Starting phenix.real_space_refine
on Sun Aug 24 07:55:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6bo4_7118/08_2025/6bo4_7118.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6bo4_7118/08_2025/6bo4_7118.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6bo4_7118/08_2025/6bo4_7118.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6bo4_7118/08_2025/6bo4_7118.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6bo4_7118/08_2025/6bo4_7118.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6bo4_7118/08_2025/6bo4_7118.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.006
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      80      5.16       5
     C   11992      2.51       5
     N    3128      2.21       5
     O    3232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18432
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4608
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 625, 4608
          Classifications: {'peptide': 625}
          Incomplete info: {'truncation_to_alanine': 121}
          Link IDs: {'CIS': 7, 'PTRANS': 25, 'TRANS': 592}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 463
          Unresolved non-hydrogen angles: 581
          Unresolved non-hydrogen dihedrals: 384
          Unresolved non-hydrogen chiralities: 32
          Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 16, 'TYR:plan': 4, 'TRP:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 11, 'GLN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 5}
          Unresolved non-hydrogen planarities: 278
  Restraints were copied for chains:
    D, B, C
  Time building chain proxies: 4.58, per 1000 atoms: 0.25
  Number of scatterers: 18432
  At special positions: 0
  Unit cell: (128.75, 128.75, 116.25, 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      80     16.00
     O    3232      8.00
     N    3128      7.00
     C   11992      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: 1.67
  Conformation dependent library (CDL) restraints added in 910.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4712

  Finding SS restraints...
    Secondary structure from input PDB file:
      104 helices and 8 sheets defined
      58.7% alpha, 1.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 87
    Processing helix  chain 'A' and resid 94 through 99
    Processing helix  chain 'A' and resid 119 through 127
      removed outlier: 4.358A  pdb=" N   ASN A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 146
    Processing helix  chain 'A' and resid 148 through 154
    Processing helix  chain 'A' and resid 166 through 174
      removed outlier: 3.656A  pdb=" N   ILE A 170 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 185
    Processing helix  chain 'A' and resid 212 through 220
    Processing helix  chain 'A' and resid 222 through 232
    Processing helix  chain 'A' and resid 248 through 257
    Processing helix  chain 'A' and resid 260 through 275
      removed outlier: 4.074A  pdb=" N   TYR A 271 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 303
    Processing helix  chain 'A' and resid 307 through 317
    Processing helix  chain 'A' and resid 323 through 327
      removed outlier: 4.286A  pdb=" N   LEU A 326 " --> pdb=" O   TYR A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 361
    Processing helix  chain 'A' and resid 369 through 374
      removed outlier: 3.642A  pdb=" N   MET A 372 " --> pdb=" O   ARG A 369 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL A 373 " --> pdb=" O   HIS A 370 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL A 374 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 369 through 374'
    Processing helix  chain 'A' and resid 375 through 389
      removed outlier: 3.791A  pdb=" N   TRP A 386 " --> pdb=" O   LEU A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 413
      removed outlier: 4.180A  pdb=" N   ASN A 396 " --> pdb=" O   ARG A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 460
      removed outlier: 4.149A  pdb=" N   TYR A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 493
      removed outlier: 3.572A  pdb=" N   ILE A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 511
      removed outlier: 4.100A  pdb=" N   LEU A 500 " --> pdb=" O   TRP A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 517
      removed outlier: 3.869A  pdb=" N   ARG A 517 " --> pdb=" O   TYR A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 558
      removed outlier: 5.618A  pdb=" N   LEU A 538 " --> pdb=" O   LEU A 534 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ARG A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 540 " --> pdb=" O   ASP A 536 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL A 543 " --> pdb=" O   ARG A 539 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   VAL A 546 " --> pdb=" O   LEU A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 604
    Processing helix  chain 'A' and resid 619 through 635
      removed outlier: 3.707A  pdb=" N   VAL A 635 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 675
      removed outlier: 4.183A  pdb=" N   LEU A 641 " --> pdb=" O   LEU A 637 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ILE A 642 " --> pdb=" O   LEU A 638 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A 653 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ASP A 654 " --> pdb=" O   ASN A 650 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ASN A 655 " --> pdb=" O   HIS A 651 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TRP A 657 " --> pdb=" O   ALA A 653 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER A 658 " --> pdb=" O   ASP A 654 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 76 through 87
    Processing helix  chain 'D' and resid 94 through 99
    Processing helix  chain 'D' and resid 119 through 127
      removed outlier: 4.359A  pdb=" N   ASN D 127 " --> pdb=" O   LYS D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 137 through 146
    Processing helix  chain 'D' and resid 148 through 154
    Processing helix  chain 'D' and resid 166 through 174
      removed outlier: 3.654A  pdb=" N   ILE D 170 " --> pdb=" O   SER D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 177 through 185
    Processing helix  chain 'D' and resid 212 through 220
    Processing helix  chain 'D' and resid 222 through 232
    Processing helix  chain 'D' and resid 248 through 257
    Processing helix  chain 'D' and resid 260 through 275
      removed outlier: 4.075A  pdb=" N   TYR D 271 " --> pdb=" O   VAL D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 297 through 303
    Processing helix  chain 'D' and resid 307 through 317
    Processing helix  chain 'D' and resid 323 through 327
      removed outlier: 4.286A  pdb=" N   LEU D 326 " --> pdb=" O   TYR D 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 355 through 361
    Processing helix  chain 'D' and resid 369 through 374
      removed outlier: 3.642A  pdb=" N   MET D 372 " --> pdb=" O   ARG D 369 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL D 373 " --> pdb=" O   HIS D 370 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL D 374 " --> pdb=" O   ARG D 371 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 369 through 374'
    Processing helix  chain 'D' and resid 375 through 389
      removed outlier: 3.791A  pdb=" N   TRP D 386 " --> pdb=" O   LEU D 382 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 392 through 413
      removed outlier: 4.181A  pdb=" N   ASN D 396 " --> pdb=" O   ARG D 392 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 428 through 460
      removed outlier: 4.148A  pdb=" N   TYR D 447 " --> pdb=" O   LEU D 443 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 470 through 493
      removed outlier: 3.572A  pdb=" N   ILE D 474 " --> pdb=" O   SER D 470 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 496 through 511
      removed outlier: 4.099A  pdb=" N   LEU D 500 " --> pdb=" O   TRP D 496 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 512 through 517
      removed outlier: 3.868A  pdb=" N   ARG D 517 " --> pdb=" O   TYR D 514 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 519 through 558
      removed outlier: 5.619A  pdb=" N   LEU D 538 " --> pdb=" O   LEU D 534 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ARG D 539 " --> pdb=" O   ARG D 535 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE D 540 " --> pdb=" O   ASP D 536 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL D 543 " --> pdb=" O   ARG D 539 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   VAL D 546 " --> pdb=" O   LEU D 542 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 594 through 604
    Processing helix  chain 'D' and resid 619 through 635
      removed outlier: 3.707A  pdb=" N   VAL D 635 " --> pdb=" O   LEU D 631 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 637 through 675
      removed outlier: 4.183A  pdb=" N   LEU D 641 " --> pdb=" O   LEU D 637 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   ILE D 642 " --> pdb=" O   LEU D 638 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA D 653 " --> pdb=" O   VAL D 649 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ASP D 654 " --> pdb=" O   ASN D 650 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ASN D 655 " --> pdb=" O   HIS D 651 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TRP D 657 " --> pdb=" O   ALA D 653 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER D 658 " --> pdb=" O   ASP D 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 87
    Processing helix  chain 'B' and resid 94 through 99
    Processing helix  chain 'B' and resid 119 through 127
      removed outlier: 4.359A  pdb=" N   ASN B 127 " --> pdb=" O   LYS B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 146
    Processing helix  chain 'B' and resid 148 through 154
    Processing helix  chain 'B' and resid 166 through 174
      removed outlier: 3.655A  pdb=" N   ILE B 170 " --> pdb=" O   SER B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 185
    Processing helix  chain 'B' and resid 212 through 220
    Processing helix  chain 'B' and resid 222 through 232
    Processing helix  chain 'B' and resid 248 through 257
    Processing helix  chain 'B' and resid 260 through 275
      removed outlier: 4.074A  pdb=" N   TYR B 271 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 303
    Processing helix  chain 'B' and resid 307 through 317
    Processing helix  chain 'B' and resid 323 through 327
      removed outlier: 4.287A  pdb=" N   LEU B 326 " --> pdb=" O   TYR B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 361
    Processing helix  chain 'B' and resid 369 through 374
      removed outlier: 3.642A  pdb=" N   MET B 372 " --> pdb=" O   ARG B 369 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   VAL B 373 " --> pdb=" O   HIS B 370 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   VAL B 374 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 369 through 374'
    Processing helix  chain 'B' and resid 375 through 389
      removed outlier: 3.790A  pdb=" N   TRP B 386 " --> pdb=" O   LEU B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 413
      removed outlier: 4.181A  pdb=" N   ASN B 396 " --> pdb=" O   ARG B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 460
      removed outlier: 4.149A  pdb=" N   TYR B 447 " --> pdb=" O   LEU B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 493
      removed outlier: 3.572A  pdb=" N   ILE B 474 " --> pdb=" O   SER B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 511
      removed outlier: 4.098A  pdb=" N   LEU B 500 " --> pdb=" O   TRP B 496 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 517
      removed outlier: 3.868A  pdb=" N   ARG B 517 " --> pdb=" O   TYR B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 558
      removed outlier: 5.620A  pdb=" N   LEU B 538 " --> pdb=" O   LEU B 534 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   ARG B 539 " --> pdb=" O   ARG B 535 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE B 540 " --> pdb=" O   ASP B 536 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL B 543 " --> pdb=" O   ARG B 539 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   VAL B 546 " --> pdb=" O   LEU B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 604
    Processing helix  chain 'B' and resid 619 through 635
      removed outlier: 3.707A  pdb=" N   VAL B 635 " --> pdb=" O   LEU B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 637 through 675
      removed outlier: 4.183A  pdb=" N   LEU B 641 " --> pdb=" O   LEU B 637 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   ILE B 642 " --> pdb=" O   LEU B 638 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA B 653 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ASP B 654 " --> pdb=" O   ASN B 650 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ASN B 655 " --> pdb=" O   HIS B 651 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TRP B 657 " --> pdb=" O   ALA B 653 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER B 658 " --> pdb=" O   ASP B 654 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 87
    Processing helix  chain 'C' and resid 94 through 99
    Processing helix  chain 'C' and resid 119 through 127
      removed outlier: 4.358A  pdb=" N   ASN C 127 " --> pdb=" O   LYS C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
    Processing helix  chain 'C' and resid 148 through 154
    Processing helix  chain 'C' and resid 166 through 174
      removed outlier: 3.655A  pdb=" N   ILE C 170 " --> pdb=" O   SER C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 185
    Processing helix  chain 'C' and resid 212 through 220
    Processing helix  chain 'C' and resid 222 through 232
    Processing helix  chain 'C' and resid 248 through 257
    Processing helix  chain 'C' and resid 260 through 275
      removed outlier: 4.074A  pdb=" N   TYR C 271 " --> pdb=" O   VAL C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 297 through 303
    Processing helix  chain 'C' and resid 307 through 317
    Processing helix  chain 'C' and resid 323 through 327
      removed outlier: 4.287A  pdb=" N   LEU C 326 " --> pdb=" O   TYR C 323 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 355 through 361
    Processing helix  chain 'C' and resid 369 through 374
      removed outlier: 3.642A  pdb=" N   MET C 372 " --> pdb=" O   ARG C 369 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL C 373 " --> pdb=" O   HIS C 370 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   VAL C 374 " --> pdb=" O   ARG C 371 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 369 through 374'
    Processing helix  chain 'C' and resid 375 through 389
      removed outlier: 3.790A  pdb=" N   TRP C 386 " --> pdb=" O   LEU C 382 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 392 through 413
      removed outlier: 4.180A  pdb=" N   ASN C 396 " --> pdb=" O   ARG C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 428 through 460
      removed outlier: 4.149A  pdb=" N   TYR C 447 " --> pdb=" O   LEU C 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 470 through 493
      removed outlier: 3.572A  pdb=" N   ILE C 474 " --> pdb=" O   SER C 470 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 511
      removed outlier: 4.099A  pdb=" N   LEU C 500 " --> pdb=" O   TRP C 496 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 512 through 517
      removed outlier: 3.868A  pdb=" N   ARG C 517 " --> pdb=" O   TYR C 514 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 519 through 558
      removed outlier: 5.618A  pdb=" N   LEU C 538 " --> pdb=" O   LEU C 534 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ARG C 539 " --> pdb=" O   ARG C 535 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE C 540 " --> pdb=" O   ASP C 536 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL C 543 " --> pdb=" O   ARG C 539 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   VAL C 546 " --> pdb=" O   LEU C 542 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 594 through 604
    Processing helix  chain 'C' and resid 619 through 635
      removed outlier: 3.707A  pdb=" N   VAL C 635 " --> pdb=" O   LEU C 631 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 637 through 675
      removed outlier: 4.183A  pdb=" N   LEU C 641 " --> pdb=" O   LEU C 637 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ILE C 642 " --> pdb=" O   LEU C 638 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA C 653 " --> pdb=" O   VAL C 649 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ASP C 654 " --> pdb=" O   ASN C 650 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   ASN C 655 " --> pdb=" O   HIS C 651 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TRP C 657 " --> pdb=" O   ALA C 653 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER C 658 " --> pdb=" O   ASP C 654 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 158
      removed outlier: 4.844A  pdb=" N   CYS A 157 " --> pdb=" O   GLY A 164 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 339 through 342
    Processing sheet with id=AA3, first strand: chain 'D' and resid 157 through 158
      removed outlier: 4.844A  pdb=" N   CYS D 157 " --> pdb=" O   GLY D 164 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 339 through 342
    Processing sheet with id=AA5, first strand: chain 'B' and resid 157 through 158
      removed outlier: 4.844A  pdb=" N   CYS B 157 " --> pdb=" O   GLY B 164 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 342
    Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 158
      removed outlier: 4.844A  pdb=" N   CYS C 157 " --> pdb=" O   GLY C 164 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 339 through 342

    980 hydrogen bonds defined for protein.
    2892 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: 2.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 4503
        1.33 -     1.45: 3997
        1.45 -     1.57: 10248
        1.57 -     1.69: 0
        1.69 -     1.81: 124
  Bond restraints: 18872
  Sorted by residual:
  bond pdb=" CA  TRP C 676 "
       pdb=" C   TRP C 676 "
    ideal  model  delta    sigma   weight residual
    1.523  1.557 -0.034 1.34e-02 5.57e+03 6.45e+00
  bond pdb=" CA  TRP B 676 "
       pdb=" C   TRP B 676 "
    ideal  model  delta    sigma   weight residual
    1.523  1.557 -0.034 1.34e-02 5.57e+03 6.31e+00
  bond pdb=" CA  TRP D 676 "
       pdb=" C   TRP D 676 "
    ideal  model  delta    sigma   weight residual
    1.523  1.557 -0.033 1.34e-02 5.57e+03 6.24e+00
  bond pdb=" CA  TRP A 676 "
       pdb=" C   TRP A 676 "
    ideal  model  delta    sigma   weight residual
    1.523  1.556 -0.033 1.34e-02 5.57e+03 5.96e+00
  bond pdb=" CB  VAL B 153 "
       pdb=" CG1 VAL B 153 "
    ideal  model  delta    sigma   weight residual
    1.521  1.450  0.071 3.30e-02 9.18e+02 4.61e+00
  ... (remaining 18867 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.64: 25176
        3.64 -     7.27: 530
        7.27 -    10.91: 66
       10.91 -    14.55: 21
       14.55 -    18.19: 7
  Bond angle restraints: 25800
  Sorted by residual:
  angle pdb=" N   TRP B 676 "
        pdb=" CA  TRP B 676 "
        pdb=" C   TRP B 676 "
      ideal   model   delta    sigma   weight residual
     110.80  122.71  -11.91 2.13e+00 2.20e-01 3.13e+01
  angle pdb=" N   TRP A 676 "
        pdb=" CA  TRP A 676 "
        pdb=" C   TRP A 676 "
      ideal   model   delta    sigma   weight residual
     110.80  122.69  -11.89 2.13e+00 2.20e-01 3.12e+01
  angle pdb=" N   TRP D 676 "
        pdb=" CA  TRP D 676 "
        pdb=" C   TRP D 676 "
      ideal   model   delta    sigma   weight residual
     110.80  122.68  -11.88 2.13e+00 2.20e-01 3.11e+01
  angle pdb=" N   TRP C 676 "
        pdb=" CA  TRP C 676 "
        pdb=" C   TRP C 676 "
      ideal   model   delta    sigma   weight residual
     110.80  122.66  -11.86 2.13e+00 2.20e-01 3.10e+01
  angle pdb=" C   TRP C 676 "
        pdb=" N   TRP C 677 "
        pdb=" CA  TRP C 677 "
      ideal   model   delta    sigma   weight residual
     121.70  131.43   -9.73 1.80e+00 3.09e-01 2.92e+01
  ... (remaining 25795 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.31: 8956
        9.31 -    18.61: 1416
       18.61 -    27.92: 356
       27.92 -    37.23: 215
       37.23 -    46.53: 73
  Dihedral angle restraints: 11016
    sinusoidal: 3728
      harmonic: 7288
  Sorted by residual:
  dihedral pdb=" CA  PHE B 519 "
           pdb=" C   PHE B 519 "
           pdb=" N   GLN B 520 "
           pdb=" CA  GLN B 520 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.06  -43.94     0      5.00e+00 4.00e-02 7.72e+01
  dihedral pdb=" CA  PHE A 519 "
           pdb=" C   PHE A 519 "
           pdb=" N   GLN A 520 "
           pdb=" CA  GLN A 520 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.11  -43.89     0      5.00e+00 4.00e-02 7.70e+01
  dihedral pdb=" CA  PHE C 519 "
           pdb=" C   PHE C 519 "
           pdb=" N   GLN C 520 "
           pdb=" CA  GLN C 520 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.13  -43.87     0      5.00e+00 4.00e-02 7.70e+01
  ... (remaining 11013 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1766
       0.045 -    0.090: 843
       0.090 -    0.135: 314
       0.135 -    0.180: 99
       0.180 -    0.225: 22
  Chirality restraints: 3044
  Sorted by residual:
  chirality pdb=" CG  LEU B 121 "
            pdb=" CB  LEU B 121 "
            pdb=" CD1 LEU B 121 "
            pdb=" CD2 LEU B 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.81    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CG  LEU D 121 "
            pdb=" CB  LEU D 121 "
            pdb=" CD1 LEU D 121 "
            pdb=" CD2 LEU D 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.81    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CG  LEU C 121 "
            pdb=" CB  LEU C 121 "
            pdb=" CD1 LEU C 121 "
            pdb=" CD2 LEU C 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.81    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 3041 not shown)

  Planarity restraints: 3264
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 366 "   -0.053 5.00e-02 4.00e+02   8.11e-02 1.05e+01
        pdb=" N   PRO B 367 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO B 367 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 367 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 366 "    0.053 5.00e-02 4.00e+02   8.11e-02 1.05e+01
        pdb=" N   PRO C 367 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO C 367 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO C 367 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 366 "   -0.053 5.00e-02 4.00e+02   8.09e-02 1.05e+01
        pdb=" N   PRO A 367 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A 367 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 367 "   -0.046 5.00e-02 4.00e+02
  ... (remaining 3261 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 2539
        2.75 -     3.28: 19395
        3.28 -     3.82: 31463
        3.82 -     4.36: 35930
        4.36 -     4.90: 56359
  Nonbonded interactions: 145686
  Sorted by model distance:
  nonbonded pdb=" O   ILE D 593 "
            pdb=" OG  SER D 597 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   ILE B 593 "
            pdb=" OG  SER B 597 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   ILE C 593 "
            pdb=" OG  SER C 597 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   ILE A 593 "
            pdb=" OG  SER A 597 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ALA A 653 "
            pdb=" OG  SER A 656 "
     model   vdw
     2.272 3.040
  ... (remaining 145681 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.380
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.050
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
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      :  0.008   0.074  18872  Z= 0.365
  Angle     :  1.323  18.187  25800  Z= 0.672
  Chirality :  0.061   0.225   3044
  Planarity :  0.008   0.081   3264
  Dihedral  : 11.915  46.533   6304
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.50 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.12 %
    Favored  : 91.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    Twisted Proline : 4.00 %
    Twisted General : 0.67 %

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 aren not related in a simple way.
  whole: -4.58 (0.14), residues: 2484
  helix: -3.13 (0.10), residues: 1244
  sheet: -4.40 (0.39), residues: 56
  loop : -2.79 (0.18), residues: 1184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 388 
 TYR   0.032   0.004   TYR B 323 
 PHE   0.027   0.004   PHE C 209 
 TRP   0.031   0.003   TRP A 454 
 HIS   0.022   0.004   HIS C 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00793 (18872)
  covalent geometry    : angle       1.32311 (25800)
  hydrogen bonds       : bond        0.14372 (  980)
  hydrogen bonds       : angle      11.74540 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 322
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8226 (m-80) cc_final: 0.8025 (m-80)
REVERT: A  351 TRP cc_start: 0.8164 (p-90) cc_final: 0.7948 (p-90)
REVERT: A  354 ASN cc_start: 0.8904 (m-40) cc_final: 0.8690 (t0)
REVERT: A  503 LEU cc_start: 0.8192 (tp) cc_final: 0.7965 (tp)
REVERT: A  644 LEU cc_start: 0.5338 (pp) cc_final: 0.4352 (pp)
REVERT: D  258 ASP cc_start: 0.7891 (m-30) cc_final: 0.7274 (m-30)
REVERT: D  351 TRP cc_start: 0.8319 (p-90) cc_final: 0.8071 (p-90)
REVERT: D  354 ASN cc_start: 0.8977 (m-40) cc_final: 0.8773 (t0)
REVERT: D  503 LEU cc_start: 0.8277 (tp) cc_final: 0.8068 (tp)
REVERT: D  644 LEU cc_start: 0.5457 (pp) cc_final: 0.4076 (pp)
REVERT: B  258 ASP cc_start: 0.7344 (m-30) cc_final: 0.6509 (m-30)
REVERT: B  351 TRP cc_start: 0.8510 (p-90) cc_final: 0.8256 (p-90)
REVERT: B  354 ASN cc_start: 0.8993 (m-40) cc_final: 0.8776 (t0)
REVERT: C  351 TRP cc_start: 0.8354 (p-90) cc_final: 0.8100 (p-90)
REVERT: C  644 LEU cc_start: 0.5108 (pp) cc_final: 0.4603 (pp)
  outliers start: 13
  outliers final: 0
  residues processed: 333
  average time/residue: 0.1488
  time to fit residues: 74.7209
Evaluate side-chains
  173 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 216 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 194 optimal weight:    0.9990
   chunk 227 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 247 optimal weight:    9.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    9.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 234 HIS
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 GLN
** D 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 520 GLN
B 234 HIS
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 520 GLN
B 650 ASN
** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 520 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.097157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.088044 restraints weight = 105925.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.089300 restraints weight = 70245.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.090223 restraints weight = 51843.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.090868 restraints weight = 41166.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.091349 restraints weight = 34666.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  18872  Z= 0.204
  Angle     :  0.871  15.124  25800  Z= 0.434
  Chirality :  0.044   0.171   3044
  Planarity :  0.006   0.052   3264
  Dihedral  :  7.055  42.484   2664
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 18.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 11.69 %
    Favored  : 84.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.54 %

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 aren not related in a simple way.
  whole: -2.99 (0.16), residues: 2484
  helix: -1.27 (0.13), residues: 1424
  sheet: -4.53 (0.41), residues: 56
  loop : -2.81 (0.19), residues: 1004

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 539 
 TYR   0.027   0.003   TYR C 323 
 PHE   0.021   0.002   PHE B 311 
 TRP   0.022   0.002   TRP C 454 
 HIS   0.007   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (18872)
  covalent geometry    : angle       0.87056 (25800)
  hydrogen bonds       : bond        0.04854 (  980)
  hydrogen bonds       : angle       6.30401 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 218
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8230 (m-80) cc_final: 0.7962 (m-80)
REVERT: A  311 PHE cc_start: 0.7049 (t80) cc_final: 0.6793 (t80)
REVERT: A  351 TRP cc_start: 0.8237 (p-90) cc_final: 0.8025 (p-90)
REVERT: A  644 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6179 (pp)
REVERT: D  311 PHE cc_start: 0.6995 (t80) cc_final: 0.6741 (t80)
REVERT: D  351 TRP cc_start: 0.8289 (p-90) cc_final: 0.8043 (p-90)
REVERT: D  360 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7289 (mm)
REVERT: D  503 LEU cc_start: 0.8356 (tp) cc_final: 0.8131 (tp)
REVERT: D  644 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6013 (pp)
REVERT: B  216 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7485 (pp)
REVERT: B  404 MET cc_start: 0.9081 (tpp) cc_final: 0.8811 (tpt)
REVERT: C  216 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7548 (pp)
REVERT: C  351 TRP cc_start: 0.8303 (p-90) cc_final: 0.8082 (p-90)
  outliers start: 59
  outliers final: 16
  residues processed: 262
  average time/residue: 0.1313
  time to fit residues: 54.5288
Evaluate side-chains
  182 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 161
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  644 LEU
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  148 ASN
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  422 ILE
Chi-restraints excluded: chain D residue  644 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  390 VAL
Chi-restraints excluded: chain B residue  621 VAL
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  390 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 202 optimal weight:    2.9990
   chunk 122 optimal weight:    5.9990
   chunk 206 optimal weight:    7.9990
   chunk 78 optimal weight:    8.9990
   chunk 162 optimal weight:    0.0970
   chunk 140 optimal weight:    6.9990
   chunk 220 optimal weight:   30.0000
   chunk 185 optimal weight:   30.0000
   chunk 196 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    4.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 234 HIS
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 HIS
** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 263 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.096387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.087051 restraints weight = 107151.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.088306 restraints weight = 72571.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.089203 restraints weight = 53906.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.089851 restraints weight = 43143.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.090317 restraints weight = 36546.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18872  Z= 0.185
  Angle     :  0.832  13.446  25800  Z= 0.412
  Chirality :  0.044   0.174   3044
  Planarity :  0.005   0.052   3264
  Dihedral  :  6.506  38.175   2664
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.42 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 13.94 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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 aren not related in a simple way.
  whole: -2.45 (0.16), residues: 2484
  helix: -0.69 (0.13), residues: 1432
  sheet: -4.58 (0.43), residues: 56
  loop : -2.83 (0.19), residues: 996

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 459 
 TYR   0.023   0.002   TYR C 323 
 PHE   0.014   0.002   PHE C 519 
 TRP   0.017   0.002   TRP A 677 
 HIS   0.009   0.001   HIS D 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (18872)
  covalent geometry    : angle       0.83215 (25800)
  hydrogen bonds       : bond        0.04501 (  980)
  hydrogen bonds       : angle       5.61653 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 190
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8267 (m-80) cc_final: 0.7922 (m-80)
REVERT: A  338 VAL cc_start: 0.8606 (t) cc_final: 0.8254 (p)
REVERT: A  351 TRP cc_start: 0.8309 (p-90) cc_final: 0.8076 (p-90)
REVERT: A  607 MET cc_start: 0.7090 (mpt) cc_final: 0.6869 (mpt)
REVERT: A  641 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7581 (tt)
REVERT: D  351 TRP cc_start: 0.8337 (p-90) cc_final: 0.8096 (p-90)
REVERT: D  360 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.7002 (mm)
REVERT: D  503 LEU cc_start: 0.8343 (tp) cc_final: 0.8127 (tp)
REVERT: D  519 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6297 (p90)
REVERT: B  404 MET cc_start: 0.9111 (tpp) cc_final: 0.8891 (tpt)
REVERT: C  351 TRP cc_start: 0.8365 (p-90) cc_final: 0.8094 (p-90)
REVERT: C  519 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.5559 (p90)
REVERT: C  539 ARG cc_start: 0.8273 (mmt180) cc_final: 0.8063 (mmm160)
  outliers start: 74
  outliers final: 30
  residues processed: 246
  average time/residue: 0.1181
  time to fit residues: 48.1562
Evaluate side-chains
  190 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 156
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  334 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  494 THR
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  148 ASN
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  334 CYS
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  422 ILE
Chi-restraints excluded: chain D residue  519 PHE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  621 VAL
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  507 LEU
Chi-restraints excluded: chain C residue  519 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 160 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   chunk 142 optimal weight:    0.2980
   chunk 29 optimal weight:    8.9990
   chunk 140 optimal weight:    0.0050
   chunk 39 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   chunk 62 optimal weight:   20.0000
   chunk 19 optimal weight:    8.9990
   chunk 103 optimal weight:    9.9990
   chunk 129 optimal weight:   20.0000
   overall best weight:    4.0600

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 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 = 0.3790 r_free = 0.3790 target = 0.095896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.086442 restraints weight = 107276.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.087689 restraints weight = 72393.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.088582 restraints weight = 54111.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.089232 restraints weight = 43547.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.089694 restraints weight = 36906.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18872  Z= 0.180
  Angle     :  0.820  14.861  25800  Z= 0.401
  Chirality :  0.044   0.209   3044
  Planarity :  0.005   0.049   3264
  Dihedral  :  6.150  35.909   2664
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 15.61 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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 aren not related in a simple way.
  whole: -2.17 (0.16), residues: 2484
  helix: -0.38 (0.13), residues: 1440
  sheet: -4.53 (0.47), residues: 56
  loop : -2.87 (0.19), residues: 988

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 459 
 TYR   0.031   0.002   TYR A 675 
 PHE   0.028   0.001   PHE B 311 
 TRP   0.018   0.002   TRP B 677 
 HIS   0.006   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (18872)
  covalent geometry    : angle       0.82012 (25800)
  hydrogen bonds       : bond        0.04261 (  980)
  hydrogen bonds       : angle       5.24186 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 194
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8419 (m-80) cc_final: 0.7948 (m-80)
REVERT: A  351 TRP cc_start: 0.8377 (p-90) cc_final: 0.8116 (p-90)
REVERT: A  607 MET cc_start: 0.6851 (mpt) cc_final: 0.6536 (mpt)
REVERT: D  351 TRP cc_start: 0.8402 (p-90) cc_final: 0.8142 (p-90)
REVERT: D  360 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7063 (mm)
REVERT: D  519 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.5637 (p90)
REVERT: B  519 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.5647 (p90)
REVERT: C  351 TRP cc_start: 0.8380 (p-90) cc_final: 0.8125 (p-90)
REVERT: C  519 PHE cc_start: 0.6649 (OUTLIER) cc_final: 0.5700 (p90)
REVERT: C  539 ARG cc_start: 0.8200 (mmt180) cc_final: 0.7955 (mmm160)
  outliers start: 82
  outliers final: 30
  residues processed: 260
  average time/residue: 0.1194
  time to fit residues: 51.0009
Evaluate side-chains
  191 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 157
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  433 MET
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  148 ASN
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  234 HIS
Chi-restraints excluded: chain D residue  334 CYS
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  422 ILE
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  519 PHE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  234 HIS
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  507 LEU
Chi-restraints excluded: chain C residue  519 PHE
Chi-restraints excluded: chain C residue  618 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 149 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 242 optimal weight:    5.9990
   chunk 217 optimal weight:   10.0000
   chunk 192 optimal weight:    0.8980
   chunk 200 optimal weight:    8.9990
   chunk 185 optimal weight:   30.0000
   chunk 174 optimal weight:   20.0000
   chunk 13 optimal weight:    5.9990
   chunk 237 optimal weight:   30.0000
   chunk 230 optimal weight:   20.0000
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 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 = 0.3748 r_free = 0.3748 target = 0.093483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.084032 restraints weight = 106694.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.085256 restraints weight = 72778.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.086126 restraints weight = 54656.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.086758 restraints weight = 44169.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.087159 restraints weight = 37540.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  18872  Z= 0.213
  Angle     :  0.867  14.118  25800  Z= 0.423
  Chirality :  0.045   0.174   3044
  Planarity :  0.005   0.053   3264
  Dihedral  :  6.158  34.355   2664
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 21.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 16.30 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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 aren not related in a simple way.
  whole: -2.17 (0.16), residues: 2484
  helix: -0.38 (0.13), residues: 1444
  sheet: -4.54 (0.50), residues: 56
  loop : -2.88 (0.19), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 539 
 TYR   0.021   0.002   TYR A 525 
 PHE   0.032   0.002   PHE D 311 
 TRP   0.015   0.002   TRP B 454 
 HIS   0.007   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (18872)
  covalent geometry    : angle       0.86651 (25800)
  hydrogen bonds       : bond        0.04462 (  980)
  hydrogen bonds       : angle       5.30197 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 178
  time to evaluate  : 0.738 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8383 (m-80) cc_final: 0.8007 (m-80)
REVERT: A  351 TRP cc_start: 0.8414 (p-90) cc_final: 0.8159 (p-90)
REVERT: A  519 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.5567 (p90)
REVERT: A  607 MET cc_start: 0.6898 (mpt) cc_final: 0.6449 (mpt)
REVERT: D  351 TRP cc_start: 0.8394 (p-90) cc_final: 0.8124 (p-90)
REVERT: D  360 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7053 (mm)
REVERT: D  519 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.5847 (p90)
REVERT: B  519 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.5570 (p90)
REVERT: B  540 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7736 (m-80)
REVERT: C  351 TRP cc_start: 0.8365 (p-90) cc_final: 0.8092 (p-90)
REVERT: C  519 PHE cc_start: 0.6445 (OUTLIER) cc_final: 0.5332 (p90)
REVERT: C  539 ARG cc_start: 0.8193 (mmt180) cc_final: 0.7804 (mmm160)
  outliers start: 81
  outliers final: 44
  residues processed: 240
  average time/residue: 0.1139
  time to fit residues: 45.8595
Evaluate side-chains
  209 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 159
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  334 CYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  618 PHE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  677 TRP
Chi-restraints excluded: chain D residue  107 THR
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  148 ASN
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  234 HIS
Chi-restraints excluded: chain D residue  334 CYS
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  519 PHE
Chi-restraints excluded: chain D residue  522 THR
Chi-restraints excluded: chain D residue  618 PHE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain D residue  677 TRP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 HIS
Chi-restraints excluded: chain B residue  374 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  540 PHE
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  234 HIS
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  507 LEU
Chi-restraints excluded: chain C residue  519 PHE
Chi-restraints excluded: chain C residue  618 PHE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  649 VAL
Chi-restraints excluded: chain C residue  677 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 109 optimal weight:    6.9990
   chunk 88 optimal weight:    7.9990
   chunk 99 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 197 optimal weight:    0.0040
   chunk 148 optimal weight:    1.9990
   chunk 184 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    2.8000

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 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 = 0.3816 r_free = 0.3816 target = 0.097414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.088031 restraints weight = 105891.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.089283 restraints weight = 71061.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.090210 restraints weight = 53338.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.090856 restraints weight = 42960.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.091320 restraints weight = 36396.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  18872  Z= 0.150
  Angle     :  0.802  13.057  25800  Z= 0.386
  Chirality :  0.043   0.175   3044
  Planarity :  0.005   0.052   3264
  Dihedral  :  5.730  30.351   2664
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 17.17 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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 aren not related in a simple way.
  whole: -1.88 (0.17), residues: 2484
  helix: -0.15 (0.13), residues: 1444
  sheet: -4.33 (0.50), residues: 56
  loop : -2.75 (0.19), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 539 
 TYR   0.022   0.002   TYR B 400 
 PHE   0.037   0.001   PHE C 311 
 TRP   0.013   0.001   TRP B 454 
 HIS   0.005   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (18872)
  covalent geometry    : angle       0.80150 (25800)
  hydrogen bonds       : bond        0.03916 (  980)
  hydrogen bonds       : angle       5.02476 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 200
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  122 MET cc_start: 0.8648 (mmm) cc_final: 0.7932 (mmm)
REVERT: A  199 PHE cc_start: 0.8223 (m-80) cc_final: 0.7661 (m-80)
REVERT: A  351 TRP cc_start: 0.8406 (p-90) cc_final: 0.8145 (p-90)
REVERT: A  519 PHE cc_start: 0.6382 (OUTLIER) cc_final: 0.5337 (p90)
REVERT: A  607 MET cc_start: 0.7126 (mpt) cc_final: 0.6868 (mpt)
REVERT: D  351 TRP cc_start: 0.8387 (p-90) cc_final: 0.8127 (p-90)
REVERT: D  360 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6857 (mm)
REVERT: D  519 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.5709 (p90)
REVERT: D  522 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.6916 (p)
REVERT: D  529 ILE cc_start: 0.8959 (pp) cc_final: 0.8747 (pt)
REVERT: B  519 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5446 (p90)
REVERT: C  351 TRP cc_start: 0.8345 (p-90) cc_final: 0.8057 (p-90)
REVERT: C  519 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.5224 (p90)
REVERT: C  539 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7625 (mmm160)
  outliers start: 75
  outliers final: 45
  residues processed: 257
  average time/residue: 0.0985
  time to fit residues: 41.4627
Evaluate side-chains
  219 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 168
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  334 CYS
Chi-restraints excluded: chain A residue  422 ILE
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  618 PHE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  677 TRP
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  148 ASN
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  234 HIS
Chi-restraints excluded: chain D residue  323 TYR
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  519 PHE
Chi-restraints excluded: chain D residue  522 THR
Chi-restraints excluded: chain D residue  618 PHE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain D residue  677 TRP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 HIS
Chi-restraints excluded: chain B residue  374 VAL
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  543 VAL
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  234 HIS
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  507 LEU
Chi-restraints excluded: chain C residue  519 PHE
Chi-restraints excluded: chain C residue  522 THR
Chi-restraints excluded: chain C residue  618 PHE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  649 VAL
Chi-restraints excluded: chain C residue  677 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 96 optimal weight:   30.0000
   chunk 57 optimal weight:    5.9990
   chunk 127 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 236 optimal weight:   20.0000
   chunk 30 optimal weight:    6.9990
   chunk 188 optimal weight:    4.9990
   chunk 234 optimal weight:   30.0000
   chunk 176 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0770
   chunk 203 optimal weight:    9.9990
   overall best weight:    5.0146

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 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 = 0.3757 r_free = 0.3757 target = 0.094051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.084526 restraints weight = 107103.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.085745 restraints weight = 72673.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.086645 restraints weight = 54849.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.087282 restraints weight = 44309.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.087737 restraints weight = 37690.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.4611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  18872  Z= 0.201
  Angle     :  0.857  14.574  25800  Z= 0.416
  Chirality :  0.045   0.220   3044
  Planarity :  0.005   0.054   3264
  Dihedral  :  5.854  31.620   2664
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 20.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.47 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 17.63 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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 aren not related in a simple way.
  whole: -1.91 (0.17), residues: 2484
  helix: -0.17 (0.13), residues: 1444
  sheet: -4.23 (0.53), residues: 56
  loop : -2.79 (0.19), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 539 
 TYR   0.026   0.002   TYR A 525 
 PHE   0.025   0.001   PHE C 311 
 TRP   0.013   0.001   TRP B 454 
 HIS   0.007   0.001   HIS A 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (18872)
  covalent geometry    : angle       0.85670 (25800)
  hydrogen bonds       : bond        0.04224 (  980)
  hydrogen bonds       : angle       5.19961 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 168
  time to evaluate  : 0.797 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8294 (m-80) cc_final: 0.7892 (m-80)
REVERT: A  351 TRP cc_start: 0.8414 (p-90) cc_final: 0.8153 (p-90)
REVERT: A  519 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.5487 (p90)
REVERT: A  607 MET cc_start: 0.6925 (mpt) cc_final: 0.6672 (mpt)
REVERT: D  351 TRP cc_start: 0.8434 (p-90) cc_final: 0.8166 (p-90)
REVERT: D  360 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6962 (mm)
REVERT: D  519 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.5835 (p90)
REVERT: B  519 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.5510 (p90)
REVERT: C  351 TRP cc_start: 0.8413 (p-90) cc_final: 0.8127 (p-90)
REVERT: C  519 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5396 (p90)
REVERT: C  522 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.6784 (p)
REVERT: C  539 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7696 (mmm160)
  outliers start: 82
  outliers final: 53
  residues processed: 234
  average time/residue: 0.1174
  time to fit residues: 45.9658
Evaluate side-chains
  223 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 164
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  334 CYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  618 PHE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  677 TRP
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  148 ASN
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  234 HIS
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  323 TYR
Chi-restraints excluded: chain D residue  334 CYS
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  519 PHE
Chi-restraints excluded: chain D residue  522 THR
Chi-restraints excluded: chain D residue  618 PHE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain D residue  677 TRP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 HIS
Chi-restraints excluded: chain B residue  323 TYR
Chi-restraints excluded: chain B residue  374 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  621 VAL
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  234 HIS
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  507 LEU
Chi-restraints excluded: chain C residue  519 PHE
Chi-restraints excluded: chain C residue  522 THR
Chi-restraints excluded: chain C residue  542 LEU
Chi-restraints excluded: chain C residue  618 PHE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  649 VAL
Chi-restraints excluded: chain C residue  677 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 173 optimal weight:   10.0000
   chunk 152 optimal weight:    2.9990
   chunk 218 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 236 optimal weight:    7.9990
   chunk 146 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0000
   chunk 24 optimal weight:    5.9990
   chunk 137 optimal weight:   20.0000
   chunk 193 optimal weight:    5.9990
   chunk 131 optimal weight:    8.9990
   overall best weight:    3.7992

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 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 = 0.3782 r_free = 0.3782 target = 0.095687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.086134 restraints weight = 106161.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.087381 restraints weight = 72067.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.088274 restraints weight = 54068.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.088921 restraints weight = 43711.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.089374 restraints weight = 37175.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.4784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18872  Z= 0.169
  Angle     :  0.834  14.324  25800  Z= 0.401
  Chirality :  0.044   0.173   3044
  Planarity :  0.005   0.055   3264
  Dihedral  :  5.694  30.526   2664
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 18.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.42 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 18.89 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.04 %

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 aren not related in a simple way.
  whole: -1.78 (0.17), residues: 2484
  helix: -0.06 (0.13), residues: 1444
  sheet: -4.04 (0.54), residues: 56
  loop : -2.74 (0.19), residues: 984

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 539 
 TYR   0.031   0.002   TYR A 525 
 PHE   0.027   0.001   PHE C 311 
 TRP   0.019   0.001   TRP B 660 
 HIS   0.006   0.001   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (18872)
  covalent geometry    : angle       0.83431 (25800)
  hydrogen bonds       : bond        0.04002 (  980)
  hydrogen bonds       : angle       5.10290 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 187
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8217 (m-80) cc_final: 0.7755 (m-80)
REVERT: A  351 TRP cc_start: 0.8422 (p-90) cc_final: 0.8144 (p-90)
REVERT: A  519 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.5209 (p90)
REVERT: A  525 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7687 (t80)
REVERT: D  351 TRP cc_start: 0.8444 (p-90) cc_final: 0.8174 (p-90)
REVERT: D  360 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7115 (mm)
REVERT: B  519 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.5387 (p90)
REVERT: B  641 LEU cc_start: 0.7685 (tt) cc_final: 0.7449 (tp)
REVERT: C  122 MET cc_start: 0.8632 (mmm) cc_final: 0.8410 (mmm)
REVERT: C  351 TRP cc_start: 0.8418 (p-90) cc_final: 0.8133 (p-90)
REVERT: C  519 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.5393 (p90)
REVERT: C  522 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.6866 (p)
  outliers start: 72
  outliers final: 52
  residues processed: 238
  average time/residue: 0.1158
  time to fit residues: 46.0559
Evaluate side-chains
  227 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 169
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  334 CYS
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  525 TYR
Chi-restraints excluded: chain A residue  618 PHE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  677 TRP
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  148 ASN
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  234 HIS
Chi-restraints excluded: chain D residue  323 TYR
Chi-restraints excluded: chain D residue  334 CYS
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  374 VAL
Chi-restraints excluded: chain D residue  507 LEU
Chi-restraints excluded: chain D residue  519 PHE
Chi-restraints excluded: chain D residue  618 PHE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain D residue  677 TRP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 HIS
Chi-restraints excluded: chain B residue  323 TYR
Chi-restraints excluded: chain B residue  374 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  677 TRP
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  234 HIS
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  334 CYS
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  507 LEU
Chi-restraints excluded: chain C residue  519 PHE
Chi-restraints excluded: chain C residue  522 THR
Chi-restraints excluded: chain C residue  542 LEU
Chi-restraints excluded: chain C residue  618 PHE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  649 VAL
Chi-restraints excluded: chain C residue  677 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 142 optimal weight:    6.9990
   chunk 190 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0970
   chunk 154 optimal weight:    9.9990
   chunk 8 optimal weight:    0.5980
   chunk 164 optimal weight:    6.9990
   chunk 205 optimal weight:    9.9990
   chunk 132 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0000
   chunk 7 optimal weight:    2.9990
   chunk 169 optimal weight:    0.6980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 133 ASN
B 222 GLN
** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.102814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.093409 restraints weight = 105244.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.094738 restraints weight = 71145.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.095646 restraints weight = 52826.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.096320 restraints weight = 42470.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.096831 restraints weight = 35777.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.5189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  18872  Z= 0.132
  Angle     :  0.804  14.468  25800  Z= 0.381
  Chirality :  0.042   0.199   3044
  Planarity :  0.005   0.056   3264
  Dihedral  :  5.278  24.354   2664
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.05 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    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 aren not related in a simple way.
  whole: -1.52 (0.17), residues: 2484
  helix:  0.12 (0.13), residues: 1448
  sheet: -3.41 (0.58), residues: 56
  loop : -2.62 (0.20), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 539 
 TYR   0.027   0.001   TYR A 525 
 PHE   0.040   0.001   PHE A 311 
 TRP   0.017   0.001   TRP B 660 
 HIS   0.004   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (18872)
  covalent geometry    : angle       0.80406 (25800)
  hydrogen bonds       : bond        0.03705 (  980)
  hydrogen bonds       : angle       4.77440 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 239
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.7964 (m-80) cc_final: 0.7245 (m-80)
REVERT: A  208 TYR cc_start: 0.5875 (t80) cc_final: 0.5531 (t80)
REVERT: A  351 TRP cc_start: 0.8397 (p-90) cc_final: 0.8122 (p-90)
REVERT: A  519 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.4866 (p90)
REVERT: A  525 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7360 (t80)
REVERT: D  122 MET cc_start: 0.8321 (mmm) cc_final: 0.7749 (mmm)
REVERT: D  208 TYR cc_start: 0.5901 (t80) cc_final: 0.5621 (t80)
REVERT: D  270 MET cc_start: 0.7953 (tpp) cc_final: 0.7660 (tpp)
REVERT: D  351 TRP cc_start: 0.8426 (p-90) cc_final: 0.8157 (p-90)
REVERT: D  360 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6301 (mm)
REVERT: B  122 MET cc_start: 0.8300 (mmm) cc_final: 0.7876 (mmm)
REVERT: B  351 TRP cc_start: 0.8513 (p-90) cc_final: 0.8208 (p-90)
REVERT: B  519 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.4705 (p90)
REVERT: B  641 LEU cc_start: 0.7543 (tt) cc_final: 0.7337 (tp)
REVERT: C  250 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7893 (mt)
REVERT: C  270 MET cc_start: 0.7844 (tpp) cc_final: 0.7430 (tpp)
REVERT: C  351 TRP cc_start: 0.8406 (p-90) cc_final: 0.8137 (p-90)
REVERT: C  519 PHE cc_start: 0.6353 (OUTLIER) cc_final: 0.5062 (p90)
REVERT: C  522 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.6969 (p)
REVERT: C  644 LEU cc_start: 0.7390 (mp) cc_final: 0.7088 (mp)
  outliers start: 56
  outliers final: 37
  residues processed: 272
  average time/residue: 0.1214
  time to fit residues: 54.2325
Evaluate side-chains
  244 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 200
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  522 THR
Chi-restraints excluded: chain A residue  525 TYR
Chi-restraints excluded: chain A residue  618 PHE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  148 ASN
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  323 TYR
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  519 PHE
Chi-restraints excluded: chain D residue  618 PHE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 HIS
Chi-restraints excluded: chain B residue  323 TYR
Chi-restraints excluded: chain B residue  374 VAL
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  522 THR
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  649 VAL
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  519 PHE
Chi-restraints excluded: chain C residue  522 THR
Chi-restraints excluded: chain C residue  618 PHE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  649 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 223 optimal weight:    8.9990
   chunk 66 optimal weight:    9.9990
   chunk 68 optimal weight:    7.9990
   chunk 117 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 GLN
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.094353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.084656 restraints weight = 106905.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.085871 restraints weight = 73006.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.086753 restraints weight = 55531.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.087397 restraints weight = 45346.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.087849 restraints weight = 38844.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.5095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  18872  Z= 0.209
  Angle     :  0.886  15.420  25800  Z= 0.427
  Chirality :  0.046   0.190   3044
  Planarity :  0.005   0.055   3264
  Dihedral  :  5.590  29.069   2664
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 21.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.68 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    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 aren not related in a simple way.
  whole: -1.61 (0.17), residues: 2484
  helix:  0.06 (0.13), residues: 1456
  sheet: -3.26 (0.60), residues: 56
  loop : -2.72 (0.19), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 312 
 TYR   0.062   0.002   TYR B 208 
 PHE   0.024   0.002   PHE A 311 
 TRP   0.038   0.001   TRP B 660 
 HIS   0.008   0.002   HIS B 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (18872)
  covalent geometry    : angle       0.88572 (25800)
  hydrogen bonds       : bond        0.04128 (  980)
  hydrogen bonds       : angle       5.14086 ( 2892)

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

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

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4968 Ramachandran restraints generated.
    2484 Oldfield, 0 Emsley, 2484 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 180
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  199 PHE cc_start: 0.8390 (m-80) cc_final: 0.7872 (m-80)
REVERT: A  270 MET cc_start: 0.8143 (tpp) cc_final: 0.7840 (tpp)
REVERT: A  351 TRP cc_start: 0.8444 (p-90) cc_final: 0.8130 (p-90)
REVERT: A  519 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.4968 (p90)
REVERT: A  525 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7881 (t80)
REVERT: D  122 MET cc_start: 0.8568 (mmm) cc_final: 0.8108 (mmm)
REVERT: D  270 MET cc_start: 0.8141 (tpp) cc_final: 0.7780 (tpp)
REVERT: D  351 TRP cc_start: 0.8455 (p-90) cc_final: 0.8166 (p-90)
REVERT: D  360 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6791 (mm)
REVERT: D  519 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.5645 (p90)
REVERT: B  208 TYR cc_start: 0.6535 (t80) cc_final: 0.6167 (t80)
REVERT: B  270 MET cc_start: 0.8136 (tpp) cc_final: 0.7821 (tpp)
REVERT: B  519 PHE cc_start: 0.6602 (OUTLIER) cc_final: 0.5117 (p90)
REVERT: C  270 MET cc_start: 0.8063 (tpp) cc_final: 0.7539 (tpp)
REVERT: C  351 TRP cc_start: 0.8475 (p-90) cc_final: 0.8198 (p-90)
REVERT: C  519 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.5499 (p90)
REVERT: C  522 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.6898 (p)
  outliers start: 54
  outliers final: 39
  residues processed: 218
  average time/residue: 0.1163
  time to fit residues: 42.3075
Evaluate side-chains
  220 residues out of total 2220 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 174
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  148 ASN
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  234 HIS
Chi-restraints excluded: chain A residue  323 TYR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  519 PHE
Chi-restraints excluded: chain A residue  525 TYR
Chi-restraints excluded: chain A residue  618 PHE
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain A residue  677 TRP
Chi-restraints excluded: chain D residue  128 LEU
Chi-restraints excluded: chain D residue  148 ASN
Chi-restraints excluded: chain D residue  152 LEU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  323 TYR
Chi-restraints excluded: chain D residue  360 ILE
Chi-restraints excluded: chain D residue  519 PHE
Chi-restraints excluded: chain D residue  522 THR
Chi-restraints excluded: chain D residue  618 PHE
Chi-restraints excluded: chain D residue  623 LEU
Chi-restraints excluded: chain D residue  677 TRP
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue  128 LEU
Chi-restraints excluded: chain B residue  148 ASN
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  234 HIS
Chi-restraints excluded: chain B residue  323 TYR
Chi-restraints excluded: chain B residue  374 VAL
Chi-restraints excluded: chain B residue  519 PHE
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  624 LEU
Chi-restraints excluded: chain B residue  677 TRP
Chi-restraints excluded: chain C residue  128 LEU
Chi-restraints excluded: chain C residue  148 ASN
Chi-restraints excluded: chain C residue  152 LEU
Chi-restraints excluded: chain C residue  216 LEU
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  374 VAL
Chi-restraints excluded: chain C residue  519 PHE
Chi-restraints excluded: chain C residue  522 THR
Chi-restraints excluded: chain C residue  618 PHE
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  632 LEU
Chi-restraints excluded: chain C residue  649 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 248
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 138 optimal weight:    3.9990
   chunk 56 optimal weight:    0.3980
   chunk 161 optimal weight:    4.9990
   chunk 87 optimal weight:    8.9990
   chunk 188 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 140 optimal weight:   10.0000
   chunk 121 optimal weight:    8.9990
   chunk 57 optimal weight:    5.9990
   chunk 137 optimal weight:    0.9990
   overall best weight:    3.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 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 = 0.3796 r_free = 0.3796 target = 0.096583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.086934 restraints weight = 106668.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.088190 restraints weight = 72705.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.089077 restraints weight = 54752.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.089735 restraints weight = 44431.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.090161 restraints weight = 37881.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.5179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  18872  Z= 0.161
  Angle     :  0.853  15.700  25800  Z= 0.407
  Chirality :  0.044   0.190   3044
  Planarity :  0.005   0.055   3264
  Dihedral  :  5.502  27.421   2664
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 18.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.51 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.17 %
    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 aren not related in a simple way.
  whole: -1.56 (0.17), residues: 2484
  helix:  0.10 (0.13), residues: 1452
  sheet: -3.05 (0.63), residues: 56
  loop : -2.70 (0.19), residues: 976

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 539 
 TYR   0.047   0.002   TYR B 208 
 PHE   0.032   0.001   PHE A 311 
 TRP   0.034   0.001   TRP B 660 
 HIS   0.008   0.001   HIS C 234 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (18872)
  covalent geometry    : angle       0.85320 (25800)
  hydrogen bonds       : bond        0.03861 (  980)
  hydrogen bonds       : angle       5.03242 ( 2892)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2749.53 seconds
wall clock time: 48 minutes 42.74 seconds (2922.74 seconds total)