.019   0.001   PHE A 462 
 TRP   0.014   0.001   TRP A 351 
 HIS   0.005   0.001   HIS C 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (20652)
  covalent geometry    : angle       0.61279 (28008)
  hydrogen bonds       : bond        0.02913 ( 1060)
  hydrogen bonds       : angle       3.62466 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  424 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 358
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.8404 (t70) cc_final: 0.7799 (m-30)
REVERT: A  122 MET cc_start: 0.8441 (mmm) cc_final: 0.8076 (mmm)
REVERT: A  215 SER cc_start: 0.9421 (m) cc_final: 0.9095 (t)
REVERT: A  243 ASP cc_start: 0.7651 (p0) cc_final: 0.7196 (p0)
REVERT: A  540 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8100 (t80)
REVERT: A  607 MET cc_start: 0.7900 (ppp) cc_final: 0.7617 (ppp)
REVERT: A  662 LEU cc_start: 0.9352 (tp) cc_final: 0.9120 (tp)
REVERT: B  108 ASP cc_start: 0.8407 (t70) cc_final: 0.7786 (m-30)
REVERT: B  122 MET cc_start: 0.8449 (mmm) cc_final: 0.8092 (mmm)
REVERT: B  215 SER cc_start: 0.9418 (m) cc_final: 0.9089 (t)
REVERT: B  243 ASP cc_start: 0.7631 (p0) cc_final: 0.7179 (p0)
REVERT: B  439 ILE cc_start: 0.8694 (mm) cc_final: 0.8354 (pt)
REVERT: B  528 MET cc_start: 0.7305 (mmm) cc_final: 0.6858 (tpp)
REVERT: B  540 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7972 (t80)
REVERT: B  599 GLU cc_start: 0.7918 (tp30) cc_final: 0.7583 (tp30)
REVERT: B  607 MET cc_start: 0.7921 (ppp) cc_final: 0.7529 (ppp)
REVERT: B  662 LEU cc_start: 0.9387 (tp) cc_final: 0.9154 (tp)
REVERT: C  108 ASP cc_start: 0.8410 (t70) cc_final: 0.7788 (m-30)
REVERT: C  122 MET cc_start: 0.8451 (mmm) cc_final: 0.8095 (mmm)
REVERT: C  215 SER cc_start: 0.9398 (m) cc_final: 0.8989 (t)
REVERT: C  243 ASP cc_start: 0.7602 (p0) cc_final: 0.7131 (p0)
REVERT: C  264 SER cc_start: 0.9285 (m) cc_final: 0.8993 (p)
REVERT: C  439 ILE cc_start: 0.8681 (mm) cc_final: 0.8346 (pt)
REVERT: C  540 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7985 (t80)
REVERT: C  597 SER cc_start: 0.9213 (m) cc_final: 0.8936 (p)
REVERT: C  599 GLU cc_start: 0.8544 (tp30) cc_final: 0.8339 (tm-30)
REVERT: C  662 LEU cc_start: 0.9391 (tp) cc_final: 0.9149 (tp)
REVERT: C  679 ARG cc_start: 0.7814 (tpp80) cc_final: 0.7549 (tpt-90)
REVERT: C  717 LYS cc_start: 0.9084 (tttt) cc_final: 0.8856 (mmtt)
REVERT: D  108 ASP cc_start: 0.8379 (t70) cc_final: 0.7769 (m-30)
REVERT: D  122 MET cc_start: 0.8466 (mmm) cc_final: 0.8096 (mmm)
REVERT: D  162 TYR cc_start: 0.9260 (m-80) cc_final: 0.8888 (m-80)
REVERT: D  215 SER cc_start: 0.9401 (m) cc_final: 0.9072 (t)
REVERT: D  243 ASP cc_start: 0.7648 (p0) cc_final: 0.7207 (p0)
REVERT: D  264 SER cc_start: 0.9292 (m) cc_final: 0.8977 (p)
REVERT: D  433 MET cc_start: 0.4856 (ttp) cc_final: 0.4525 (ttt)
REVERT: D  479 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8718 (tm-30)
REVERT: D  540 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.8076 (t80)
REVERT: D  597 SER cc_start: 0.8861 (m) cc_final: 0.8562 (p)
REVERT: D  598 LEU cc_start: 0.8725 (tt) cc_final: 0.8316 (tp)
REVERT: D  662 LEU cc_start: 0.9399 (tp) cc_final: 0.9163 (tp)
  outliers start: 66
  outliers final: 53
  residues processed: 400
  average time/residue: 0.1078
  time to fit residues: 72.6677
Evaluate side-chains
  395 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 338
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  639 ASN
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  291 SER
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain B residue  639 ASN
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  291 SER
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  356 VAL
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  438 HIS
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  538 LEU
Chi-restraints excluded: chain C residue  540 PHE
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  605 ILE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  242 THR
Chi-restraints excluded: chain D residue  277 MET
Chi-restraints excluded: chain D residue  291 SER
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  356 VAL
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 HIS
Chi-restraints excluded: chain D residue  456 PHE
Chi-restraints excluded: chain D residue  484 VAL
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  540 PHE
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  605 ILE
Chi-restraints excluded: chain D residue  627 LEU
Chi-restraints excluded: chain D residue  639 ASN
Chi-restraints excluded: chain D residue  718 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 179 optimal weight:    0.5980
   chunk 21 optimal weight:    6.9990
   chunk 213 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 149 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 114 optimal weight:    4.9990
   chunk 228 optimal weight:    4.9990
   chunk 101 optimal weight:    1.9990
   chunk 241 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
A 413 HIS
A 452 GLN
B 154 ASN
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 154 ASN
C 452 GLN
D 154 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.108931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.095315 restraints weight = 42215.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.097858 restraints weight = 24300.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.099624 restraints weight = 16219.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.100796 restraints weight = 11968.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.101713 restraints weight = 9542.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.5233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  20652  Z= 0.115
  Angle     :  0.624  10.163  28008  Z= 0.280
  Chirality :  0.037   0.123   3140
  Planarity :  0.003   0.035   3468
  Dihedral  :  3.489  15.089   2696
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 26.14 %
    Favored  : 70.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.17), residues: 2432
  helix:  1.87 (0.14), residues: 1468
  sheet:  None (None), residues: 0
  loop : -0.80 (0.19), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 684 
 TYR   0.020   0.001   TYR B 525 
 PHE   0.033   0.001   PHE C 462 
 TRP   0.015   0.001   TRP A 351 
 HIS   0.005   0.001   HIS C 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (20652)
  covalent geometry    : angle       0.62429 (28008)
  hydrogen bonds       : bond        0.03040 ( 1060)
  hydrogen bonds       : angle       3.68935 ( 3084)

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

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

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4864 Ramachandran restraints generated.
    2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  392 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 329
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 ASP cc_start: 0.8441 (t70) cc_final: 0.7815 (m-30)
REVERT: A  122 MET cc_start: 0.8498 (mmm) cc_final: 0.8122 (mmm)
REVERT: A  215 SER cc_start: 0.9451 (m) cc_final: 0.9101 (t)
REVERT: A  243 ASP cc_start: 0.7709 (p0) cc_final: 0.7266 (p0)
REVERT: A  479 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8712 (tm-30)
REVERT: A  540 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8133 (t80)
REVERT: A  640 MET cc_start: 0.7640 (tmm) cc_final: 0.7057 (tmm)
REVERT: A  662 LEU cc_start: 0.9378 (tp) cc_final: 0.9121 (tp)
REVERT: A  679 ARG cc_start: 0.7795 (tpp80) cc_final: 0.7534 (tpt-90)
REVERT: B  108 ASP cc_start: 0.8424 (t70) cc_final: 0.7767 (m-30)
REVERT: B  122 MET cc_start: 0.8522 (mmm) cc_final: 0.8139 (mmm)
REVERT: B  215 SER cc_start: 0.9431 (m) cc_final: 0.9077 (t)
REVERT: B  243 ASP cc_start: 0.7674 (p0) cc_final: 0.7216 (p0)
REVERT: B  439 ILE cc_start: 0.8687 (mm) cc_final: 0.8366 (pt)
REVERT: B  540 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8026 (t80)
REVERT: B  599 GLU cc_start: 0.7987 (tp30) cc_final: 0.7720 (tp30)
REVERT: B  662 LEU cc_start: 0.9399 (tp) cc_final: 0.9165 (tp)
REVERT: B  679 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7565 (tpt-90)
REVERT: C  108 ASP cc_start: 0.8434 (t70) cc_final: 0.7767 (m-30)
REVERT: C  122 MET cc_start: 0.8505 (mmm) cc_final: 0.8150 (mmm)
REVERT: C  215 SER cc_start: 0.9422 (m) cc_final: 0.9073 (t)
REVERT: C  243 ASP cc_start: 0.7633 (p0) cc_final: 0.7156 (p0)
REVERT: C  264 SER cc_start: 0.9311 (m) cc_final: 0.8998 (p)
REVERT: C  439 ILE cc_start: 0.8678 (mm) cc_final: 0.8358 (pt)
REVERT: C  528 MET cc_start: 0.7334 (mmm) cc_final: 0.6857 (tpp)
REVERT: C  540 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7954 (t80)
REVERT: C  597 SER cc_start: 0.9216 (m) cc_final: 0.8937 (p)
REVERT: C  599 GLU cc_start: 0.8526 (tp30) cc_final: 0.8310 (tm-30)
REVERT: C  607 MET cc_start: 0.7797 (ppp) cc_final: 0.7200 (ppp)
REVERT: C  662 LEU cc_start: 0.9402 (tp) cc_final: 0.9176 (tp)
REVERT: C  679 ARG cc_start: 0.7808 (tpp80) cc_final: 0.7540 (tpt-90)
REVERT: C  717 LYS cc_start: 0.9112 (tttt) cc_final: 0.8885 (mmtt)
REVERT: D  108 ASP cc_start: 0.8442 (t70) cc_final: 0.7772 (m-30)
REVERT: D  122 MET cc_start: 0.8517 (mmm) cc_final: 0.8137 (mmm)
REVERT: D  162 TYR cc_start: 0.9276 (m-80) cc_final: 0.8921 (m-80)
REVERT: D  215 SER cc_start: 0.9431 (m) cc_final: 0.9071 (t)
REVERT: D  243 ASP cc_start: 0.7677 (p0) cc_final: 0.7238 (p0)
REVERT: D  264 SER cc_start: 0.9311 (m) cc_final: 0.8994 (p)
REVERT: D  433 MET cc_start: 0.4912 (ttp) cc_final: 0.4575 (ttt)
REVERT: D  479 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8781 (tm-30)
REVERT: D  540 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8127 (t80)
REVERT: D  597 SER cc_start: 0.8909 (m) cc_final: 0.8638 (p)
REVERT: D  598 LEU cc_start: 0.8760 (tt) cc_final: 0.8356 (tp)
REVERT: D  662 LEU cc_start: 0.9414 (tp) cc_final: 0.9179 (tp)
  outliers start: 63
  outliers final: 55
  residues processed: 380
  average time/residue: 0.1067
  time to fit residues: 68.8505
Evaluate side-chains
  384 residues out of total 2212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 325
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  438 HIS
Chi-restraints excluded: chain A residue  456 PHE
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  540 PHE
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain B residue  284 THR
Chi-restraints excluded: chain B residue  291 SER
Chi-restraints excluded: chain B residue  308 ILE
Chi-restraints excluded: chain B residue  356 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  438 HIS
Chi-restraints excluded: chain B residue  456 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  605 ILE
Chi-restraints excluded: chain B residue  639 ASN
Chi-restraints excluded: chain C residue   84 VAL
Chi-restraints excluded: chain C residue  205 THR
Chi-restraints excluded: chain C residue  242 THR
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  291 SER
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  402 VAL
Chi-restraints excluded: chain C residue  438 HIS
Chi-restraints excluded: chain C residue  456 PHE
Chi-restraints excluded: chain C residue  538 LEU
Chi-restraints excluded: chain C residue  540 PHE
Chi-restraints excluded: chain C residue  548 LEU
Chi-restraints excluded: chain C residue  605 ILE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain D residue   75 PHE
Chi-restraints excluded: chain D residue  205 THR
Chi-restraints excluded: chain D residue  242 THR
Chi-restraints excluded: chain D residue  277 MET
Chi-restraints excluded: chain D residue  308 ILE
Chi-restraints excluded: chain D residue  310 ILE
Chi-restraints excluded: chain D residue  356 VAL
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  434 LEU
Chi-restraints excluded: chain D residue  438 HIS
Chi-restraints excluded: chain D residue  456 PHE
Chi-restraints excluded: chain D residue  484 VAL
Chi-restraints excluded: chain D residue  538 LEU
Chi-restraints excluded: chain D residue  540 PHE
Chi-restraints excluded: chain D residue  548 LEU
Chi-restraints excluded: chain D residue  605 ILE
Chi-restraints excluded: chain D residue  627 LEU
Chi-restraints excluded: chain D residue  639 ASN
Chi-restraints excluded: chain D residue  718 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 236 optimal weight:    0.3980
   chunk 233 optimal weight:    0.8980
   chunk 174 optimal weight:    4.9990
   chunk 115 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 205 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 160 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 208 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
B 154 ASN
** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 530 GLN
C 154 ASN
** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.110232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.096694 restraints weight = 41915.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.099252 restraints weight = 24033.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.101032 restraints weight = 16041.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.102254 restraints weight = 11811.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.103035 restraints weight = 9363.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.5313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  20652  Z= 0.102
  Angle     :  0.628  12.092  28008  Z= 0.277
  Chirality :  0.037   0.142   3140
  Planarity :  0.003   0.033   3468
  Dihedral  :  3.429  14.957   2696
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 26.37 %
    Favored  : 70.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.17), residues: 2432
  helix:  1.92 (0.14), residues: 1468
  sheet:  None (None), residues: 0
  loop : -0.77 (0.19), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 684 
 TYR   0.018   0.001   TYR B 525 
 PHE   0.020   0.001   PHE B 612 
 TRP   0.015   0.001   TRP A 351 
 HIS   0.004   0.000   HIS C 438 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (20652)
  covalent geometry    : angle       0.62761 (28008)
  hydrogen bonds       : bond        0.02910 ( 1060)
  hydrogen bonds       : angle       3.66004 ( 3084)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2671.49 seconds
wall clock time: 47 minutes 16.65 seconds (2836.65 seconds total)