Starting phenix.real_space_refine
on Thu Mar  5 06:14:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7aa5_11690/03_2026/7aa5_11690_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7aa5_11690/03_2026/7aa5_11690.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7aa5_11690/03_2026/7aa5_11690_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7aa5_11690/03_2026/7aa5_11690_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7aa5_11690/03_2026/7aa5_11690.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7aa5_11690/03_2026/7aa5_11690.map"
  }
  resolution = 4.18
  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=   0.025
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     S     108      5.16       5
     C   12804      2.51       5
     N    3268      2.21       5
     O    3516      1.98       5
     H       8      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 168 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 19705
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4926
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 22, 'TRANS': 589}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4926
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 22, 'TRANS': 589}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 4926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4926
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 22, 'TRANS': 589}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 4926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4926
          Classifications: {'peptide': 612}
          Link IDs: {'PTRANS': 22, 'TRANS': 589}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.08, per 1000 atoms: 0.21
  Number of scatterers: 19705
  At special positions: 0
  Unit cell: (147.609, 147.609, 116.937, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S     108     16.00
     O    3516      8.00
     N    3268      7.00
     C   12804      6.00
     H       8      1.00
    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: 1.62
  Conformation dependent library (CDL) restraints added in 753.5 milliseconds
  

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4632

  Finding SS restraints...
    Secondary structure from input PDB file:
      124 helices and 4 sheets defined
      61.4% alpha, 2.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 150 through 161
      removed outlier: 3.734A  pdb=" N   LEU A 154 " --> pdb=" O   ASN A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 166
      removed outlier: 3.999A  pdb=" N   ASP A 165 " --> pdb=" O   SER A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 176
    Processing helix  chain 'A' and resid 193 through 201
      removed outlier: 3.699A  pdb=" N   ASN A 201 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 221
    Processing helix  chain 'A' and resid 223 through 228
    Processing helix  chain 'A' and resid 240 through 249
      removed outlier: 3.939A  pdb=" N   ILE A 244 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 261
    Processing helix  chain 'A' and resid 270 through 274
    Processing helix  chain 'A' and resid 287 through 295
    Processing helix  chain 'A' and resid 297 through 306
    Processing helix  chain 'A' and resid 323 through 331
    Processing helix  chain 'A' and resid 336 through 357
      removed outlier: 3.736A  pdb=" N   PHE A 341 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   VAL A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LYS A 344 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 380
    Processing helix  chain 'A' and resid 382 through 392
      removed outlier: 3.791A  pdb=" N   ARG A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 400
      removed outlier: 3.691A  pdb=" N   THR A 399 " --> pdb=" O   ASP A 396 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG A 400 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 396 through 400'
    Processing helix  chain 'A' and resid 432 through 439
      removed outlier: 3.515A  pdb=" N   ILE A 436 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 450
      removed outlier: 3.623A  pdb=" N   LEU A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 464
      removed outlier: 4.119A  pdb=" N   LEU A 458 " --> pdb=" O   PRO A 454 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ARG A 460 " --> pdb=" O   ASN A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 491
      removed outlier: 3.904A  pdb=" N   PHE A 471 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 530
      removed outlier: 3.554A  pdb=" N   ILE A 516 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 570
      removed outlier: 3.546A  pdb=" N   SER A 557 " --> pdb=" O   TYR A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 593
      removed outlier: 3.897A  pdb=" N   VAL A 579 " --> pdb=" O   LEU A 575 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE A 580 " --> pdb=" O   ALA A 576 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LEU A 590 " --> pdb=" O   TRP A 586 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   TYR A 591 " --> pdb=" O   MET A 587 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE A 592 " --> pdb=" O   ASN A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 599
      removed outlier: 3.625A  pdb=" N   LEU A 598 " --> pdb=" O   GLY A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 610
      removed outlier: 4.006A  pdb=" N   GLN A 607 " --> pdb=" O   SER A 603 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LYS A 608 " --> pdb=" O   ILE A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 635
    Processing helix  chain 'A' and resid 667 through 678
    Processing helix  chain 'A' and resid 693 through 709
      removed outlier: 4.254A  pdb=" N   ILE A 697 " --> pdb=" O   VAL A 693 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU A 698 " --> pdb=" O   VAL A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 722
    Processing helix  chain 'A' and resid 723 through 725
      No H-bonds generated for 'chain 'A' and resid 723 through 725'
    Processing helix  chain 'A' and resid 729 through 748
      removed outlier: 3.638A  pdb=" N   PHE A 748 " --> pdb=" O   ILE A 744 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 161
      removed outlier: 3.735A  pdb=" N   LEU B 154 " --> pdb=" O   ASN B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 166
      removed outlier: 4.000A  pdb=" N   ASP B 165 " --> pdb=" O   SER B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 176
    Processing helix  chain 'B' and resid 193 through 201
      removed outlier: 3.699A  pdb=" N   ASN B 201 " --> pdb=" O   LYS B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 221
    Processing helix  chain 'B' and resid 223 through 228
    Processing helix  chain 'B' and resid 240 through 249
      removed outlier: 3.939A  pdb=" N   ILE B 244 " --> pdb=" O   THR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 261
    Processing helix  chain 'B' and resid 270 through 274
    Processing helix  chain 'B' and resid 287 through 295
    Processing helix  chain 'B' and resid 297 through 306
    Processing helix  chain 'B' and resid 323 through 331
    Processing helix  chain 'B' and resid 336 through 357
      removed outlier: 3.735A  pdb=" N   PHE B 341 " --> pdb=" O   GLU B 337 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   VAL B 342 " --> pdb=" O   ASN B 338 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LYS B 344 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 380
    Processing helix  chain 'B' and resid 382 through 392
      removed outlier: 3.791A  pdb=" N   ARG B 391 " --> pdb=" O   GLN B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 400
      removed outlier: 3.692A  pdb=" N   THR B 399 " --> pdb=" O   ASP B 396 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG B 400 " --> pdb=" O   GLU B 397 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 396 through 400'
    Processing helix  chain 'B' and resid 432 through 439
      removed outlier: 3.515A  pdb=" N   ILE B 436 " --> pdb=" O   SER B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 450
      removed outlier: 3.624A  pdb=" N   LEU B 450 " --> pdb=" O   ARG B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 464
      removed outlier: 4.120A  pdb=" N   LEU B 458 " --> pdb=" O   PRO B 454 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG B 460 " --> pdb=" O   ASN B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 491
      removed outlier: 3.904A  pdb=" N   PHE B 471 " --> pdb=" O   GLY B 467 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 530
      removed outlier: 3.554A  pdb=" N   ILE B 516 " --> pdb=" O   ALA B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 570
      removed outlier: 3.544A  pdb=" N   SER B 557 " --> pdb=" O   TYR B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 575 through 593
      removed outlier: 3.898A  pdb=" N   VAL B 579 " --> pdb=" O   LEU B 575 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE B 580 " --> pdb=" O   ALA B 576 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LEU B 590 " --> pdb=" O   TRP B 586 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   TYR B 591 " --> pdb=" O   MET B 587 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE B 592 " --> pdb=" O   ASN B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 599
      removed outlier: 3.626A  pdb=" N   LEU B 598 " --> pdb=" O   GLY B 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 610
      removed outlier: 4.007A  pdb=" N   GLN B 607 " --> pdb=" O   SER B 603 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LYS B 608 " --> pdb=" O   ILE B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 635
    Processing helix  chain 'B' and resid 667 through 678
    Processing helix  chain 'B' and resid 693 through 709
      removed outlier: 4.254A  pdb=" N   ILE B 697 " --> pdb=" O   VAL B 693 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B 698 " --> pdb=" O   VAL B 694 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 722
    Processing helix  chain 'B' and resid 723 through 725
      No H-bonds generated for 'chain 'B' and resid 723 through 725'
    Processing helix  chain 'B' and resid 729 through 748
      removed outlier: 3.639A  pdb=" N   PHE B 748 " --> pdb=" O   ILE B 744 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 161
      removed outlier: 3.734A  pdb=" N   LEU C 154 " --> pdb=" O   ASN C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 166
      removed outlier: 4.000A  pdb=" N   ASP C 165 " --> pdb=" O   SER C 162 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 176
    Processing helix  chain 'C' and resid 193 through 201
      removed outlier: 3.698A  pdb=" N   ASN C 201 " --> pdb=" O   LYS C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 221
    Processing helix  chain 'C' and resid 223 through 228
    Processing helix  chain 'C' and resid 240 through 249
      removed outlier: 3.939A  pdb=" N   ILE C 244 " --> pdb=" O   THR C 240 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 261
    Processing helix  chain 'C' and resid 270 through 274
    Processing helix  chain 'C' and resid 287 through 295
    Processing helix  chain 'C' and resid 297 through 306
    Processing helix  chain 'C' and resid 323 through 331
    Processing helix  chain 'C' and resid 336 through 357
      removed outlier: 3.735A  pdb=" N   PHE C 341 " --> pdb=" O   GLU C 337 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   VAL C 342 " --> pdb=" O   ASN C 338 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LYS C 344 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 372 through 380
    Processing helix  chain 'C' and resid 382 through 392
      removed outlier: 3.791A  pdb=" N   ARG C 391 " --> pdb=" O   GLN C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 396 through 400
      removed outlier: 3.691A  pdb=" N   THR C 399 " --> pdb=" O   ASP C 396 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ARG C 400 " --> pdb=" O   GLU C 397 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 396 through 400'
    Processing helix  chain 'C' and resid 432 through 439
      removed outlier: 3.514A  pdb=" N   ILE C 436 " --> pdb=" O   SER C 432 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 445 through 450
      removed outlier: 3.624A  pdb=" N   LEU C 450 " --> pdb=" O   ARG C 446 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 464
      removed outlier: 4.120A  pdb=" N   LEU C 458 " --> pdb=" O   PRO C 454 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG C 460 " --> pdb=" O   ASN C 456 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 467 through 491
      removed outlier: 3.904A  pdb=" N   PHE C 471 " --> pdb=" O   GLY C 467 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 507 through 530
      removed outlier: 3.554A  pdb=" N   ILE C 516 " --> pdb=" O   ALA C 512 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 551 through 570
      removed outlier: 3.545A  pdb=" N   SER C 557 " --> pdb=" O   TYR C 553 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 575 through 593
      removed outlier: 3.898A  pdb=" N   VAL C 579 " --> pdb=" O   LEU C 575 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE C 580 " --> pdb=" O   ALA C 576 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LEU C 590 " --> pdb=" O   TRP C 586 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   TYR C 591 " --> pdb=" O   MET C 587 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE C 592 " --> pdb=" O   ASN C 588 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 595 through 599
      removed outlier: 3.626A  pdb=" N   LEU C 598 " --> pdb=" O   GLY C 595 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 600 through 610
      removed outlier: 4.007A  pdb=" N   GLN C 607 " --> pdb=" O   SER C 603 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LYS C 608 " --> pdb=" O   ILE C 604 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 612 through 635
    Processing helix  chain 'C' and resid 667 through 678
    Processing helix  chain 'C' and resid 693 through 709
      removed outlier: 4.255A  pdb=" N   ILE C 697 " --> pdb=" O   VAL C 693 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU C 698 " --> pdb=" O   VAL C 694 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 709 through 722
    Processing helix  chain 'C' and resid 723 through 725
      No H-bonds generated for 'chain 'C' and resid 723 through 725'
    Processing helix  chain 'C' and resid 729 through 748
      removed outlier: 3.639A  pdb=" N   PHE C 748 " --> pdb=" O   ILE C 744 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 150 through 161
      removed outlier: 3.734A  pdb=" N   LEU D 154 " --> pdb=" O   ASN D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 166
      removed outlier: 4.000A  pdb=" N   ASP D 165 " --> pdb=" O   SER D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 176
    Processing helix  chain 'D' and resid 193 through 201
      removed outlier: 3.699A  pdb=" N   ASN D 201 " --> pdb=" O   LYS D 197 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 221
    Processing helix  chain 'D' and resid 223 through 228
    Processing helix  chain 'D' and resid 240 through 249
      removed outlier: 3.939A  pdb=" N   ILE D 244 " --> pdb=" O   THR D 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 250 through 261
    Processing helix  chain 'D' and resid 270 through 274
    Processing helix  chain 'D' and resid 287 through 295
    Processing helix  chain 'D' and resid 297 through 306
    Processing helix  chain 'D' and resid 323 through 331
    Processing helix  chain 'D' and resid 336 through 357
      removed outlier: 3.735A  pdb=" N   PHE D 341 " --> pdb=" O   GLU D 337 " (cutoff:3.500A)
      removed outlier: 5.149A  pdb=" N   VAL D 342 " --> pdb=" O   ASN D 338 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LYS D 344 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 372 through 380
    Processing helix  chain 'D' and resid 382 through 392
      removed outlier: 3.791A  pdb=" N   ARG D 391 " --> pdb=" O   GLN D 387 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 396 through 400
      removed outlier: 3.691A  pdb=" N   THR D 399 " --> pdb=" O   ASP D 396 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ARG D 400 " --> pdb=" O   GLU D 397 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 396 through 400'
    Processing helix  chain 'D' and resid 432 through 439
      removed outlier: 3.514A  pdb=" N   ILE D 436 " --> pdb=" O   SER D 432 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 445 through 450
      removed outlier: 3.623A  pdb=" N   LEU D 450 " --> pdb=" O   ARG D 446 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 452 through 464
      removed outlier: 4.120A  pdb=" N   LEU D 458 " --> pdb=" O   PRO D 454 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG D 460 " --> pdb=" O   ASN D 456 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 467 through 491
      removed outlier: 3.904A  pdb=" N   PHE D 471 " --> pdb=" O   GLY D 467 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 507 through 530
      removed outlier: 3.553A  pdb=" N   ILE D 516 " --> pdb=" O   ALA D 512 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 551 through 570
      removed outlier: 3.544A  pdb=" N   SER D 557 " --> pdb=" O   TYR D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 575 through 593
      removed outlier: 3.898A  pdb=" N   VAL D 579 " --> pdb=" O   LEU D 575 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   PHE D 580 " --> pdb=" O   ALA D 576 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LEU D 590 " --> pdb=" O   TRP D 586 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   TYR D 591 " --> pdb=" O   MET D 587 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE D 592 " --> pdb=" O   ASN D 588 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 595 through 599
      removed outlier: 3.626A  pdb=" N   LEU D 598 " --> pdb=" O   GLY D 595 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 600 through 610
      removed outlier: 4.006A  pdb=" N   GLN D 607 " --> pdb=" O   SER D 603 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LYS D 608 " --> pdb=" O   ILE D 604 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 612 through 635
    Processing helix  chain 'D' and resid 667 through 678
    Processing helix  chain 'D' and resid 693 through 709
      removed outlier: 4.254A  pdb=" N   ILE D 697 " --> pdb=" O   VAL D 693 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU D 698 " --> pdb=" O   VAL D 694 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 709 through 722
    Processing helix  chain 'D' and resid 723 through 725
      No H-bonds generated for 'chain 'D' and resid 723 through 725'
    Processing helix  chain 'D' and resid 729 through 748
      removed outlier: 3.639A  pdb=" N   PHE D 748 " --> pdb=" O   ILE D 744 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 406
      removed outlier: 3.651A  pdb=" N   LEU A 418 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 406
      removed outlier: 3.652A  pdb=" N   LEU B 418 " --> pdb=" O   PHE B 406 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 406
      removed outlier: 3.651A  pdb=" N   LEU C 418 " --> pdb=" O   PHE C 406 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 406
      removed outlier: 3.651A  pdb=" N   LEU D 418 " --> pdb=" O   PHE D 406 " (cutoff:3.500A)

    944 hydrogen bonds defined for protein.
    2784 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.61

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        1.01 -     1.17: 8
        1.17 -     1.33: 4161
        1.33 -     1.49: 7284
        1.49 -     1.65: 8513
        1.65 -     1.81: 178
  Bond restraints: 20144
  Sorted by residual:
  bond pdb=" N   PRO D 772 "
       pdb=" CD  PRO D 772 "
    ideal  model  delta    sigma   weight residual
    1.473  1.714 -0.241 1.40e-02 5.10e+03 2.96e+02
  bond pdb=" N   PRO B 772 "
       pdb=" CD  PRO B 772 "
    ideal  model  delta    sigma   weight residual
    1.473  1.714 -0.241 1.40e-02 5.10e+03 2.96e+02
  bond pdb=" N   PRO D 772 "
       pdb=" CA  PRO D 772 "
    ideal  model  delta    sigma   weight residual
    1.469  1.292  0.177 1.28e-02 6.10e+03 1.91e+02
  bond pdb=" N   PRO B 772 "
       pdb=" CA  PRO B 772 "
    ideal  model  delta    sigma   weight residual
    1.469  1.292  0.177 1.28e-02 6.10e+03 1.90e+02
  bond pdb=" N   PRO C 772 "
       pdb=" CD  PRO C 772 "
    ideal  model  delta    sigma   weight residual
    1.473  1.629 -0.156 1.40e-02 5.10e+03 1.25e+02
  ... (remaining 20139 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.99: 27222
        5.99 -    11.97: 62
       11.97 -    17.96: 5
       17.96 -    23.94: 6
       23.94 -    29.93: 1
  Bond angle restraints: 27296
  Sorted by residual:
  angle pdb=" C   THR C 771 "
        pdb=" N   PRO C 772 "
        pdb=" CA  PRO C 772 "
      ideal   model   delta    sigma   weight residual
     119.84   99.71   20.13 1.25e+00 6.40e-01 2.59e+02
  angle pdb=" CA  THR B 771 "
        pdb=" C   THR B 771 "
        pdb=" O   THR B 771 "
      ideal   model   delta    sigma   weight residual
     120.16  100.91   19.25 1.37e+00 5.33e-01 1.97e+02
  angle pdb=" CA  THR D 771 "
        pdb=" C   THR D 771 "
        pdb=" O   THR D 771 "
      ideal   model   delta    sigma   weight residual
     120.16  100.93   19.23 1.37e+00 5.33e-01 1.97e+02
  angle pdb=" C   THR D 771 "
        pdb=" N   PRO D 772 "
        pdb=" CA  PRO D 772 "
      ideal   model   delta    sigma   weight residual
     119.84  102.33   17.51 1.25e+00 6.40e-01 1.96e+02
  angle pdb=" C   THR B 771 "
        pdb=" N   PRO B 772 "
        pdb=" CA  PRO B 772 "
      ideal   model   delta    sigma   weight residual
     119.84  102.34   17.50 1.25e+00 6.40e-01 1.96e+02
  ... (remaining 27291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 10620
       17.58 -    35.16: 1116
       35.16 -    52.73: 209
       52.73 -    70.31: 46
       70.31 -    87.89: 9
  Dihedral angle restraints: 12000
    sinusoidal: 4820
      harmonic: 7180
  Sorted by residual:
  dihedral pdb=" CA  GLY C 770 "
           pdb=" C   GLY C 770 "
           pdb=" N   THR C 771 "
           pdb=" CA  THR C 771 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  106.78   73.22     0      5.00e+00 4.00e-02 2.14e+02
  dihedral pdb=" CA  GLY D 770 "
           pdb=" C   GLY D 770 "
           pdb=" N   THR D 771 "
           pdb=" CA  THR D 771 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  122.37   57.63     0      5.00e+00 4.00e-02 1.33e+02
  dihedral pdb=" CA  GLY B 770 "
           pdb=" C   GLY B 770 "
           pdb=" N   THR B 771 "
           pdb=" CA  THR B 771 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  122.41   57.59     0      5.00e+00 4.00e-02 1.33e+02
  ... (remaining 11997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 3052
       0.095 -    0.190: 78
       0.190 -    0.286: 2
       0.286 -    0.381: 1
       0.381 -    0.476: 3
  Chirality restraints: 3136
  Sorted by residual:
  chirality pdb=" CA  PRO B 772 "
            pdb=" N   PRO B 772 "
            pdb=" C   PRO B 772 "
            pdb=" CB  PRO B 772 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.24    0.48 2.00e-01 2.50e+01 5.67e+00
  chirality pdb=" CA  PRO D 772 "
            pdb=" N   PRO D 772 "
            pdb=" C   PRO D 772 "
            pdb=" CB  PRO D 772 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.24    0.48 2.00e-01 2.50e+01 5.66e+00
  chirality pdb=" CB  THR A 771 "
            pdb=" CA  THR A 771 "
            pdb=" OG1 THR A 771 "
            pdb=" CG2 THR A 771 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.11    0.45 2.00e-01 2.50e+01 4.99e+00
  ... (remaining 3133 not shown)

  Planarity restraints: 3408
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 770 "    0.024 2.00e-02 2.50e+03   5.43e-02 2.95e+01
        pdb=" C   GLY A 770 "   -0.094 2.00e-02 2.50e+03
        pdb=" O   GLY A 770 "    0.037 2.00e-02 2.50e+03
        pdb=" N   THR A 771 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 771 "   -0.021 2.00e-02 2.50e+03   4.34e-02 1.88e+01
        pdb=" C   THR B 771 "    0.075 2.00e-02 2.50e+03
        pdb=" O   THR B 771 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   PRO B 772 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 771 "    0.021 2.00e-02 2.50e+03   4.32e-02 1.87e+01
        pdb=" C   THR D 771 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   THR D 771 "    0.026 2.00e-02 2.50e+03
        pdb=" N   PRO D 772 "    0.028 2.00e-02 2.50e+03
  ... (remaining 3405 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.62: 403
        2.62 -     3.11: 17172
        3.11 -     3.61: 25393
        3.61 -     4.10: 32478
        4.10 -     4.60: 47585
  Nonbonded interactions: 123031
  Sorted by model distance:
  nonbonded pdb=" O   THR A 339 "
            pdb=" OG1 THR A 343 "
     model   vdw
     2.119 2.800
  nonbonded pdb=" O   THR B 339 "
            pdb=" OG1 THR B 343 "
     model   vdw
     2.120 2.800
  nonbonded pdb=" O   THR C 339 "
            pdb=" OG1 THR C 343 "
     model   vdw
     2.120 2.800
  nonbonded pdb=" O   THR D 339 "
            pdb=" OG1 THR D 343 "
     model   vdw
     2.120 2.800
  nonbonded pdb=" O   ALA D 217 "
            pdb=" OG1 THR D 220 "
     model   vdw
     2.199 2.800
  ... (remaining 123026 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 148 through 786)
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.660
  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:             0.170
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     15.470
  Find NCS groups from input model:        0.390
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
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      :  0.006   0.241  20136  Z= 0.336
  Angle     :  0.921  29.930  27288  Z= 0.544
  Chirality :  0.045   0.476   3136
  Planarity :  0.005   0.072   3408
  Dihedral  : 14.673  87.890   7360
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 21.41
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 15.06 %
    Favored  : 84.74 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  4.72 %
    Favored  : 93.24 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.27 %
    Twisted General : 0.34 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.78 (0.13), residues: 2424
  helix: -2.43 (0.11), residues: 1336
  sheet: -1.80 (0.54), residues: 76
  loop : -4.33 (0.15), residues: 1012

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 757 
 TYR   0.012   0.001   TYR C 500 
 PHE   0.012   0.001   PHE B 756 
 TRP   0.022   0.002   TRP C 733 
 HIS   0.004   0.001   HIS C 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 (20136)
  covalent geometry    : angle       0.92061 (27288)
  hydrogen bonds       : bond        0.15361 (  944)
  hydrogen bonds       : angle       7.01976 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  288 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 244
  time to evaluate  : 0.704 
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  223 MET cc_start: 0.7127 (mmm) cc_final: 0.6823 (mmm)
REVERT: A  482 MET cc_start: 0.8206 (mmm) cc_final: 0.7707 (mmt)
REVERT: A  578 MET cc_start: 0.6533 (mtp) cc_final: 0.6286 (tpp)
REVERT: A  757 ARG cc_start: 0.8177 (ppt170) cc_final: 0.7956 (ppt170)
REVERT: B  176 HIS cc_start: 0.8619 (t-170) cc_final: 0.8132 (m90)
REVERT: B  482 MET cc_start: 0.7450 (mmm) cc_final: 0.6929 (mmt)
REVERT: B  556 TYR cc_start: 0.9269 (t80) cc_final: 0.8726 (t80)
REVERT: B  761 MET cc_start: 0.8316 (mmp) cc_final: 0.8035 (mmp)
REVERT: C  223 MET cc_start: 0.7257 (mmm) cc_final: 0.6986 (mmm)
REVERT: C  225 GLU cc_start: 0.7495 (tt0) cc_final: 0.7281 (tt0)
REVERT: C  482 MET cc_start: 0.8305 (mmm) cc_final: 0.7802 (mmt)
REVERT: D  223 MET cc_start: 0.7133 (mmm) cc_final: 0.6838 (mmm)
REVERT: D  225 GLU cc_start: 0.7508 (tt0) cc_final: 0.7265 (tt0)
REVERT: D  482 MET cc_start: 0.8211 (mmm) cc_final: 0.7717 (mmt)
REVERT: D  713 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.9099 (mmt)
REVERT: D  757 ARG cc_start: 0.8230 (ppt170) cc_final: 0.7976 (ppt170)
  outliers start: 44
  outliers final: 19
  residues processed: 280
  average time/residue: 0.1318
  time to fit residues: 58.2115
Evaluate side-chains
  205 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 216 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 194 optimal weight:    5.9990
   chunk 227 optimal weight:    0.0770
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   chunk 235 optimal weight:    0.9990
   overall best weight:    2.5544

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

Flipped N/Q/H residues before XYZ refinement:
A 326 HIS
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 HIS
** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 326 HIS
** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 326 HIS
** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.084990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.064114 restraints weight = 106220.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.066417 restraints weight = 69034.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.067417 restraints weight = 43024.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.067725 restraints weight = 35486.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.067826 restraints weight = 32821.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  20136  Z= 0.178
  Angle     :  0.618   8.515  27288  Z= 0.328
  Chirality :  0.037   0.147   3136
  Planarity :  0.004   0.043   3408
  Dihedral  :  5.814  40.892   2692
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 47.49
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 13.70 %
    Favored  : 86.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -2.96 (0.15), residues: 2424
  helix: -0.66 (0.13), residues: 1368
  sheet: -1.51 (0.54), residues: 76
  loop : -4.03 (0.16), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 160 
 TYR   0.013   0.001   TYR D 628 
 PHE   0.041   0.002   PHE B 615 
 TRP   0.014   0.001   TRP B 586 
 HIS   0.006   0.001   HIS C 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (20136)
  covalent geometry    : angle       0.61829 (27288)
  hydrogen bonds       : bond        0.03917 (  944)
  hydrogen bonds       : angle       5.56836 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  223 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.719 
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  176 HIS cc_start: 0.9301 (t-90) cc_final: 0.8579 (t-90)
REVERT: A  178 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8437 (mmmt)
REVERT: A  397 GLU cc_start: 0.9248 (pm20) cc_final: 0.8633 (tm-30)
REVERT: A  482 MET cc_start: 0.8209 (mmm) cc_final: 0.7786 (mmt)
REVERT: A  578 MET cc_start: 0.6288 (mtp) cc_final: 0.6004 (mtt)
REVERT: A  587 MET cc_start: 0.9124 (mtm) cc_final: 0.8853 (mtp)
REVERT: A  624 PHE cc_start: 0.9298 (m-80) cc_final: 0.9030 (m-80)
REVERT: B  482 MET cc_start: 0.7467 (mmm) cc_final: 0.7239 (mmt)
REVERT: B  578 MET cc_start: 0.4556 (mtt) cc_final: 0.4312 (tpp)
REVERT: B  587 MET cc_start: 0.8907 (mtm) cc_final: 0.8546 (mtp)
REVERT: B  624 PHE cc_start: 0.9250 (m-80) cc_final: 0.8970 (m-80)
REVERT: B  761 MET cc_start: 0.8769 (mmp) cc_final: 0.8545 (mmp)
REVERT: C  176 HIS cc_start: 0.9320 (t-90) cc_final: 0.8593 (t-90)
REVERT: C  178 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8371 (mmmt)
REVERT: C  397 GLU cc_start: 0.9219 (pm20) cc_final: 0.8568 (tm-30)
REVERT: C  587 MET cc_start: 0.9149 (mtm) cc_final: 0.8877 (mtp)
REVERT: C  624 PHE cc_start: 0.9213 (m-80) cc_final: 0.8990 (m-80)
REVERT: D  176 HIS cc_start: 0.9325 (t-90) cc_final: 0.8623 (t-90)
REVERT: D  178 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8429 (mmmt)
REVERT: D  397 GLU cc_start: 0.9254 (pm20) cc_final: 0.8665 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1255
  time to fit residues: 44.9387
Evaluate side-chains
  184 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 223 optimal weight:    5.9990
   chunk 108 optimal weight:    5.9990
   chunk 135 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 50 optimal weight:   20.0000
   chunk 169 optimal weight:   20.0000
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 274 GLN
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 274 GLN
** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 274 GLN
** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.084945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.064367 restraints weight = 105962.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.066539 restraints weight = 68271.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.067594 restraints weight = 43050.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.067931 restraints weight = 36863.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.068060 restraints weight = 32025.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.2185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  20136  Z= 0.182
  Angle     :  0.603   7.272  27288  Z= 0.318
  Chirality :  0.037   0.138   3136
  Planarity :  0.004   0.037   3408
  Dihedral  :  5.561  36.542   2692
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 57.04
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 14.36 %
    Favored  : 85.44 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.54 %
    Favored  : 95.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -2.48 (0.16), residues: 2424
  helix: -0.15 (0.13), residues: 1396
  sheet: -1.33 (0.56), residues: 76
  loop : -4.12 (0.17), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 446 
 TYR   0.016   0.002   TYR C 303 
 PHE   0.021   0.001   PHE B 615 
 TRP   0.010   0.001   TRP A 586 
 HIS   0.006   0.001   HIS C 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (20136)
  covalent geometry    : angle       0.60279 (27288)
  hydrogen bonds       : bond        0.03492 (  944)
  hydrogen bonds       : angle       5.26573 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  233 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 229
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 HIS cc_start: 0.9332 (t-90) cc_final: 0.9085 (t-90)
REVERT: A  178 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8507 (mtpp)
REVERT: A  587 MET cc_start: 0.9113 (mtm) cc_final: 0.8873 (mtp)
REVERT: A  624 PHE cc_start: 0.9253 (m-80) cc_final: 0.8996 (m-80)
REVERT: A  761 MET cc_start: 0.8684 (mmp) cc_final: 0.8374 (mmp)
REVERT: B  219 ARG cc_start: 0.8009 (mmt90) cc_final: 0.7800 (mmt90)
REVERT: B  482 MET cc_start: 0.7600 (mmm) cc_final: 0.7317 (mmt)
REVERT: B  578 MET cc_start: 0.4400 (mtt) cc_final: 0.4179 (tpp)
REVERT: B  587 MET cc_start: 0.8919 (mtm) cc_final: 0.8605 (mpp)
REVERT: B  624 PHE cc_start: 0.9219 (m-80) cc_final: 0.8966 (m-80)
REVERT: B  761 MET cc_start: 0.8766 (mmp) cc_final: 0.8531 (mmp)
REVERT: C  176 HIS cc_start: 0.9312 (t-90) cc_final: 0.9097 (t-90)
REVERT: C  587 MET cc_start: 0.9129 (mtm) cc_final: 0.8902 (mtp)
REVERT: C  624 PHE cc_start: 0.9210 (m-80) cc_final: 0.8998 (m-80)
REVERT: C  761 MET cc_start: 0.8766 (mmp) cc_final: 0.8510 (mmp)
REVERT: D  176 HIS cc_start: 0.9308 (t-90) cc_final: 0.9090 (t-90)
REVERT: D  397 GLU cc_start: 0.9248 (pm20) cc_final: 0.8656 (tm-30)
REVERT: D  587 MET cc_start: 0.9039 (mtm) cc_final: 0.8746 (mtp)
REVERT: D  625 MET cc_start: 0.8995 (ptp) cc_final: 0.8709 (ptp)
REVERT: D  761 MET cc_start: 0.8733 (mmp) cc_final: 0.8487 (mmp)
REVERT: D  778 PHE cc_start: 0.7411 (t80) cc_final: 0.7194 (t80)
  outliers start: 4
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1295
  time to fit residues: 48.1220
Evaluate side-chains
  188 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 211 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 220 optimal weight:    9.9990
   chunk 127 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   chunk 158 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 231 optimal weight:    0.0870
   overall best weight:    1.3562

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 731 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 = 0.3755 r_free = 0.3755 target = 0.092587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.069406 restraints weight = 89713.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.071161 restraints weight = 57198.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.072385 restraints weight = 42235.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.073263 restraints weight = 34255.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.073901 restraints weight = 29584.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  20136  Z= 0.110
  Angle     :  0.502   6.102  27288  Z= 0.268
  Chirality :  0.035   0.132   3136
  Planarity :  0.004   0.054   3408
  Dihedral  :  5.141  32.770   2692
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 53.23
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 12.50 %
    Favored  : 87.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.17), residues: 2424
  helix:  0.44 (0.14), residues: 1400
  sheet: -0.94 (0.57), residues: 76
  loop : -3.82 (0.18), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 160 
 TYR   0.012   0.001   TYR D 621 
 PHE   0.019   0.001   PHE D 624 
 TRP   0.011   0.001   TRP A 586 
 HIS   0.006   0.001   HIS A 731 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (20136)
  covalent geometry    : angle       0.50206 (27288)
  hydrogen bonds       : bond        0.02987 (  944)
  hydrogen bonds       : angle       4.71328 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  227 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 HIS cc_start: 0.9204 (t-90) cc_final: 0.8898 (t-90)
REVERT: A  397 GLU cc_start: 0.9138 (pm20) cc_final: 0.8622 (tm-30)
REVERT: A  449 MET cc_start: 0.9415 (mtt) cc_final: 0.9136 (mtt)
REVERT: A  587 MET cc_start: 0.8975 (mtm) cc_final: 0.8772 (mtp)
REVERT: A  624 PHE cc_start: 0.9146 (m-80) cc_final: 0.8912 (m-80)
REVERT: A  713 MET cc_start: 0.9088 (tpp) cc_final: 0.8742 (tpp)
REVERT: A  761 MET cc_start: 0.8656 (mmp) cc_final: 0.8406 (mmp)
REVERT: A  778 PHE cc_start: 0.7364 (t80) cc_final: 0.7136 (t80)
REVERT: B  176 HIS cc_start: 0.9193 (t-90) cc_final: 0.8992 (t-90)
REVERT: B  219 ARG cc_start: 0.8028 (mmt90) cc_final: 0.7788 (mmt90)
REVERT: B  482 MET cc_start: 0.7569 (mmm) cc_final: 0.7304 (mmt)
REVERT: B  578 MET cc_start: 0.4442 (mtt) cc_final: 0.4238 (tpp)
REVERT: B  587 MET cc_start: 0.8777 (mtm) cc_final: 0.8500 (mtp)
REVERT: B  624 PHE cc_start: 0.9148 (m-80) cc_final: 0.8877 (m-80)
REVERT: B  710 LEU cc_start: 0.9837 (mm) cc_final: 0.9546 (mp)
REVERT: B  761 MET cc_start: 0.8663 (mmp) cc_final: 0.8440 (mmp)
REVERT: B  778 PHE cc_start: 0.7693 (t80) cc_final: 0.7467 (t80)
REVERT: C  397 GLU cc_start: 0.9109 (pm20) cc_final: 0.8613 (tm-30)
REVERT: C  449 MET cc_start: 0.9397 (mtt) cc_final: 0.9110 (mtt)
REVERT: C  482 MET cc_start: 0.8285 (mmm) cc_final: 0.7623 (mmt)
REVERT: C  621 TYR cc_start: 0.9249 (t80) cc_final: 0.9037 (t80)
REVERT: C  622 LEU cc_start: 0.9159 (tp) cc_final: 0.8908 (tp)
REVERT: C  761 MET cc_start: 0.8694 (mmp) cc_final: 0.8494 (mmp)
REVERT: C  778 PHE cc_start: 0.7302 (t80) cc_final: 0.7095 (t80)
REVERT: D  397 GLU cc_start: 0.9136 (pm20) cc_final: 0.8615 (tm-30)
REVERT: D  587 MET cc_start: 0.8889 (mtm) cc_final: 0.8588 (mtp)
REVERT: D  778 PHE cc_start: 0.7344 (t80) cc_final: 0.7074 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.1296
  time to fit residues: 47.0367
Evaluate side-chains
  196 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 189 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 207 optimal weight:    4.9990
   chunk 146 optimal weight:    4.9990
   chunk 230 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 203 optimal weight:    5.9990
   chunk 155 optimal weight:   20.0000
   chunk 43 optimal weight:   20.0000
   chunk 59 optimal weight:    1.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 731 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 = 0.3701 r_free = 0.3701 target = 0.085136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.064014 restraints weight = 105640.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.065848 restraints weight = 65576.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.067060 restraints weight = 47175.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.067869 restraints weight = 37451.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.068415 restraints weight = 31870.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  20136  Z= 0.168
  Angle     :  0.575   5.793  27288  Z= 0.301
  Chirality :  0.036   0.166   3136
  Planarity :  0.004   0.041   3408
  Dihedral  :  5.162  31.439   2692
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 60.31
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 14.81 %
    Favored  : 85.02 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  2.55 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.17), residues: 2424
  helix:  0.51 (0.14), residues: 1396
  sheet: -1.11 (0.56), residues: 76
  loop : -3.88 (0.18), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 160 
 TYR   0.018   0.001   TYR C 303 
 PHE   0.025   0.001   PHE A 172 
 TRP   0.012   0.001   TRP A 586 
 HIS   0.005   0.001   HIS D 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (20136)
  covalent geometry    : angle       0.57499 (27288)
  hydrogen bonds       : bond        0.03120 (  944)
  hydrogen bonds       : angle       4.82427 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  221 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 220
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 HIS cc_start: 0.9244 (t-90) cc_final: 0.8931 (t-170)
REVERT: A  397 GLU cc_start: 0.9160 (pm20) cc_final: 0.8631 (tm-30)
REVERT: A  482 MET cc_start: 0.8216 (mmm) cc_final: 0.7407 (mmt)
REVERT: A  587 MET cc_start: 0.9100 (mtm) cc_final: 0.8884 (mtp)
REVERT: A  621 TYR cc_start: 0.9385 (t80) cc_final: 0.9179 (t80)
REVERT: A  624 PHE cc_start: 0.9206 (m-80) cc_final: 0.8985 (m-80)
REVERT: A  761 MET cc_start: 0.8553 (mmp) cc_final: 0.8123 (mmp)
REVERT: A  778 PHE cc_start: 0.7398 (t80) cc_final: 0.7169 (t80)
REVERT: B  176 HIS cc_start: 0.9216 (t-90) cc_final: 0.8912 (t-90)
REVERT: B  482 MET cc_start: 0.7626 (mmm) cc_final: 0.7268 (mmt)
REVERT: B  578 MET cc_start: 0.4324 (mtt) cc_final: 0.4119 (tpp)
REVERT: B  587 MET cc_start: 0.8930 (mtm) cc_final: 0.8646 (mtp)
REVERT: B  624 PHE cc_start: 0.9175 (m-80) cc_final: 0.8956 (m-80)
REVERT: B  642 MET cc_start: 0.8613 (tpt) cc_final: 0.8394 (tpp)
REVERT: B  761 MET cc_start: 0.8636 (mmp) cc_final: 0.8410 (mmp)
REVERT: C  397 GLU cc_start: 0.9158 (pm20) cc_final: 0.8637 (tm-30)
REVERT: C  482 MET cc_start: 0.8316 (mmm) cc_final: 0.7596 (mmt)
REVERT: C  621 TYR cc_start: 0.9445 (t80) cc_final: 0.9218 (t80)
REVERT: C  622 LEU cc_start: 0.9186 (tp) cc_final: 0.8978 (tp)
REVERT: C  761 MET cc_start: 0.8606 (mmp) cc_final: 0.8394 (mmp)
REVERT: D  397 GLU cc_start: 0.9155 (pm20) cc_final: 0.8647 (tm-30)
REVERT: D  587 MET cc_start: 0.9016 (mtm) cc_final: 0.8737 (mtp)
REVERT: D  624 PHE cc_start: 0.9160 (m-80) cc_final: 0.8941 (m-80)
REVERT: D  778 PHE cc_start: 0.7360 (t80) cc_final: 0.7120 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 221
  average time/residue: 0.1219
  time to fit residues: 44.1760
Evaluate side-chains
  184 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 163 optimal weight:    7.9990
   chunk 188 optimal weight:    3.9990
   chunk 186 optimal weight:    5.9990
   chunk 222 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 194 optimal weight:    3.9990
   chunk 210 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 492 GLN
** A 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 274 GLN
B 401 HIS
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 492 GLN
** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 368 ASN
** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 492 GLN
** D 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.082829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.061616 restraints weight = 106679.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.063344 restraints weight = 67048.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.064484 restraints weight = 48810.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.065246 restraints weight = 39146.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.065770 restraints weight = 33593.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.080  20136  Z= 0.260
  Angle     :  0.711   8.896  27288  Z= 0.368
  Chirality :  0.040   0.220   3136
  Planarity :  0.004   0.040   3408
  Dihedral  :  5.598  30.757   2692
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 71.75
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 16.67 %
    Favored  : 83.17 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  3.56 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.21 (0.16), residues: 2424
  helix:  0.10 (0.14), residues: 1392
  sheet: -1.11 (0.57), residues: 76
  loop : -4.06 (0.17), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 316 
 TYR   0.034   0.002   TYR D 303 
 PHE   0.024   0.002   PHE B 172 
 TRP   0.009   0.001   TRP C 785 
 HIS   0.009   0.002   HIS D 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (20136)
  covalent geometry    : angle       0.71144 (27288)
  hydrogen bonds       : bond        0.03713 (  944)
  hydrogen bonds       : angle       5.40092 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  215 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 214
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 HIS cc_start: 0.9236 (t-90) cc_final: 0.9025 (t-90)
REVERT: A  449 MET cc_start: 0.9290 (mtt) cc_final: 0.9043 (mtt)
REVERT: A  587 MET cc_start: 0.9054 (mtm) cc_final: 0.8816 (mtp)
REVERT: A  624 PHE cc_start: 0.9266 (m-80) cc_final: 0.9010 (m-80)
REVERT: A  713 MET cc_start: 0.9167 (tpp) cc_final: 0.8897 (tpp)
REVERT: A  761 MET cc_start: 0.8567 (mmp) cc_final: 0.8250 (mmp)
REVERT: B  176 HIS cc_start: 0.9202 (t-90) cc_final: 0.8877 (t-170)
REVERT: B  482 MET cc_start: 0.7910 (mmm) cc_final: 0.7420 (mmt)
REVERT: B  582 LEU cc_start: 0.8893 (tp) cc_final: 0.8688 (tp)
REVERT: B  587 MET cc_start: 0.8929 (mtm) cc_final: 0.8640 (mtp)
REVERT: B  624 PHE cc_start: 0.9235 (m-80) cc_final: 0.9008 (m-80)
REVERT: B  761 MET cc_start: 0.8686 (mmp) cc_final: 0.8262 (mmp)
REVERT: C  449 MET cc_start: 0.9289 (mtt) cc_final: 0.9068 (mtt)
REVERT: C  587 MET cc_start: 0.9046 (mtm) cc_final: 0.8821 (mtp)
REVERT: C  621 TYR cc_start: 0.9451 (t80) cc_final: 0.9224 (t80)
REVERT: C  622 LEU cc_start: 0.9211 (tp) cc_final: 0.8996 (tp)
REVERT: C  624 PHE cc_start: 0.9253 (m-80) cc_final: 0.8996 (m-80)
REVERT: C  761 MET cc_start: 0.8561 (mmp) cc_final: 0.7992 (mmp)
REVERT: D  368 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8978 (m-40)
REVERT: D  587 MET cc_start: 0.8982 (mtm) cc_final: 0.8696 (mtp)
REVERT: D  624 PHE cc_start: 0.9233 (m-80) cc_final: 0.8952 (m-80)
REVERT: D  761 MET cc_start: 0.8535 (mmp) cc_final: 0.8273 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1235
  time to fit residues: 43.3881
Evaluate side-chains
  177 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    0.4980
   chunk 117 optimal weight:    4.9990
   chunk 96 optimal weight:    0.0050
   chunk 177 optimal weight:   10.0000
   chunk 187 optimal weight:    0.9980
   chunk 219 optimal weight:    5.9990
   chunk 229 optimal weight:    2.9990
   overall best weight:    1.0998

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 492 GLN
B 588 ASN
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 401 HIS
** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 588 ASN
D 401 HIS
** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 588 ASN
** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.096601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.072647 restraints weight = 85203.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.074511 restraints weight = 54848.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.075698 restraints weight = 40727.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.076559 restraints weight = 33124.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.077132 restraints weight = 28733.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  20136  Z= 0.102
  Angle     :  0.522   6.649  27288  Z= 0.276
  Chirality :  0.035   0.132   3136
  Planarity :  0.004   0.049   3408
  Dihedral  :  5.014  31.034   2692
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 59.20
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 12.21 %
    Favored  : 87.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.17), residues: 2424
  helix:  0.77 (0.14), residues: 1388
  sheet: -0.95 (0.58), residues: 76
  loop : -3.83 (0.17), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 320 
 TYR   0.012   0.001   TYR A 628 
 PHE   0.018   0.001   PHE C 624 
 TRP   0.012   0.001   TRP C 586 
 HIS   0.004   0.001   HIS B 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 (20136)
  covalent geometry    : angle       0.52226 (27288)
  hydrogen bonds       : bond        0.02898 (  944)
  hydrogen bonds       : angle       4.71184 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  230 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 GLU cc_start: 0.7748 (tt0) cc_final: 0.7533 (tt0)
REVERT: A  397 GLU cc_start: 0.9142 (pm20) cc_final: 0.8626 (tm-30)
REVERT: A  449 MET cc_start: 0.9373 (mtt) cc_final: 0.9089 (mtt)
REVERT: A  482 MET cc_start: 0.8263 (mmm) cc_final: 0.7601 (mmp)
REVERT: A  621 TYR cc_start: 0.9310 (t80) cc_final: 0.9101 (t80)
REVERT: A  624 PHE cc_start: 0.9138 (m-80) cc_final: 0.8912 (m-80)
REVERT: A  710 LEU cc_start: 0.9857 (mm) cc_final: 0.9620 (mp)
REVERT: A  761 MET cc_start: 0.8575 (mmp) cc_final: 0.8146 (mmp)
REVERT: A  778 PHE cc_start: 0.7421 (t80) cc_final: 0.7198 (t80)
REVERT: B  176 HIS cc_start: 0.9158 (t-90) cc_final: 0.8919 (t70)
REVERT: B  397 GLU cc_start: 0.9171 (pm20) cc_final: 0.8606 (tm-30)
REVERT: B  482 MET cc_start: 0.7861 (mmm) cc_final: 0.7464 (mmt)
REVERT: B  587 MET cc_start: 0.8799 (mtm) cc_final: 0.8534 (mtp)
REVERT: B  624 PHE cc_start: 0.9118 (m-80) cc_final: 0.8898 (m-80)
REVERT: B  761 MET cc_start: 0.8678 (mmp) cc_final: 0.8427 (mmp)
REVERT: B  778 PHE cc_start: 0.7544 (t80) cc_final: 0.7304 (t80)
REVERT: C  176 HIS cc_start: 0.9075 (t-90) cc_final: 0.8707 (t-90)
REVERT: C  397 GLU cc_start: 0.9115 (pm20) cc_final: 0.8654 (tm-30)
REVERT: C  449 MET cc_start: 0.9376 (mtt) cc_final: 0.9106 (mtt)
REVERT: C  482 MET cc_start: 0.8384 (mmm) cc_final: 0.7582 (mmt)
REVERT: C  622 LEU cc_start: 0.9198 (tp) cc_final: 0.8943 (tp)
REVERT: C  624 PHE cc_start: 0.9138 (m-80) cc_final: 0.8902 (m-80)
REVERT: C  778 PHE cc_start: 0.7413 (t80) cc_final: 0.7180 (t80)
REVERT: D  176 HIS cc_start: 0.9097 (t-90) cc_final: 0.8754 (t-90)
REVERT: D  397 GLU cc_start: 0.9094 (pm20) cc_final: 0.8690 (tm-30)
REVERT: D  482 MET cc_start: 0.8179 (mmm) cc_final: 0.7665 (mmt)
REVERT: D  587 MET cc_start: 0.8862 (mtm) cc_final: 0.8647 (mtp)
REVERT: D  624 PHE cc_start: 0.9113 (m-80) cc_final: 0.8856 (m-80)
REVERT: D  778 PHE cc_start: 0.7453 (t80) cc_final: 0.7183 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1206
  time to fit residues: 45.3924
Evaluate side-chains
  185 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 126 optimal weight:    1.9990
   chunk 210 optimal weight:    5.9990
   chunk 20 optimal weight:    0.3980
   chunk 238 optimal weight:    6.9990
   chunk 148 optimal weight:    0.8980
   chunk 121 optimal weight:    9.9990
   chunk 214 optimal weight:    3.9990
   chunk 120 optimal weight:    8.9990
   chunk 128 optimal weight:    0.8980
   chunk 180 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 588 ASN
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 447 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 = 0.3734 r_free = 0.3734 target = 0.096408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.072966 restraints weight = 91461.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.074923 restraints weight = 55701.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.076246 restraints weight = 40423.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.077156 restraints weight = 32517.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.077727 restraints weight = 27987.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  20136  Z= 0.114
  Angle     :  0.507   5.637  27288  Z= 0.268
  Chirality :  0.035   0.134   3136
  Planarity :  0.003   0.039   3408
  Dihedral  :  4.838  29.908   2692
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 60.79
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 12.42 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.17), residues: 2424
  helix:  1.02 (0.14), residues: 1392
  sheet: -0.79 (0.60), residues: 76
  loop : -3.67 (0.18), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 316 
 TYR   0.014   0.001   TYR B 628 
 PHE   0.025   0.001   PHE A 707 
 TRP   0.012   0.001   TRP D 586 
 HIS   0.003   0.001   HIS D 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (20136)
  covalent geometry    : angle       0.50718 (27288)
  hydrogen bonds       : bond        0.02746 (  944)
  hydrogen bonds       : angle       4.55542 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  219 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 HIS cc_start: 0.9230 (t-90) cc_final: 0.8960 (t70)
REVERT: A  225 GLU cc_start: 0.7689 (tt0) cc_final: 0.7464 (tt0)
REVERT: A  397 GLU cc_start: 0.9246 (pm20) cc_final: 0.8699 (tm-30)
REVERT: A  449 MET cc_start: 0.9351 (mtt) cc_final: 0.9105 (mtt)
REVERT: A  482 MET cc_start: 0.8313 (mmm) cc_final: 0.7586 (mmt)
REVERT: A  622 LEU cc_start: 0.9227 (tp) cc_final: 0.9008 (tp)
REVERT: A  761 MET cc_start: 0.8539 (mmp) cc_final: 0.8231 (mmp)
REVERT: A  778 PHE cc_start: 0.7372 (t80) cc_final: 0.7139 (t80)
REVERT: B  397 GLU cc_start: 0.9257 (pm20) cc_final: 0.8675 (tm-30)
REVERT: B  482 MET cc_start: 0.7910 (mmm) cc_final: 0.7500 (mmt)
REVERT: B  587 MET cc_start: 0.9017 (mtm) cc_final: 0.8771 (mtp)
REVERT: B  761 MET cc_start: 0.8584 (mmp) cc_final: 0.8360 (mmp)
REVERT: B  778 PHE cc_start: 0.7488 (t80) cc_final: 0.7266 (t80)
REVERT: C  176 HIS cc_start: 0.9090 (t-90) cc_final: 0.8726 (t-90)
REVERT: C  397 GLU cc_start: 0.9296 (pm20) cc_final: 0.8774 (tm-30)
REVERT: C  449 MET cc_start: 0.9379 (mtt) cc_final: 0.9125 (mtt)
REVERT: C  482 MET cc_start: 0.8388 (mmm) cc_final: 0.7522 (mmt)
REVERT: C  622 LEU cc_start: 0.9163 (tp) cc_final: 0.8854 (tp)
REVERT: C  778 PHE cc_start: 0.7358 (t80) cc_final: 0.7135 (t80)
REVERT: D  176 HIS cc_start: 0.9155 (t-90) cc_final: 0.8792 (t-90)
REVERT: D  397 GLU cc_start: 0.9253 (pm20) cc_final: 0.8802 (tm-30)
REVERT: D  587 MET cc_start: 0.9142 (mtm) cc_final: 0.8892 (mtp)
REVERT: D  778 PHE cc_start: 0.7407 (t80) cc_final: 0.7171 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 219
  average time/residue: 0.1180
  time to fit residues: 42.9510
Evaluate side-chains
  184 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 183 optimal weight:   10.0000
   chunk 238 optimal weight:   10.0000
   chunk 186 optimal weight:    0.8980
   chunk 114 optimal weight:    0.6980
   chunk 193 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 160 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0870
   chunk 229 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0170
   chunk 240 optimal weight:    0.1980
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 712 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.086640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.065172 restraints weight = 98517.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.067335 restraints weight = 55616.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.068751 restraints weight = 37737.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.069687 restraints weight = 28727.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.070313 restraints weight = 23795.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  20136  Z= 0.076
  Angle     :  0.471   6.166  27288  Z= 0.247
  Chirality :  0.035   0.133   3136
  Planarity :  0.003   0.035   3408
  Dihedral  :  4.424  29.697   2692
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 54.90
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 10.11 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.05 %
    Favored  : 99.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.18), residues: 2424
  helix:  1.67 (0.14), residues: 1376
  sheet: -0.59 (0.58), residues: 76
  loop : -3.41 (0.19), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 757 
 TYR   0.013   0.001   TYR B 628 
 PHE   0.020   0.001   PHE D 624 
 TRP   0.014   0.001   TRP C 586 
 HIS   0.003   0.001   HIS C 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00168 (20136)
  covalent geometry    : angle       0.47115 (27288)
  hydrogen bonds       : bond        0.02394 (  944)
  hydrogen bonds       : angle       4.10769 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  245 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 HIS cc_start: 0.9141 (t-90) cc_final: 0.8870 (t70)
REVERT: A  397 GLU cc_start: 0.8997 (pm20) cc_final: 0.8641 (tm-30)
REVERT: A  449 MET cc_start: 0.9425 (mtt) cc_final: 0.9147 (mtt)
REVERT: A  482 MET cc_start: 0.8288 (mmm) cc_final: 0.7293 (mmt)
REVERT: A  556 TYR cc_start: 0.9113 (t80) cc_final: 0.8813 (t80)
REVERT: A  621 TYR cc_start: 0.9271 (t80) cc_final: 0.8896 (t80)
REVERT: A  622 LEU cc_start: 0.9177 (tp) cc_final: 0.8945 (tp)
REVERT: A  710 LEU cc_start: 0.9845 (mm) cc_final: 0.9571 (mp)
REVERT: A  761 MET cc_start: 0.8429 (mmp) cc_final: 0.8208 (mmp)
REVERT: B  397 GLU cc_start: 0.9065 (pm20) cc_final: 0.8673 (tm-30)
REVERT: B  482 MET cc_start: 0.7881 (mmm) cc_final: 0.7337 (mmt)
REVERT: B  621 TYR cc_start: 0.9168 (t80) cc_final: 0.8838 (t80)
REVERT: B  622 LEU cc_start: 0.9200 (tp) cc_final: 0.8989 (tp)
REVERT: B  761 MET cc_start: 0.8467 (mmp) cc_final: 0.8074 (mmp)
REVERT: B  778 PHE cc_start: 0.7458 (t80) cc_final: 0.7252 (t80)
REVERT: C  176 HIS cc_start: 0.9073 (t-90) cc_final: 0.8728 (t-90)
REVERT: C  397 GLU cc_start: 0.9062 (pm20) cc_final: 0.8712 (tm-30)
REVERT: C  449 MET cc_start: 0.9413 (mtt) cc_final: 0.9136 (mtt)
REVERT: C  482 MET cc_start: 0.8449 (mmm) cc_final: 0.7359 (mmt)
REVERT: C  556 TYR cc_start: 0.9112 (t80) cc_final: 0.8794 (t80)
REVERT: C  622 LEU cc_start: 0.9116 (tp) cc_final: 0.8841 (tp)
REVERT: C  713 MET cc_start: 0.8516 (mtt) cc_final: 0.8255 (mtt)
REVERT: D  176 HIS cc_start: 0.9043 (t-90) cc_final: 0.8714 (t-90)
REVERT: D  397 GLU cc_start: 0.9039 (pm20) cc_final: 0.8733 (tm-30)
REVERT: D  482 MET cc_start: 0.8227 (mmm) cc_final: 0.7367 (mmt)
REVERT: D  556 TYR cc_start: 0.9156 (t80) cc_final: 0.8775 (t80)
REVERT: D  778 PHE cc_start: 0.7362 (t80) cc_final: 0.7139 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.1187
  time to fit residues: 48.4519
Evaluate side-chains
  194 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 159 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 169 optimal weight:    5.9990
   chunk 76 optimal weight:    0.8980
   chunk 214 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 175 optimal weight:    0.1980
   chunk 139 optimal weight:    0.0770
   chunk 118 optimal weight:    0.2980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 712 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.086336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.065093 restraints weight = 97943.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.067285 restraints weight = 54395.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.068720 restraints weight = 36487.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.069679 restraints weight = 27645.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.070327 restraints weight = 22753.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  20136  Z= 0.078
  Angle     :  0.468   5.660  27288  Z= 0.247
  Chirality :  0.035   0.170   3136
  Planarity :  0.003   0.037   3408
  Dihedral  :  4.287  31.931   2692
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 55.50
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 10.60 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.05 %
    Favored  : 99.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -0.20 (0.18), residues: 2424
  helix:  1.84 (0.14), residues: 1376
  sheet: -0.44 (0.60), residues: 76
  loop : -3.27 (0.19), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 224 
 TYR   0.013   0.001   TYR B 628 
 PHE   0.027   0.001   PHE B 624 
 TRP   0.012   0.001   TRP C 586 
 HIS   0.002   0.001   HIS B 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00179 (20136)
  covalent geometry    : angle       0.46817 (27288)
  hydrogen bonds       : bond        0.02314 (  944)
  hydrogen bonds       : angle       4.05968 ( 2784)

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

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

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4848 Ramachandran restraints generated.
    2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Residue SER  659 is missing expected H atoms. Skipping.
Evaluate side-chains
  229 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 HIS cc_start: 0.9126 (t-90) cc_final: 0.8863 (t70)
REVERT: A  397 GLU cc_start: 0.8913 (pm20) cc_final: 0.8606 (tm-30)
REVERT: A  449 MET cc_start: 0.9379 (mtt) cc_final: 0.9179 (mtt)
REVERT: A  482 MET cc_start: 0.8203 (mmm) cc_final: 0.7347 (mmt)
REVERT: A  556 TYR cc_start: 0.9088 (t80) cc_final: 0.8797 (t80)
REVERT: A  622 LEU cc_start: 0.9207 (tp) cc_final: 0.8952 (tp)
REVERT: B  397 GLU cc_start: 0.9031 (pm20) cc_final: 0.8684 (tm-30)
REVERT: B  482 MET cc_start: 0.7820 (mmm) cc_final: 0.7415 (mmt)
REVERT: B  622 LEU cc_start: 0.9229 (tp) cc_final: 0.8963 (tp)
REVERT: B  761 MET cc_start: 0.8367 (mmp) cc_final: 0.8032 (mmp)
REVERT: C  176 HIS cc_start: 0.9034 (t-90) cc_final: 0.8696 (t-90)
REVERT: C  397 GLU cc_start: 0.8960 (pm20) cc_final: 0.8674 (tm-30)
REVERT: C  482 MET cc_start: 0.8442 (mmm) cc_final: 0.7413 (mmt)
REVERT: C  556 TYR cc_start: 0.9095 (t80) cc_final: 0.8773 (t80)
REVERT: C  622 LEU cc_start: 0.9137 (tp) cc_final: 0.8830 (tp)
REVERT: D  176 HIS cc_start: 0.9006 (t-90) cc_final: 0.8703 (t-90)
REVERT: D  225 GLU cc_start: 0.8682 (mp0) cc_final: 0.7700 (tt0)
REVERT: D  397 GLU cc_start: 0.8947 (pm20) cc_final: 0.8703 (tm-30)
REVERT: D  482 MET cc_start: 0.8199 (mmm) cc_final: 0.7474 (mmt)
REVERT: D  556 TYR cc_start: 0.9128 (t80) cc_final: 0.8818 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1093
  time to fit residues: 42.0956
Evaluate side-chains
  193 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 244
   random chunks:
   chunk 165 optimal weight:    3.9990
   chunk 215 optimal weight:    0.8980
   chunk 238 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 99 optimal weight:    9.9990
   chunk 112 optimal weight:    0.3980
   chunk 173 optimal weight:    0.0170
   chunk 20 optimal weight:    0.0870
   chunk 46 optimal weight:    3.9990
   chunk 159 optimal weight:    5.9990
   chunk 146 optimal weight:    2.9990
   overall best weight:    0.8798

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

Flipped N/Q/H residues before XYZ refinement:
** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 712 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.086275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.064992 restraints weight = 99735.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.067150 restraints weight = 56484.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.068547 restraints weight = 38454.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.069482 restraints weight = 29416.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.070098 restraints weight = 24385.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  20136  Z= 0.085
  Angle     :  0.464   5.470  27288  Z= 0.244
  Chirality :  0.034   0.115   3136
  Planarity :  0.003   0.034   3408
  Dihedral  :  4.215  28.492   2692
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 56.26
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 10.27 %
    Favored  : 89.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.18), residues: 2424
  helix:  1.87 (0.14), residues: 1400
  sheet: -0.20 (0.62), residues: 76
  loop : -3.20 (0.20), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 224 
 TYR   0.011   0.001   TYR D 628 
 PHE   0.021   0.001   PHE B 695 
 TRP   0.011   0.001   TRP C 586 
 HIS   0.003   0.001   HIS D 265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 (20136)
  covalent geometry    : angle       0.46431 (27288)
  hydrogen bonds       : bond        0.02297 (  944)
  hydrogen bonds       : angle       4.03764 ( 2784)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3268.49 seconds
wall clock time: 58 minutes 10.07 seconds (3490.07 seconds total)