Starting phenix.real_space_refine
on Thu Mar  5 06:10:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xeo_33157/03_2026/7xeo_33157.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xeo_33157/03_2026/7xeo_33157.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xeo_33157/03_2026/7xeo_33157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xeo_33157/03_2026/7xeo_33157.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xeo_33157/03_2026/7xeo_33157.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xeo_33157/03_2026/7xeo_33157.cif"
  }
  resolution = 2.89
  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=   0.003
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     108      5.16       5
     C   13064      2.51       5
     N    3372      2.21       5
     O    3436      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 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: 19980
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4995
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 20, 'TRANS': 593}
          Chain breaks: 2
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 4.62, per 1000 atoms: 0.23
  Number of scatterers: 19980
  At special positions: 0
  Unit cell: (157.17, 157.17, 117.624, 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     108     16.00
     O    3436      8.00
     N    3372      7.00
     C   13064      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: 1.68
  Conformation dependent library (CDL) restraints added in 808.3 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:  4624

  Finding SS restraints...
    Secondary structure from input PDB file:
      116 helices and 4 sheets defined
      63.4% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 82
      removed outlier: 3.554A  pdb=" N   LEU A  75 " --> pdb=" O   ASP A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 85
      No H-bonds generated for 'chain 'A' and resid 83 through 85'
    Processing helix  chain 'A' and resid 86 through 96
      removed outlier: 4.070A  pdb=" N   LEU A  90 " --> pdb=" O   GLU A  86 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 99
      No H-bonds generated for 'chain 'A' and resid 97 through 99'
    Processing helix  chain 'A' and resid 114 through 121
    Processing helix  chain 'A' and resid 130 through 142
      removed outlier: 3.539A  pdb=" N   ASP A 140 " --> pdb=" O   GLN A 136 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   SER A 141 " --> pdb=" O   ILE A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 169
      removed outlier: 3.609A  pdb=" N   ILE A 165 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 182
      removed outlier: 3.566A  pdb=" N   VAL A 175 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 215
    Processing helix  chain 'A' and resid 217 through 226
      removed outlier: 3.551A  pdb=" N   TYR A 223 " --> pdb=" O   ASP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 251
    Processing helix  chain 'A' and resid 255 through 277
      removed outlier: 3.523A  pdb=" N   ARG A 275 " --> pdb=" O   GLN A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 301
    Processing helix  chain 'A' and resid 302 through 311
    Processing helix  chain 'A' and resid 350 through 358
    Processing helix  chain 'A' and resid 363 through 368
      removed outlier: 3.745A  pdb=" N   ARG A 366 " --> pdb=" O   HIS A 363 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 368 " --> pdb=" O   HIS A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 408
      Proline residue:  A 386  - end of helix
    Processing helix  chain 'A' and resid 424 through 454
    Processing helix  chain 'A' and resid 455 through 458
      removed outlier: 3.842A  pdb=" N   ILE A 458 " --> pdb=" O   ARG A 455 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 455 through 458'
    Processing helix  chain 'A' and resid 467 through 488
      removed outlier: 3.975A  pdb=" N   PHE A 486 " --> pdb=" O   GLN A 482 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL A 487 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 506
      removed outlier: 3.568A  pdb=" N   LEU A 495 " --> pdb=" O   TRP A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 510
    Processing helix  chain 'A' and resid 514 through 531
      removed outlier: 4.150A  pdb=" N   ILE A 519 " --> pdb=" O   GLN A 515 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   TYR A 520 " --> pdb=" O   HIS A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 553
      removed outlier: 3.529A  pdb=" N   ALA A 549 " --> pdb=" O   GLY A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 601
      removed outlier: 3.553A  pdb=" N   SER A 592 " --> pdb=" O   ILE A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 613 through 630
      removed outlier: 3.522A  pdb=" N   LEU A 627 " --> pdb=" O   ALA A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 648
      removed outlier: 3.523A  pdb=" N   ASN A 645 " --> pdb=" O   SER A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 668
      removed outlier: 3.804A  pdb=" N   ASN A 668 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 713
      removed outlier: 3.699A  pdb=" N   TRP A 710 " --> pdb=" O   ASN A 706 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS A 712 " --> pdb=" O   ALA A 708 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   THR A 713 " --> pdb=" O   ALA A 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 82
      removed outlier: 3.554A  pdb=" N   LEU B  75 " --> pdb=" O   ASP B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 85
      No H-bonds generated for 'chain 'B' and resid 83 through 85'
    Processing helix  chain 'B' and resid 86 through 96
      removed outlier: 4.070A  pdb=" N   LEU B  90 " --> pdb=" O   GLU B  86 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG B  95 " --> pdb=" O   LEU B  91 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 99
      No H-bonds generated for 'chain 'B' and resid 97 through 99'
    Processing helix  chain 'B' and resid 114 through 121
    Processing helix  chain 'B' and resid 130 through 142
      removed outlier: 3.539A  pdb=" N   ASP B 140 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   SER B 141 " --> pdb=" O   ILE B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 161 through 169
      removed outlier: 3.609A  pdb=" N   ILE B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 182
      removed outlier: 3.567A  pdb=" N   VAL B 175 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 215
    Processing helix  chain 'B' and resid 217 through 226
      removed outlier: 3.500A  pdb=" N   VAL B 221 " --> pdb=" O   GLN B 217 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   TYR B 223 " --> pdb=" O   ASP B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 251
    Processing helix  chain 'B' and resid 255 through 277
      removed outlier: 3.523A  pdb=" N   ARG B 275 " --> pdb=" O   GLN B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 301
    Processing helix  chain 'B' and resid 302 through 311
    Processing helix  chain 'B' and resid 350 through 358
    Processing helix  chain 'B' and resid 363 through 368
      removed outlier: 3.746A  pdb=" N   ARG B 366 " --> pdb=" O   HIS B 363 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL B 368 " --> pdb=" O   HIS B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 408
      Proline residue:  B 386  - end of helix
    Processing helix  chain 'B' and resid 424 through 454
    Processing helix  chain 'B' and resid 455 through 458
      removed outlier: 3.842A  pdb=" N   ILE B 458 " --> pdb=" O   ARG B 455 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 455 through 458'
    Processing helix  chain 'B' and resid 467 through 488
      removed outlier: 3.975A  pdb=" N   PHE B 486 " --> pdb=" O   GLN B 482 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL B 487 " --> pdb=" O   VAL B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 506
      removed outlier: 3.567A  pdb=" N   LEU B 495 " --> pdb=" O   TRP B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 510
    Processing helix  chain 'B' and resid 514 through 531
      removed outlier: 4.150A  pdb=" N   ILE B 519 " --> pdb=" O   GLN B 515 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TYR B 520 " --> pdb=" O   HIS B 516 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 553
      removed outlier: 3.529A  pdb=" N   ALA B 549 " --> pdb=" O   GLY B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 601
      removed outlier: 3.552A  pdb=" N   SER B 592 " --> pdb=" O   ILE B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 613 through 630
      removed outlier: 3.522A  pdb=" N   LEU B 627 " --> pdb=" O   ALA B 623 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 648
      removed outlier: 3.523A  pdb=" N   ASN B 645 " --> pdb=" O   SER B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 668
      removed outlier: 3.803A  pdb=" N   ASN B 668 " --> pdb=" O   LEU B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 706 through 713
      removed outlier: 3.699A  pdb=" N   TRP B 710 " --> pdb=" O   ASN B 706 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   LYS B 712 " --> pdb=" O   ALA B 708 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   THR B 713 " --> pdb=" O   ALA B 709 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 82
      removed outlier: 3.554A  pdb=" N   LEU C  75 " --> pdb=" O   ASP C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 85
      No H-bonds generated for 'chain 'C' and resid 83 through 85'
    Processing helix  chain 'C' and resid 86 through 96
      removed outlier: 4.069A  pdb=" N   LEU C  90 " --> pdb=" O   GLU C  86 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU C  92 " --> pdb=" O   THR C  88 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG C  95 " --> pdb=" O   LEU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 99
      No H-bonds generated for 'chain 'C' and resid 97 through 99'
    Processing helix  chain 'C' and resid 114 through 121
    Processing helix  chain 'C' and resid 130 through 142
      removed outlier: 3.539A  pdb=" N   ASP C 140 " --> pdb=" O   GLN C 136 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   SER C 141 " --> pdb=" O   ILE C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 161 through 169
      removed outlier: 3.609A  pdb=" N   ILE C 165 " --> pdb=" O   SER C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 171 through 182
      removed outlier: 3.566A  pdb=" N   VAL C 175 " --> pdb=" O   SER C 171 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 207 through 215
    Processing helix  chain 'C' and resid 217 through 226
      removed outlier: 3.551A  pdb=" N   TYR C 223 " --> pdb=" O   ASP C 219 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 251
    Processing helix  chain 'C' and resid 255 through 277
      removed outlier: 3.522A  pdb=" N   ARG C 275 " --> pdb=" O   GLN C 271 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 292 through 301
    Processing helix  chain 'C' and resid 302 through 311
    Processing helix  chain 'C' and resid 350 through 358
    Processing helix  chain 'C' and resid 363 through 368
      removed outlier: 3.744A  pdb=" N   ARG C 366 " --> pdb=" O   HIS C 363 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL C 368 " --> pdb=" O   HIS C 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 408
      Proline residue:  C 386  - end of helix
    Processing helix  chain 'C' and resid 424 through 454
    Processing helix  chain 'C' and resid 455 through 458
      removed outlier: 3.842A  pdb=" N   ILE C 458 " --> pdb=" O   ARG C 455 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 455 through 458'
    Processing helix  chain 'C' and resid 467 through 488
      removed outlier: 3.976A  pdb=" N   PHE C 486 " --> pdb=" O   GLN C 482 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL C 487 " --> pdb=" O   VAL C 483 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 491 through 506
      removed outlier: 3.568A  pdb=" N   LEU C 495 " --> pdb=" O   TRP C 491 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 507 through 510
    Processing helix  chain 'C' and resid 514 through 531
      removed outlier: 4.151A  pdb=" N   ILE C 519 " --> pdb=" O   GLN C 515 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   TYR C 520 " --> pdb=" O   HIS C 516 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 532 through 553
      removed outlier: 3.529A  pdb=" N   ALA C 549 " --> pdb=" O   GLY C 545 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 587 through 601
      removed outlier: 3.552A  pdb=" N   SER C 592 " --> pdb=" O   ILE C 588 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 613 through 630
      removed outlier: 3.521A  pdb=" N   LEU C 627 " --> pdb=" O   ALA C 623 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 631 through 648
      removed outlier: 3.523A  pdb=" N   ASN C 645 " --> pdb=" O   SER C 641 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 650 through 668
      removed outlier: 3.804A  pdb=" N   ASN C 668 " --> pdb=" O   LEU C 664 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 706 through 713
      removed outlier: 3.700A  pdb=" N   TRP C 710 " --> pdb=" O   ASN C 706 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS C 712 " --> pdb=" O   ALA C 708 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   THR C 713 " --> pdb=" O   ALA C 709 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 71 through 82
      removed outlier: 3.554A  pdb=" N   LEU D  75 " --> pdb=" O   ASP D  71 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 85
      No H-bonds generated for 'chain 'D' and resid 83 through 85'
    Processing helix  chain 'D' and resid 86 through 96
      removed outlier: 4.070A  pdb=" N   LEU D  90 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU D  92 " --> pdb=" O   THR D  88 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG D  95 " --> pdb=" O   LEU D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 99
      No H-bonds generated for 'chain 'D' and resid 97 through 99'
    Processing helix  chain 'D' and resid 114 through 121
    Processing helix  chain 'D' and resid 130 through 142
      removed outlier: 3.538A  pdb=" N   ASP D 140 " --> pdb=" O   GLN D 136 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   SER D 141 " --> pdb=" O   ILE D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 161 through 169
      removed outlier: 3.609A  pdb=" N   ILE D 165 " --> pdb=" O   SER D 161 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 182
      removed outlier: 3.567A  pdb=" N   VAL D 175 " --> pdb=" O   SER D 171 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 207 through 215
    Processing helix  chain 'D' and resid 217 through 226
      removed outlier: 3.552A  pdb=" N   TYR D 223 " --> pdb=" O   ASP D 219 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 251
    Processing helix  chain 'D' and resid 255 through 277
      removed outlier: 3.523A  pdb=" N   ARG D 275 " --> pdb=" O   GLN D 271 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 292 through 301
    Processing helix  chain 'D' and resid 302 through 311
    Processing helix  chain 'D' and resid 350 through 358
    Processing helix  chain 'D' and resid 363 through 368
      removed outlier: 3.745A  pdb=" N   ARG D 366 " --> pdb=" O   HIS D 363 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL D 368 " --> pdb=" O   HIS D 365 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 372 through 408
      Proline residue:  D 386  - end of helix
    Processing helix  chain 'D' and resid 424 through 454
    Processing helix  chain 'D' and resid 455 through 458
      removed outlier: 3.843A  pdb=" N   ILE D 458 " --> pdb=" O   ARG D 455 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 455 through 458'
    Processing helix  chain 'D' and resid 467 through 488
      removed outlier: 3.976A  pdb=" N   PHE D 486 " --> pdb=" O   GLN D 482 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL D 487 " --> pdb=" O   VAL D 483 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 491 through 506
      removed outlier: 3.568A  pdb=" N   LEU D 495 " --> pdb=" O   TRP D 491 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 507 through 510
    Processing helix  chain 'D' and resid 514 through 531
      removed outlier: 4.150A  pdb=" N   ILE D 519 " --> pdb=" O   GLN D 515 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   TYR D 520 " --> pdb=" O   HIS D 516 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 532 through 553
      removed outlier: 3.529A  pdb=" N   ALA D 549 " --> pdb=" O   GLY D 545 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 587 through 601
      removed outlier: 3.552A  pdb=" N   SER D 592 " --> pdb=" O   ILE D 588 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 613 through 630
      removed outlier: 3.522A  pdb=" N   LEU D 627 " --> pdb=" O   ALA D 623 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 631 through 648
      removed outlier: 3.523A  pdb=" N   ASN D 645 " --> pdb=" O   SER D 641 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 650 through 668
      removed outlier: 3.804A  pdb=" N   ASN D 668 " --> pdb=" O   LEU D 664 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 706 through 713
      removed outlier: 3.699A  pdb=" N   TRP D 710 " --> pdb=" O   ASN D 706 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LYS D 712 " --> pdb=" O   ALA D 708 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   THR D 713 " --> pdb=" O   ALA D 709 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 333 through 339
      removed outlier: 4.094A  pdb=" N   ARG A 697 " --> pdb=" O   LEU A 684 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 684 " --> pdb=" O   ARG A 697 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 333 through 339
      removed outlier: 4.094A  pdb=" N   ARG B 697 " --> pdb=" O   LEU B 684 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B 684 " --> pdb=" O   ARG B 697 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 333 through 339
      removed outlier: 4.094A  pdb=" N   ARG C 697 " --> pdb=" O   LEU C 684 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU C 684 " --> pdb=" O   ARG C 697 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 333 through 339
      removed outlier: 4.094A  pdb=" N   ARG D 697 " --> pdb=" O   LEU D 684 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU D 684 " --> pdb=" O   ARG D 697 " (cutoff:3.500A)

    1027 hydrogen bonds defined for protein.
    3045 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: 3.25

  Time building geometry restraints manager: 2.25 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: 6019
        1.34 -     1.46: 3242
        1.46 -     1.57: 11063
        1.57 -     1.69: 0
        1.69 -     1.81: 160
  Bond restraints: 20484
  Sorted by residual:
  bond pdb=" CA  GLU A 371 "
       pdb=" CB  GLU A 371 "
    ideal  model  delta    sigma   weight residual
    1.530  1.490  0.040 1.58e-02 4.01e+03 6.34e+00
  bond pdb=" CA  GLU D 371 "
       pdb=" CB  GLU D 371 "
    ideal  model  delta    sigma   weight residual
    1.530  1.490  0.040 1.58e-02 4.01e+03 6.25e+00
  bond pdb=" CA  GLU C 371 "
       pdb=" CB  GLU C 371 "
    ideal  model  delta    sigma   weight residual
    1.530  1.491  0.039 1.58e-02 4.01e+03 6.10e+00
  bond pdb=" CA  GLU B 371 "
       pdb=" CB  GLU B 371 "
    ideal  model  delta    sigma   weight residual
    1.530  1.491  0.039 1.58e-02 4.01e+03 5.94e+00
  bond pdb=" CA  GLU C 371 "
       pdb=" C   GLU C 371 "
    ideal  model  delta    sigma   weight residual
    1.524  1.496  0.028 1.26e-02 6.30e+03 5.02e+00
  ... (remaining 20479 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 27229
        2.06 -     4.11: 480
        4.11 -     6.17: 71
        6.17 -     8.22: 8
        8.22 -    10.28: 8
  Bond angle restraints: 27796
  Sorted by residual:
  angle pdb=" N   VAL A 148 "
        pdb=" CA  VAL A 148 "
        pdb=" C   VAL A 148 "
      ideal   model   delta    sigma   weight residual
     113.53  108.75    4.78 9.80e-01 1.04e+00 2.38e+01
  angle pdb=" N   VAL B 148 "
        pdb=" CA  VAL B 148 "
        pdb=" C   VAL B 148 "
      ideal   model   delta    sigma   weight residual
     113.53  108.75    4.78 9.80e-01 1.04e+00 2.38e+01
  angle pdb=" N   VAL C 148 "
        pdb=" CA  VAL C 148 "
        pdb=" C   VAL C 148 "
      ideal   model   delta    sigma   weight residual
     113.53  108.75    4.78 9.80e-01 1.04e+00 2.38e+01
  angle pdb=" N   VAL D 148 "
        pdb=" CA  VAL D 148 "
        pdb=" C   VAL D 148 "
      ideal   model   delta    sigma   weight residual
     113.53  108.79    4.74 9.80e-01 1.04e+00 2.34e+01
  angle pdb=" N   LEU B 532 "
        pdb=" CA  LEU B 532 "
        pdb=" C   LEU B 532 "
      ideal   model   delta    sigma   weight residual
     114.75  108.88    5.87 1.26e+00 6.30e-01 2.17e+01
  ... (remaining 27791 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 10948
       17.21 -    34.43: 887
       34.43 -    51.64: 153
       51.64 -    68.85: 16
       68.85 -    86.07: 20
  Dihedral angle restraints: 12024
    sinusoidal: 4856
      harmonic: 7168
  Sorted by residual:
  dihedral pdb=" N   GLU A 371 "
           pdb=" C   GLU A 371 "
           pdb=" CA  GLU A 371 "
           pdb=" CB  GLU A 371 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.19  -15.39     0      2.50e+00 1.60e-01 3.79e+01
  dihedral pdb=" N   GLU B 371 "
           pdb=" C   GLU B 371 "
           pdb=" CA  GLU B 371 "
           pdb=" CB  GLU B 371 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.17  -15.37     0      2.50e+00 1.60e-01 3.78e+01
  dihedral pdb=" N   GLU C 371 "
           pdb=" C   GLU C 371 "
           pdb=" CA  GLU C 371 "
           pdb=" CB  GLU C 371 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.15  -15.35     0      2.50e+00 1.60e-01 3.77e+01
  ... (remaining 12021 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.140: 3123
       0.140 -    0.280: 13
       0.280 -    0.420: 0
       0.420 -    0.560: 0
       0.560 -    0.700: 4
  Chirality restraints: 3140
  Sorted by residual:
  chirality pdb=" CA  GLU A 371 "
            pdb=" N   GLU A 371 "
            pdb=" C   GLU A 371 "
            pdb=" CB  GLU A 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.81    0.70 2.00e-01 2.50e+01 1.22e+01
  chirality pdb=" CA  GLU C 371 "
            pdb=" N   GLU C 371 "
            pdb=" C   GLU C 371 "
            pdb=" CB  GLU C 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.81    0.70 2.00e-01 2.50e+01 1.22e+01
  chirality pdb=" CA  GLU B 371 "
            pdb=" N   GLU B 371 "
            pdb=" C   GLU B 371 "
            pdb=" CB  GLU B 371 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.81    0.70 2.00e-01 2.50e+01 1.22e+01
  ... (remaining 3137 not shown)

  Planarity restraints: 3432
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  70 "    0.019 2.00e-02 2.50e+03   1.82e-02 5.78e+00
        pdb=" CG  PHE C  70 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  70 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  70 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  70 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  70 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  70 "   -0.019 2.00e-02 2.50e+03   1.82e-02 5.78e+00
        pdb=" CG  PHE B  70 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  70 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  70 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  70 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  70 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  70 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  70 "    0.019 2.00e-02 2.50e+03   1.81e-02 5.76e+00
        pdb=" CG  PHE D  70 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  70 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  70 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  70 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  70 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  70 "    0.000 2.00e-02 2.50e+03
  ... (remaining 3429 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 2311
        2.75 -     3.29: 20093
        3.29 -     3.83: 33115
        3.83 -     4.36: 37144
        4.36 -     4.90: 65414
  Nonbonded interactions: 158077
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 143 "
            pdb=" CD  PRO A 144 "
     model   vdw
     2.214 3.440
  nonbonded pdb=" OD1 ASN C 143 "
            pdb=" CD  PRO C 144 "
     model   vdw
     2.214 3.440
  nonbonded pdb=" OD1 ASN B 143 "
            pdb=" CD  PRO B 144 "
     model   vdw
     2.214 3.440
  nonbonded pdb=" OD1 ASN D 143 "
            pdb=" CD  PRO D 144 "
     model   vdw
     2.215 3.440
  nonbonded pdb=" N   GLN C 145 "
            pdb=" OE1 GLN C 145 "
     model   vdw
     2.252 3.120
  ... (remaining 158072 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.070
  Set scattering table:                    0.050
  Process input model:                     18.390
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
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      :  0.003   0.040  20484  Z= 0.148
  Angle     :  0.698  10.281  27796  Z= 0.412
  Chirality :  0.046   0.700   3140
  Planarity :  0.003   0.031   3432
  Dihedral  : 12.941  86.069   7400
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.99 %
    Allowed  :  4.28 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  0.37 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.18), residues: 2432
  helix:  1.74 (0.14), residues: 1444
  sheet: -4.18 (0.42), residues: 84
  loop : -2.56 (0.20), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 485 
 TYR   0.010   0.001   TYR C  93 
 PHE   0.042   0.001   PHE B  70 
 TRP   0.010   0.001   TRP B 652 
 HIS   0.005   0.001   HIS B 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (20484)
  covalent geometry    : angle       0.69789 (27796)
  hydrogen bonds       : bond        0.15825 ( 1027)
  hydrogen bonds       : angle       5.55115 ( 3045)

*********************** 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
  301 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 285
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 GLN cc_start: 0.8200 (tp-100) cc_final: 0.7983 (tp40)
REVERT: A  272 MET cc_start: 0.8626 (tpp) cc_final: 0.8407 (tpp)
REVERT: B  539 TYR cc_start: 0.8375 (t80) cc_final: 0.8035 (t80)
REVERT: C   70 PHE cc_start: 0.2820 (m-80) cc_final: 0.2468 (m-10)
REVERT: C  188 ARG cc_start: 0.7369 (mmt90) cc_final: 0.6861 (mmt90)
REVERT: D   76 PHE cc_start: 0.8075 (m-10) cc_final: 0.7854 (m-80)
REVERT: D  539 TYR cc_start: 0.8394 (t80) cc_final: 0.8052 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 300
  average time/residue: 0.6142
  time to fit residues: 208.5405
Evaluate side-chains
  200 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 192
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  371 GLU
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain B residue  371 GLU
Chi-restraints excluded: chain B residue  373 LEU
Chi-restraints excluded: chain C residue  371 GLU
Chi-restraints excluded: chain C residue  373 LEU
Chi-restraints excluded: chain D residue  371 GLU
Chi-restraints excluded: chain D residue  373 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 216 optimal weight:    0.8980
   chunk 98 optimal weight:    4.9990
   chunk 194 optimal weight:    8.9990
   chunk 227 optimal weight:    3.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    7.9990
   chunk 235 optimal weight:    0.7980
   overall best weight:    2.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.110593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.080329 restraints weight = 40495.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.81
r_work: 0.3036 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087  20484  Z= 0.188
  Angle     :  0.656   9.483  27796  Z= 0.332
  Chirality :  0.041   0.230   3140
  Planarity :  0.004   0.039   3432
  Dihedral  :  5.987 101.049   2716
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.06 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.53 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.18), residues: 2432
  helix:  2.08 (0.14), residues: 1432
  sheet: -3.99 (0.40), residues: 84
  loop : -2.42 (0.19), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  96 
 TYR   0.014   0.001   TYR A 223 
 PHE   0.035   0.001   PHE A  70 
 TRP   0.007   0.001   TRP D 698 
 HIS   0.007   0.001   HIS C 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (20484)
  covalent geometry    : angle       0.65618 (27796)
  hydrogen bonds       : bond        0.04717 ( 1027)
  hydrogen bonds       : angle       4.25978 ( 3045)

*********************** 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
  244 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 185
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 GLN cc_start: 0.8307 (tp-100) cc_final: 0.7995 (tp40)
REVERT: A  409 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8086 (tt0)
REVERT: B  409 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8102 (tt0)
REVERT: C   70 PHE cc_start: 0.3494 (m-80) cc_final: 0.3031 (m-10)
REVERT: C  409 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8021 (tt0)
REVERT: C  431 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8295 (tm)
REVERT: D   76 PHE cc_start: 0.8046 (m-10) cc_final: 0.7815 (m-80)
  outliers start: 59
  outliers final: 27
  residues processed: 223
  average time/residue: 0.5251
  time to fit residues: 135.6753
Evaluate side-chains
  191 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 160
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  165 ILE
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  219 ASP
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  409 GLN
Chi-restraints excluded: chain B residue  476 LEU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  668 ASN
Chi-restraints excluded: chain C residue  131 ILE
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  435 LEU
Chi-restraints excluded: chain C residue  529 LEU
Chi-restraints excluded: chain D residue  131 ILE
Chi-restraints excluded: chain D residue  219 ASP
Chi-restraints excluded: chain D residue  317 LEU
Chi-restraints excluded: chain D residue  476 LEU
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  626 LEU
Chi-restraints excluded: chain D residue  668 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 135 optimal weight:    7.9990
   chunk 117 optimal weight:    5.9990
   chunk 176 optimal weight:    0.1980
   chunk 196 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9990
   chunk 188 optimal weight:    0.9980
   chunk 156 optimal weight:    0.7980
   chunk 184 optimal weight:    7.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.112275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.081984 restraints weight = 40588.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 2.84
r_work: 0.3082 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  20484  Z= 0.115
  Angle     :  0.566   8.332  27796  Z= 0.287
  Chirality :  0.039   0.210   3140
  Planarity :  0.004   0.058   3432
  Dihedral  :  3.849  25.985   2696
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.26 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 13.69 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.18), residues: 2432
  helix:  2.26 (0.14), residues: 1460
  sheet: -3.78 (0.41), residues: 84
  loop : -2.39 (0.20), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  74 
 TYR   0.014   0.001   TYR A 466 
 PHE   0.025   0.001   PHE A  70 
 TRP   0.006   0.001   TRP D 173 
 HIS   0.005   0.001   HIS D 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (20484)
  covalent geometry    : angle       0.56551 (27796)
  hydrogen bonds       : bond        0.03684 ( 1027)
  hydrogen bonds       : angle       3.92486 ( 3045)

*********************** 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
  240 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 182
  time to evaluate  : 0.844 
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: A   92 GLU cc_start: 0.8755 (mp0) cc_final: 0.8445 (pm20)
REVERT: A  121 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8778 (mt)
REVERT: A  132 LEU cc_start: 0.9231 (tt) cc_final: 0.9013 (tp)
REVERT: A  230 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7976 (tp40)
REVERT: A  370 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7870 (pp)
REVERT: B  121 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8815 (mt)
REVERT: B  370 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7826 (pp)
REVERT: C  132 LEU cc_start: 0.9256 (tt) cc_final: 0.9051 (tp)
REVERT: C  370 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7875 (pp)
REVERT: C  431 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8259 (tm)
REVERT: D  188 ARG cc_start: 0.7524 (mmt90) cc_final: 0.7094 (mtt180)
REVERT: D  370 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7809 (pp)
REVERT: D  431 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8474 (tt)
REVERT: D  635 MET cc_start: 0.8603 (ttp) cc_final: 0.8260 (ttt)
  outliers start: 58
  outliers final: 16
  residues processed: 224
  average time/residue: 0.5004
  time to fit residues: 130.9770
Evaluate side-chains
  183 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 TYR
Chi-restraints excluded: chain A residue  121 LEU
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain B residue  100 TYR
Chi-restraints excluded: chain B residue  121 LEU
Chi-restraints excluded: chain B residue  136 GLN
Chi-restraints excluded: chain B residue  219 ASP
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain D residue  100 TYR
Chi-restraints excluded: chain D residue  219 ASP
Chi-restraints excluded: chain D residue  317 LEU
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  431 LEU
Chi-restraints excluded: chain D residue  497 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 223 optimal weight:    6.9990
   chunk 151 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 149 optimal weight:    3.9990
   chunk 168 optimal weight:    0.9980
   chunk 190 optimal weight:    8.9990
   chunk 189 optimal weight:    0.9980
   chunk 197 optimal weight:    7.9990
   chunk 229 optimal weight:    0.9980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 525 GLN
B 258 ASN
B 525 GLN
B 668 ASN
** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 525 GLN
D 668 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.111262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.080850 restraints weight = 40830.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.84
r_work: 0.3063 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  20484  Z= 0.119
  Angle     :  0.569  14.465  27796  Z= 0.281
  Chirality :  0.039   0.163   3140
  Planarity :  0.004   0.067   3432
  Dihedral  :  3.702  26.342   2696
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.06 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 15.21 %
    Favored  : 81.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.18), residues: 2432
  helix:  2.46 (0.14), residues: 1428
  sheet: -3.54 (0.44), residues: 84
  loop : -2.27 (0.20), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  74 
 TYR   0.008   0.001   TYR C 106 
 PHE   0.020   0.001   PHE C  70 
 TRP   0.007   0.001   TRP D 173 
 HIS   0.004   0.001   HIS D 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (20484)
  covalent geometry    : angle       0.56866 (27796)
  hydrogen bonds       : bond        0.03652 ( 1027)
  hydrogen bonds       : angle       3.84213 ( 3045)

*********************** 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
  239 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 172
  time to evaluate  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7363 (t0)
REVERT: A  230 GLN cc_start: 0.8271 (tp-100) cc_final: 0.7965 (tp40)
REVERT: A  370 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7754 (pp)
REVERT: A  431 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8510 (tt)
REVERT: A  486 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8378 (m-80)
REVERT: B  143 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7250 (t0)
REVERT: B  370 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7777 (pp)
REVERT: B  431 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8515 (tt)
REVERT: B  486 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8383 (m-80)
REVERT: C   70 PHE cc_start: 0.3619 (m-80) cc_final: 0.3182 (m-10)
REVERT: C   99 LYS cc_start: 0.6536 (ptpt) cc_final: 0.5972 (pttp)
REVERT: C  370 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7750 (pp)
REVERT: C  431 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8228 (tm)
REVERT: C  486 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8293 (m-80)
REVERT: D  143 ASN cc_start: 0.7629 (OUTLIER) cc_final: 0.7228 (t0)
REVERT: D  188 ARG cc_start: 0.7511 (mmt90) cc_final: 0.7105 (mtt180)
REVERT: D  370 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7759 (pp)
REVERT: D  486 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8384 (m-80)
REVERT: D  635 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8400 (ttt)
  outliers start: 67
  outliers final: 20
  residues processed: 211
  average time/residue: 0.4890
  time to fit residues: 120.0435
Evaluate side-chains
  190 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 155
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 TYR
Chi-restraints excluded: chain A residue  143 ASN
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain B residue  100 TYR
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  219 ASP
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  476 LEU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  486 PHE
Chi-restraints excluded: chain C residue  492 TYR
Chi-restraints excluded: chain C residue  702 VAL
Chi-restraints excluded: chain D residue  143 ASN
Chi-restraints excluded: chain D residue  219 ASP
Chi-restraints excluded: chain D residue  317 LEU
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  486 PHE
Chi-restraints excluded: chain D residue  492 TYR
Chi-restraints excluded: chain D residue  626 LEU
Chi-restraints excluded: chain D residue  635 MET
Chi-restraints excluded: chain D residue  702 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 232 optimal weight:    0.9980
   chunk 146 optimal weight:    5.9990
   chunk 220 optimal weight:    1.9990
   chunk 64 optimal weight:    6.9990
   chunk 169 optimal weight:    5.9990
   chunk 226 optimal weight:    2.9990
   chunk 230 optimal weight:    2.9990
   chunk 152 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 118 optimal weight:   10.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
B 515 GLN
** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 258 ASN
C 515 GLN
C 525 GLN
** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 258 ASN
D 515 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.107996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.077188 restraints weight = 40858.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.86
r_work: 0.2997 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  20484  Z= 0.173
  Angle     :  0.607  12.029  27796  Z= 0.305
  Chirality :  0.040   0.189   3140
  Planarity :  0.005   0.068   3432
  Dihedral  :  3.794  26.734   2696
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.17 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 14.80 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.18), residues: 2432
  helix:  2.55 (0.14), residues: 1400
  sheet: -3.26 (0.47), residues: 84
  loop : -2.24 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  72 
 TYR   0.009   0.001   TYR D 466 
 PHE   0.022   0.001   PHE C  70 
 TRP   0.010   0.001   TRP C 698 
 HIS   0.004   0.001   HIS B 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (20484)
  covalent geometry    : angle       0.60716 (27796)
  hydrogen bonds       : bond        0.04264 ( 1027)
  hydrogen bonds       : angle       3.92148 ( 3045)

*********************** 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
  258 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 170
  time to evaluate  : 0.692 
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: A   92 GLU cc_start: 0.8704 (mp0) cc_final: 0.8378 (pm20)
REVERT: A  143 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7495 (t0)
REVERT: A  230 GLN cc_start: 0.8286 (tp-100) cc_final: 0.7979 (tp40)
REVERT: A  370 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7829 (pp)
REVERT: A  431 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8508 (tt)
REVERT: A  486 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8314 (m-80)
REVERT: A  511 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9084 (p)
REVERT: B   76 PHE cc_start: 0.8021 (m-10) cc_final: 0.7810 (m-80)
REVERT: B   92 GLU cc_start: 0.8703 (mp0) cc_final: 0.8357 (pm20)
REVERT: B  143 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7386 (t0)
REVERT: B  370 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7837 (pp)
REVERT: B  431 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8511 (tt)
REVERT: B  486 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8337 (m-80)
REVERT: B  511 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9115 (p)
REVERT: C   70 PHE cc_start: 0.3688 (m-80) cc_final: 0.3014 (m-10)
REVERT: C   99 LYS cc_start: 0.6787 (ptpt) cc_final: 0.6246 (pttp)
REVERT: C  121 LEU cc_start: 0.8869 (mt) cc_final: 0.8658 (mp)
REVERT: C  188 ARG cc_start: 0.7664 (mmt90) cc_final: 0.7110 (mmt90)
REVERT: C  370 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7813 (pp)
REVERT: C  431 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8320 (tm)
REVERT: C  486 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8305 (m-80)
REVERT: C  511 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.9078 (p)
REVERT: D  143 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7238 (t0)
REVERT: D  370 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7820 (pp)
REVERT: D  431 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8510 (tt)
REVERT: D  486 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8339 (m-80)
REVERT: D  511 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9103 (p)
  outliers start: 88
  outliers final: 37
  residues processed: 232
  average time/residue: 0.4748
  time to fit residues: 128.4249
Evaluate side-chains
  209 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 153
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 TYR
Chi-restraints excluded: chain A residue  143 ASN
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  626 LEU
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain B residue  100 TYR
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  219 ASP
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  476 LEU
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  511 THR
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  626 LEU
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain C residue  143 ASN
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  476 LEU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  486 PHE
Chi-restraints excluded: chain C residue  492 TYR
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain C residue  511 THR
Chi-restraints excluded: chain C residue  529 LEU
Chi-restraints excluded: chain C residue  702 VAL
Chi-restraints excluded: chain D residue  143 ASN
Chi-restraints excluded: chain D residue  219 ASP
Chi-restraints excluded: chain D residue  317 LEU
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  431 LEU
Chi-restraints excluded: chain D residue  476 LEU
Chi-restraints excluded: chain D residue  483 VAL
Chi-restraints excluded: chain D residue  486 PHE
Chi-restraints excluded: chain D residue  492 TYR
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  511 THR
Chi-restraints excluded: chain D residue  626 LEU
Chi-restraints excluded: chain D residue  702 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    0.1980
   chunk 203 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 204 optimal weight:    4.9990
   chunk 242 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   chunk 232 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 162 optimal weight:    7.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 515 GLN
** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.109912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.079534 restraints weight = 40484.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 2.81
r_work: 0.3041 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  20484  Z= 0.121
  Angle     :  0.597  14.752  27796  Z= 0.295
  Chirality :  0.040   0.293   3140
  Planarity :  0.004   0.065   3432
  Dihedral  :  3.744  27.397   2696
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.76 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.96 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.18), residues: 2432
  helix:  2.64 (0.14), residues: 1400
  sheet: -2.80 (0.51), residues: 84
  loop : -2.18 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  72 
 TYR   0.008   0.001   TYR C 466 
 PHE   0.029   0.001   PHE C  76 
 TRP   0.009   0.001   TRP C 173 
 HIS   0.004   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (20484)
  covalent geometry    : angle       0.59662 (27796)
  hydrogen bonds       : bond        0.03724 ( 1027)
  hydrogen bonds       : angle       3.87661 ( 3045)

*********************** 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
  233 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 160
  time to evaluate  : 0.809 
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: A  143 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.7359 (t0)
REVERT: A  230 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7955 (tp40)
REVERT: A  370 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7786 (pp)
REVERT: A  431 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8533 (tt)
REVERT: A  486 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8344 (m-80)
REVERT: B   92 GLU cc_start: 0.8652 (mp0) cc_final: 0.8342 (pm20)
REVERT: B  143 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7307 (t0)
REVERT: B  370 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7764 (pp)
REVERT: B  431 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8528 (tt)
REVERT: B  486 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8359 (m-80)
REVERT: C   70 PHE cc_start: 0.3336 (m-80) cc_final: 0.3108 (m-10)
REVERT: C   99 LYS cc_start: 0.6734 (ptpt) cc_final: 0.6200 (pttp)
REVERT: C  118 LYS cc_start: 0.8824 (tptt) cc_final: 0.8577 (tptp)
REVERT: C  121 LEU cc_start: 0.8859 (mt) cc_final: 0.8641 (mp)
REVERT: C  143 ASN cc_start: 0.7536 (OUTLIER) cc_final: 0.7097 (t0)
REVERT: C  370 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7743 (pp)
REVERT: C  431 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8319 (tm)
REVERT: C  486 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8322 (m-80)
REVERT: C  604 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7845 (mp0)
REVERT: D   75 LEU cc_start: 0.7031 (mm) cc_final: 0.6802 (mp)
REVERT: D  370 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7769 (pp)
REVERT: D  431 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8524 (tt)
REVERT: D  486 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8360 (m-80)
  outliers start: 73
  outliers final: 26
  residues processed: 210
  average time/residue: 0.4785
  time to fit residues: 117.5611
Evaluate side-chains
  195 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 153
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ASN
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  219 ASP
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain C residue  143 ASN
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  486 PHE
Chi-restraints excluded: chain C residue  492 TYR
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain C residue  529 LEU
Chi-restraints excluded: chain C residue  604 GLU
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain D residue  143 ASN
Chi-restraints excluded: chain D residue  219 ASP
Chi-restraints excluded: chain D residue  317 LEU
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  431 LEU
Chi-restraints excluded: chain D residue  486 PHE
Chi-restraints excluded: chain D residue  492 TYR
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain D residue  611 LEU
Chi-restraints excluded: chain D residue  702 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 212 optimal weight:    9.9990
   chunk 176 optimal weight:    6.9990
   chunk 171 optimal weight:    0.9980
   chunk 219 optimal weight:    3.9990
   chunk 119 optimal weight:    8.9990
   chunk 194 optimal weight:    9.9990
   chunk 175 optimal weight:    0.9990
   chunk 155 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 123 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.109470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.079088 restraints weight = 40732.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.81
r_work: 0.3029 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  20484  Z= 0.134
  Angle     :  0.599  14.296  27796  Z= 0.298
  Chirality :  0.040   0.441   3140
  Planarity :  0.004   0.063   3432
  Dihedral  :  3.734  27.274   2696
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.80 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.11 %
    Favored  : 79.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.18), residues: 2432
  helix:  2.60 (0.14), residues: 1400
  sheet: -2.50 (0.56), residues: 84
  loop : -2.14 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B  72 
 TYR   0.007   0.001   TYR D 266 
 PHE   0.017   0.001   PHE C  70 
 TRP   0.010   0.001   TRP C 173 
 HIS   0.004   0.001   HIS D 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (20484)
  covalent geometry    : angle       0.59922 (27796)
  hydrogen bonds       : bond        0.03789 ( 1027)
  hydrogen bonds       : angle       3.86750 ( 3045)

*********************** 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
  229 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 168
  time to evaluate  : 0.748 
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: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8626 (pm20)
REVERT: A  143 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7290 (t0)
REVERT: A  230 GLN cc_start: 0.8264 (tp-100) cc_final: 0.7958 (tp40)
REVERT: A  370 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7808 (pp)
REVERT: A  431 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8528 (tt)
REVERT: A  486 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8328 (m-80)
REVERT: B  143 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7232 (t0)
REVERT: B  370 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7803 (pp)
REVERT: B  431 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8525 (tt)
REVERT: B  486 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8341 (m-80)
REVERT: C  118 LYS cc_start: 0.8846 (tptt) cc_final: 0.8585 (tptp)
REVERT: C  121 LEU cc_start: 0.8883 (mt) cc_final: 0.8672 (mp)
REVERT: C  188 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7631 (mtt90)
REVERT: C  370 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7701 (pp)
REVERT: C  431 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8356 (tm)
REVERT: C  486 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8323 (m-80)
REVERT: C  604 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7856 (mp0)
REVERT: D  370 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7728 (pp)
REVERT: D  431 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8524 (tt)
REVERT: D  486 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8321 (m-80)
REVERT: D  635 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8374 (ttt)
  outliers start: 61
  outliers final: 31
  residues processed: 212
  average time/residue: 0.4957
  time to fit residues: 122.4182
Evaluate side-chains
  199 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 151
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  143 ASN
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  219 ASP
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain C residue  143 ASN
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  476 LEU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  486 PHE
Chi-restraints excluded: chain C residue  492 TYR
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain C residue  529 LEU
Chi-restraints excluded: chain C residue  604 GLU
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  702 VAL
Chi-restraints excluded: chain D residue  143 ASN
Chi-restraints excluded: chain D residue  219 ASP
Chi-restraints excluded: chain D residue  317 LEU
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  431 LEU
Chi-restraints excluded: chain D residue  486 PHE
Chi-restraints excluded: chain D residue  492 TYR
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain D residue  611 LEU
Chi-restraints excluded: chain D residue  635 MET
Chi-restraints excluded: chain D residue  702 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 153 optimal weight:    0.8980
   chunk 184 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.110177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.079804 restraints weight = 40973.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.84
r_work: 0.3043 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  20484  Z= 0.119
  Angle     :  0.591  15.344  27796  Z= 0.292
  Chirality :  0.040   0.346   3140
  Planarity :  0.004   0.060   3432
  Dihedral  :  3.689  27.403   2696
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.35 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.47 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.11 (0.18), residues: 2432
  helix:  2.65 (0.14), residues: 1400
  sheet: -2.52 (0.55), residues: 84
  loop : -2.07 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  74 
 TYR   0.009   0.001   TYR D 466 
 PHE   0.026   0.001   PHE B  70 
 TRP   0.010   0.001   TRP D 173 
 HIS   0.004   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (20484)
  covalent geometry    : angle       0.59147 (27796)
  hydrogen bonds       : bond        0.03584 ( 1027)
  hydrogen bonds       : angle       3.86916 ( 3045)

*********************** 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
  238 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 171
  time to evaluate  : 0.731 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7195 (t0)
REVERT: A  230 GLN cc_start: 0.8262 (tp-100) cc_final: 0.7946 (tp40)
REVERT: A  370 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7724 (pp)
REVERT: A  431 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8528 (tt)
REVERT: A  486 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8313 (m-80)
REVERT: A  635 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8415 (ttt)
REVERT: B  370 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7730 (pp)
REVERT: B  431 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8525 (tt)
REVERT: B  486 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8315 (m-80)
REVERT: C  118 LYS cc_start: 0.8860 (tptt) cc_final: 0.8592 (tptp)
REVERT: C  121 LEU cc_start: 0.8852 (mt) cc_final: 0.8631 (mp)
REVERT: C  370 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7627 (pp)
REVERT: C  431 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8354 (tm)
REVERT: C  486 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8350 (m-80)
REVERT: D  370 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7642 (pp)
REVERT: D  431 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8520 (tt)
REVERT: D  486 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8304 (m-80)
REVERT: D  635 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8355 (ttt)
  outliers start: 67
  outliers final: 32
  residues processed: 216
  average time/residue: 0.4663
  time to fit residues: 117.7894
Evaluate side-chains
  202 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 155
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ASN
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  219 ASP
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain C residue  143 ASN
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  486 PHE
Chi-restraints excluded: chain C residue  492 TYR
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain C residue  501 VAL
Chi-restraints excluded: chain C residue  529 LEU
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  702 VAL
Chi-restraints excluded: chain D residue  143 ASN
Chi-restraints excluded: chain D residue  219 ASP
Chi-restraints excluded: chain D residue  317 LEU
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  431 LEU
Chi-restraints excluded: chain D residue  486 PHE
Chi-restraints excluded: chain D residue  492 TYR
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain D residue  611 LEU
Chi-restraints excluded: chain D residue  635 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 66 optimal weight:    0.2980
   chunk 147 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 120 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0770
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6342

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

Flipped N/Q/H residues before XYZ refinement:
** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.111383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.081373 restraints weight = 40503.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 2.80
r_work: 0.3076 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  20484  Z= 0.109
  Angle     :  0.612  21.240  27796  Z= 0.299
  Chirality :  0.040   0.397   3140
  Planarity :  0.004   0.054   3432
  Dihedral  :  3.678  27.252   2696
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.35 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 19.76 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.18), residues: 2432
  helix:  2.55 (0.14), residues: 1424
  sheet: -2.45 (0.55), residues: 84
  loop : -2.08 (0.20), residues: 924

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  74 
 TYR   0.027   0.001   TYR C 223 
 PHE   0.021   0.001   PHE B  70 
 TRP   0.012   0.001   TRP C 491 
 HIS   0.005   0.001   HIS B 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (20484)
  covalent geometry    : angle       0.61194 (27796)
  hydrogen bonds       : bond        0.03386 ( 1027)
  hydrogen bonds       : angle       3.85705 ( 3045)

*********************** 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
  230 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 176
  time to evaluate  : 0.677 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7937 (tp40)
REVERT: A  370 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7627 (pp)
REVERT: B  370 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7629 (pp)
REVERT: B  486 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8326 (m-80)
REVERT: C  118 LYS cc_start: 0.8887 (tptt) cc_final: 0.8610 (tptp)
REVERT: C  121 LEU cc_start: 0.8858 (mt) cc_final: 0.8652 (mp)
REVERT: C  188 ARG cc_start: 0.7556 (mmm-85) cc_final: 0.7341 (mtt90)
REVERT: C  370 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7604 (pp)
REVERT: C  431 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8316 (tm)
REVERT: D  370 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7642 (pp)
REVERT: D  486 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8333 (m-80)
REVERT: D  635 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8253 (ttt)
  outliers start: 54
  outliers final: 35
  residues processed: 213
  average time/residue: 0.4599
  time to fit residues: 115.2191
Evaluate side-chains
  208 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 165
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ASN
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  219 ASP
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  600 ILE
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain C residue  143 ASN
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  492 TYR
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain C residue  501 VAL
Chi-restraints excluded: chain C residue  529 LEU
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  702 VAL
Chi-restraints excluded: chain D residue  143 ASN
Chi-restraints excluded: chain D residue  219 ASP
Chi-restraints excluded: chain D residue  317 LEU
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  486 PHE
Chi-restraints excluded: chain D residue  492 TYR
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain D residue  611 LEU
Chi-restraints excluded: chain D residue  635 MET
Chi-restraints excluded: chain D residue  702 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 164 optimal weight:    3.9990
   chunk 183 optimal weight:   20.0000
   chunk 101 optimal weight:    5.9990
   chunk 136 optimal weight:    3.9990
   chunk 163 optimal weight:    5.9990
   chunk 121 optimal weight:    2.9990
   chunk 173 optimal weight:    4.9990
   chunk 216 optimal weight:    0.9990
   chunk 12 optimal weight:    9.9990
   chunk 212 optimal weight:    9.9990
   chunk 167 optimal weight:    4.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.106467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.076086 restraints weight = 41034.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.79
r_work: 0.2969 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  20484  Z= 0.222
  Angle     :  0.679  19.386  27796  Z= 0.337
  Chirality :  0.043   0.387   3140
  Planarity :  0.005   0.058   3432
  Dihedral  :  3.882  27.530   2696
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.54 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.04 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.18), residues: 2432
  helix:  2.38 (0.14), residues: 1396
  sheet: -2.58 (0.54), residues: 84
  loop : -2.02 (0.20), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  72 
 TYR   0.017   0.002   TYR B 223 
 PHE   0.018   0.002   PHE B  70 
 TRP   0.014   0.002   TRP B 698 
 HIS   0.004   0.001   HIS B 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00537 (20484)
  covalent geometry    : angle       0.67928 (27796)
  hydrogen bonds       : bond        0.04635 ( 1027)
  hydrogen bonds       : angle       4.10067 ( 3045)

********************** 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
  217 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 156
  time to evaluate  : 0.760 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 PHE cc_start: 0.7886 (m-80) cc_final: 0.7610 (m-80)
REVERT: A  230 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7907 (tp40)
REVERT: A  370 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7776 (pp)
REVERT: A  431 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8554 (tt)
REVERT: A  486 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8278 (m-80)
REVERT: B   76 PHE cc_start: 0.7708 (m-80) cc_final: 0.7353 (m-80)
REVERT: B  370 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7790 (pp)
REVERT: B  431 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8544 (tt)
REVERT: B  486 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8286 (m-80)
REVERT: C  188 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7503 (mtt90)
REVERT: C  370 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7784 (pp)
REVERT: C  431 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8440 (tm)
REVERT: C  486 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8383 (m-80)
REVERT: D  370 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7814 (pp)
REVERT: D  431 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8541 (tt)
REVERT: D  486 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8284 (m-80)
  outliers start: 61
  outliers final: 35
  residues processed: 196
  average time/residue: 0.4811
  time to fit residues: 110.5901
Evaluate side-chains
  190 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 142
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 ASN
Chi-restraints excluded: chain A residue  219 ASP
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  492 TYR
Chi-restraints excluded: chain A residue  497 VAL
Chi-restraints excluded: chain A residue  600 ILE
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain B residue  143 ASN
Chi-restraints excluded: chain B residue  219 ASP
Chi-restraints excluded: chain B residue  317 LEU
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  431 LEU
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  486 PHE
Chi-restraints excluded: chain B residue  492 TYR
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  600 ILE
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  702 VAL
Chi-restraints excluded: chain C residue  188 ARG
Chi-restraints excluded: chain C residue  219 ASP
Chi-restraints excluded: chain C residue  317 LEU
Chi-restraints excluded: chain C residue  370 LEU
Chi-restraints excluded: chain C residue  431 LEU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  486 PHE
Chi-restraints excluded: chain C residue  492 TYR
Chi-restraints excluded: chain C residue  497 VAL
Chi-restraints excluded: chain C residue  600 ILE
Chi-restraints excluded: chain C residue  611 LEU
Chi-restraints excluded: chain C residue  702 VAL
Chi-restraints excluded: chain D residue  143 ASN
Chi-restraints excluded: chain D residue  219 ASP
Chi-restraints excluded: chain D residue  317 LEU
Chi-restraints excluded: chain D residue  370 LEU
Chi-restraints excluded: chain D residue  431 LEU
Chi-restraints excluded: chain D residue  483 VAL
Chi-restraints excluded: chain D residue  486 PHE
Chi-restraints excluded: chain D residue  492 TYR
Chi-restraints excluded: chain D residue  497 VAL
Chi-restraints excluded: chain D residue  600 ILE
Chi-restraints excluded: chain D residue  611 LEU
Chi-restraints excluded: chain D residue  702 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 113 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0870
   chunk 62 optimal weight:   10.0000
   chunk 171 optimal weight:    3.9990
   chunk 178 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 143 optimal weight:    5.9990
   overall best weight:    1.8166

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

Flipped N/Q/H residues before XYZ refinement:
** A 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.108107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.077828 restraints weight = 41005.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.80
r_work: 0.3004 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  20484  Z= 0.147
  Angle     :  0.634  19.101  27796  Z= 0.315
  Chirality :  0.042   0.367   3140
  Planarity :  0.004   0.053   3432
  Dihedral  :  3.856  28.038   2696
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.00 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.96 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.18), residues: 2432
  helix:  2.46 (0.14), residues: 1400
  sheet: -2.45 (0.54), residues: 84
  loop : -2.04 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 679 
 TYR   0.018   0.001   TYR C 223 
 PHE   0.016   0.001   PHE B  70 
 TRP   0.012   0.001   TRP C 173 
 HIS   0.004   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (20484)
  covalent geometry    : angle       0.63439 (27796)
  hydrogen bonds       : bond        0.04031 ( 1027)
  hydrogen bonds       : angle       4.01743 ( 3045)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 5089.03 seconds
wall clock time: 87 minutes 52.33 seconds (5272.33 seconds total)