Starting phenix.real_space_refine
on Wed Mar  4 01:44:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p48_20246/03_2026/6p48_20246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p48_20246/03_2026/6p48_20246.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p48_20246/03_2026/6p48_20246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p48_20246/03_2026/6p48_20246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p48_20246/03_2026/6p48_20246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p48_20246/03_2026/6p48_20246.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     S      68      5.16       5
     C    6592      2.51       5
     N    1586      2.21       5
     O    1688      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 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: 9936
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 604, 4967
          Classifications: {'peptide': 604}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 577}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.21, per 1000 atoms: 0.42
  Number of scatterers: 9936
  At special positions: 0
  Unit cell: (85.779, 112.254, 109.077, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      2     19.99
     S      68     16.00
     O    1688      8.00
     N    1586      7.00
     C    6592      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 338 " - pdb=" SG  CYS A 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 349 " - pdb=" SG  CYS A 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 352 " - pdb=" SG  CYS A 356 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 338 " - pdb=" SG  CYS B 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 349 " - pdb=" SG  CYS B 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 352 " - pdb=" SG  CYS B 356 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 596 " - pdb=" SG  CYS B 601 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 574.2 milliseconds
  

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2296

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 2 sheets defined
      60.1% alpha, 1.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 104
      removed outlier: 3.994A  pdb=" N   LYS A  97 " --> pdb=" O   LYS A  93 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ALA A 100 " --> pdb=" O   ARG A  96 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   TYR A 101 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLU A 102 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   SER A 103 " --> pdb=" O   GLN A  99 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ASN A 104 " --> pdb=" O   ALA A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 220
      removed outlier: 3.787A  pdb=" N   ARG A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL A 213 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   ARG A 219 " --> pdb=" O   PHE A 215 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   VAL A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.626A  pdb=" N   VAL A 237 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A 238 " --> pdb=" O   ASN A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 272
    Processing helix  chain 'A' and resid 285 through 290
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.685A  pdb=" N   TRP A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN A 308 " --> pdb=" O   GLY A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 326
      removed outlier: 3.834A  pdb=" N   VAL A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   CYS A 320 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TYR A 325 " --> pdb=" O   PHE A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 376
      removed outlier: 3.837A  pdb=" N   SER A 376 " --> pdb=" O   CYS A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 408
      removed outlier: 3.856A  pdb=" N   GLU A 395 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 456
      removed outlier: 3.558A  pdb=" N   CYS A 456 " --> pdb=" O   ARG A 452 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 452 through 456'
    Processing helix  chain 'A' and resid 456 through 480
      removed outlier: 3.729A  pdb=" N   PHE A 462 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TRP A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU A 465 " --> pdb=" O   PHE A 461 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ALA A 469 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   SER A 470 " --> pdb=" O   LEU A 466 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE A 475 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR A 477 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 486
      removed outlier: 3.648A  pdb=" N   VAL A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 537
      removed outlier: 3.818A  pdb=" N   PHE A 518 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   THR A 526 " --> pdb=" O   MET A 522 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE A 527 " --> pdb=" O   ILE A 523 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA A 532 " --> pdb=" O   TYR A 528 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 535 " --> pdb=" O   VAL A 531 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 551
      removed outlier: 3.906A  pdb=" N   TYR A 547 " --> pdb=" O   THR A 543 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ASN A 549 " --> pdb=" O   THR A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 573
      removed outlier: 4.589A  pdb=" N   LEU A 557 " --> pdb=" O   MET A 553 " (cutoff:3.500A)
      removed outlier: 4.836A  pdb=" N   SER A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   CYS A 567 " --> pdb=" O   TYR A 563 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   TYR A 569 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   PHE A 572 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 3.583A  pdb=" N   LEU A 588 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 614
      removed outlier: 3.535A  pdb=" N   LEU A 605 " --> pdb=" O   CYS A 601 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN A 608 " --> pdb=" O   GLU A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 620
    Processing helix  chain 'A' and resid 638 through 646
      removed outlier: 3.555A  pdb=" N   GLY A 642 " --> pdb=" O   LYS A 638 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   GLU A 644 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 654
      removed outlier: 3.543A  pdb=" N   ASP A 653 " --> pdb=" O   ARG A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 679
      removed outlier: 3.765A  pdb=" N   GLU A 670 " --> pdb=" O   TYR A 666 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   MET A 671 " --> pdb=" O   GLU A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 709
      removed outlier: 3.597A  pdb=" N   ASN A 696 " --> pdb=" O   ALA A 692 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ILE A 700 " --> pdb=" O   ASN A 696 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ARG A 701 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A 704 " --> pdb=" O   ILE A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 747
      removed outlier: 3.518A  pdb=" N   ALA A 741 " --> pdb=" O   VAL A 737 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 760
      removed outlier: 3.603A  pdb=" N   TYR A 756 " --> pdb=" O   PRO A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 857
      removed outlier: 3.511A  pdb=" N   SER A 848 " --> pdb=" O   HIS A 844 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 104
      removed outlier: 3.995A  pdb=" N   LYS B  97 " --> pdb=" O   LYS B  93 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ALA B 100 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   TYR B 101 " --> pdb=" O   LYS B  97 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLU B 102 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   SER B 103 " --> pdb=" O   GLN B  99 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   ASN B 104 " --> pdb=" O   ALA B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 220
      removed outlier: 3.787A  pdb=" N   ARG B 211 " --> pdb=" O   ALA B 207 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL B 213 " --> pdb=" O   ARG B 209 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ARG B 219 " --> pdb=" O   PHE B 215 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   VAL B 220 " --> pdb=" O   ILE B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 239
      removed outlier: 3.626A  pdb=" N   VAL B 237 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER B 238 " --> pdb=" O   ASN B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 272
    Processing helix  chain 'B' and resid 285 through 290
    Processing helix  chain 'B' and resid 296 through 310
      removed outlier: 3.685A  pdb=" N   TRP B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN B 308 " --> pdb=" O   GLY B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 311 through 326
      removed outlier: 3.834A  pdb=" N   VAL B 316 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY B 317 " --> pdb=" O   ALA B 313 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   CYS B 320 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TYR B 325 " --> pdb=" O   PHE B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 376
      removed outlier: 3.837A  pdb=" N   SER B 376 " --> pdb=" O   CYS B 372 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 408
      removed outlier: 3.856A  pdb=" N   GLU B 395 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 456
      removed outlier: 3.557A  pdb=" N   CYS B 456 " --> pdb=" O   ARG B 452 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 452 through 456'
    Processing helix  chain 'B' and resid 456 through 480
      removed outlier: 3.728A  pdb=" N   PHE B 462 " --> pdb=" O   SER B 458 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TRP B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU B 465 " --> pdb=" O   PHE B 461 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ALA B 469 " --> pdb=" O   LEU B 465 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   SER B 470 " --> pdb=" O   LEU B 466 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE B 474 " --> pdb=" O   SER B 470 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ILE B 475 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   TYR B 477 " --> pdb=" O   GLY B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 486
      removed outlier: 3.648A  pdb=" N   VAL B 484 " --> pdb=" O   SER B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 537
      removed outlier: 3.818A  pdb=" N   PHE B 518 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   THR B 526 " --> pdb=" O   MET B 522 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   ILE B 527 " --> pdb=" O   ILE B 523 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA B 532 " --> pdb=" O   TYR B 528 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE B 535 " --> pdb=" O   VAL B 531 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR B 536 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 551
      removed outlier: 3.906A  pdb=" N   TYR B 547 " --> pdb=" O   THR B 543 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ASN B 549 " --> pdb=" O   THR B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 551 through 573
      removed outlier: 4.590A  pdb=" N   LEU B 557 " --> pdb=" O   MET B 553 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   SER B 566 " --> pdb=" O   ASN B 562 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS B 567 " --> pdb=" O   TYR B 563 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TYR B 569 " --> pdb=" O   SER B 565 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   PHE B 572 " --> pdb=" O   PHE B 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.583A  pdb=" N   LEU B 588 " --> pdb=" O   VAL B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 614
      removed outlier: 3.535A  pdb=" N   LEU B 605 " --> pdb=" O   CYS B 601 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN B 608 " --> pdb=" O   GLU B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 615 through 620
    Processing helix  chain 'B' and resid 638 through 646
      removed outlier: 3.555A  pdb=" N   GLY B 642 " --> pdb=" O   LYS B 638 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 644 " --> pdb=" O   VAL B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 649 through 654
      removed outlier: 3.542A  pdb=" N   ASP B 653 " --> pdb=" O   ARG B 649 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 664 through 679
      removed outlier: 3.765A  pdb=" N   GLU B 670 " --> pdb=" O   TYR B 666 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   MET B 671 " --> pdb=" O   GLU B 667 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 709
      removed outlier: 3.597A  pdb=" N   ASN B 696 " --> pdb=" O   ALA B 692 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   ILE B 700 " --> pdb=" O   ASN B 696 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ARG B 701 " --> pdb=" O   ILE B 697 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ALA B 704 " --> pdb=" O   ILE B 700 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 725 through 747
      removed outlier: 3.518A  pdb=" N   ALA B 741 " --> pdb=" O   VAL B 737 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 760
      removed outlier: 3.602A  pdb=" N   TYR B 756 " --> pdb=" O   PRO B 752 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 825 through 857
      removed outlier: 3.510A  pdb=" N   SER B 848 " --> pdb=" O   HIS B 844 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 76
      removed outlier: 3.534A  pdb=" N   ALA A 244 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 73 through 76
      removed outlier: 3.534A  pdb=" N   ALA B 244 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)

    418 hydrogen bonds defined for protein.
    1248 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: 1.20

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2934
        1.34 -     1.47: 2832
        1.47 -     1.59: 4334
        1.59 -     1.72: 0
        1.72 -     1.84: 106
  Bond restraints: 10206
  Sorted by residual:
  bond pdb=" CA  ALA A 571 "
       pdb=" C   ALA A 571 "
    ideal  model  delta    sigma   weight residual
    1.524  1.577 -0.054 1.16e-02 7.43e+03 2.15e+01
  bond pdb=" CA  ALA B 571 "
       pdb=" C   ALA B 571 "
    ideal  model  delta    sigma   weight residual
    1.524  1.577 -0.053 1.16e-02 7.43e+03 2.12e+01
  bond pdb=" CA  PHE A 812 "
       pdb=" CB  PHE A 812 "
    ideal  model  delta    sigma   weight residual
    1.526  1.464  0.063 1.53e-02 4.27e+03 1.68e+01
  bond pdb=" CA  PHE B 812 "
       pdb=" CB  PHE B 812 "
    ideal  model  delta    sigma   weight residual
    1.526  1.464  0.063 1.53e-02 4.27e+03 1.68e+01
  bond pdb=" N   PRO B 648 "
       pdb=" CD  PRO B 648 "
    ideal  model  delta    sigma   weight residual
    1.473  1.527 -0.054 1.40e-02 5.10e+03 1.51e+01
  ... (remaining 10201 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.04: 13089
        3.04 -     6.08: 614
        6.08 -     9.12: 103
        9.12 -    12.16: 26
       12.16 -    15.19: 12
  Bond angle restraints: 13844
  Sorted by residual:
  angle pdb=" N   ARG A 478 "
        pdb=" CA  ARG A 478 "
        pdb=" C   ARG A 478 "
      ideal   model   delta    sigma   weight residual
     113.88  100.31   13.57 1.23e+00 6.61e-01 1.22e+02
  angle pdb=" N   ARG B 478 "
        pdb=" CA  ARG B 478 "
        pdb=" C   ARG B 478 "
      ideal   model   delta    sigma   weight residual
     113.88  100.33   13.55 1.23e+00 6.61e-01 1.21e+02
  angle pdb=" N   ALA A 274 "
        pdb=" CA  ALA A 274 "
        pdb=" C   ALA A 274 "
      ideal   model   delta    sigma   weight residual
     112.68  126.47  -13.79 1.33e+00 5.65e-01 1.07e+02
  angle pdb=" N   ALA B 274 "
        pdb=" CA  ALA B 274 "
        pdb=" C   ALA B 274 "
      ideal   model   delta    sigma   weight residual
     112.68  126.44  -13.76 1.33e+00 5.65e-01 1.07e+02
  angle pdb=" N   LEU B 664 "
        pdb=" CA  LEU B 664 "
        pdb=" C   LEU B 664 "
      ideal   model   delta    sigma   weight residual
     112.59  100.75   11.84 1.22e+00 6.72e-01 9.42e+01
  ... (remaining 13839 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.48: 5026
       16.48 -    32.95: 728
       32.95 -    49.43: 164
       49.43 -    65.90: 50
       65.90 -    82.38: 8
  Dihedral angle restraints: 5976
    sinusoidal: 2410
      harmonic: 3566
  Sorted by residual:
  dihedral pdb=" CA  ILE A 786 "
           pdb=" C   ILE A 786 "
           pdb=" N   THR A 787 "
           pdb=" CA  THR A 787 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.07   27.93     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  ILE B 786 "
           pdb=" C   ILE B 786 "
           pdb=" N   THR B 787 "
           pdb=" CA  THR B 787 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.09   27.91     0      5.00e+00 4.00e-02 3.12e+01
  dihedral pdb=" CA  ASP A 375 "
           pdb=" C   ASP A 375 "
           pdb=" N   SER A 376 "
           pdb=" CA  SER A 376 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.43  -27.57     0      5.00e+00 4.00e-02 3.04e+01
  ... (remaining 5973 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1318
       0.105 -    0.210: 162
       0.210 -    0.315: 30
       0.315 -    0.421: 24
       0.421 -    0.526: 4
  Chirality restraints: 1538
  Sorted by residual:
  chirality pdb=" CA  ALA B 274 "
            pdb=" N   ALA B 274 "
            pdb=" C   ALA B 274 "
            pdb=" CB  ALA B 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.96    0.53 2.00e-01 2.50e+01 6.91e+00
  chirality pdb=" CA  ALA A 274 "
            pdb=" N   ALA A 274 "
            pdb=" C   ALA A 274 "
            pdb=" CB  ALA A 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.96    0.53 2.00e-01 2.50e+01 6.90e+00
  chirality pdb=" CA  PRO A 340 "
            pdb=" N   PRO A 340 "
            pdb=" C   PRO A 340 "
            pdb=" CB  PRO A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.24    0.48 2.00e-01 2.50e+01 5.67e+00
  ... (remaining 1535 not shown)

  Planarity restraints: 1686
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 541 "    0.021 2.00e-02 2.50e+03   4.27e-02 1.83e+01
        pdb=" C   PRO A 541 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   PRO A 541 "    0.030 2.00e-02 2.50e+03
        pdb=" N   ARG A 542 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 541 "    0.021 2.00e-02 2.50e+03   4.27e-02 1.82e+01
        pdb=" C   PRO B 541 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   PRO B 541 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ARG B 542 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 647 "   -0.069 5.00e-02 4.00e+02   1.03e-01 1.70e+01
        pdb=" N   PRO A 648 "    0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO A 648 "   -0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 648 "   -0.055 5.00e-02 4.00e+02
  ... (remaining 1683 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 156
        2.59 -     3.17: 8430
        3.17 -     3.75: 16032
        3.75 -     4.32: 22064
        4.32 -     4.90: 34337
  Nonbonded interactions: 81019
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU A 627 "
            pdb=" CD  PRO A 628 "
     model   vdw
     2.014 3.860
  nonbonded pdb=" CD1 LEU B 627 "
            pdb=" CD  PRO B 628 "
     model   vdw
     2.014 3.860
  nonbonded pdb=" CB  HIS B 275 "
            pdb=" CD  PRO B 276 "
     model   vdw
     2.171 3.840
  nonbonded pdb=" CB  HIS A 275 "
            pdb=" CD  PRO A 276 "
     model   vdw
     2.171 3.840
  nonbonded pdb=" O   HIS B 275 "
            pdb=" O   SER B 278 "
     model   vdw
     2.200 3.040
  ... (remaining 81014 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.910
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.260
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6472
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      :  0.011   0.100  10214  Z= 0.493
  Angle     :  1.557  15.195  13860  Z= 0.962
  Chirality :  0.091   0.526   1538
  Planarity :  0.011   0.103   1686
  Dihedral  : 16.573  82.380   3656
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 22.33
  Ramachandran Plot:
    Outliers :  0.86 %
    Allowed  :  6.51 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 14.68 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.05 (0.17), residues: 1168
  helix: -4.12 (0.11), residues: 696
  sheet: -3.70 (1.03), residues: 18
  loop : -3.59 (0.25), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 209 
 TYR   0.037   0.004   TYR A 809 
 PHE   0.028   0.004   PHE B 760 
 TRP   0.039   0.004   TRP B 463 
 HIS   0.008   0.002   HIS A 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.01065 (10206)
  covalent geometry    : angle       1.55569 (13844)
  SS BOND              : bond        0.00385 (    8)
  SS BOND              : angle       2.24811 (   16)
  hydrogen bonds       : bond        0.30919 (  418)
  hydrogen bonds       : angle      12.12342 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 200
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 HIS cc_start: 0.5230 (OUTLIER) cc_final: 0.4889 (t70)
REVERT: A  298 ILE cc_start: 0.8456 (tp) cc_final: 0.8144 (tt)
REVERT: A  396 PHE cc_start: 0.6698 (t80) cc_final: 0.6483 (t80)
REVERT: A  403 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7517 (tm-30)
REVERT: A  588 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5903 (mm)
REVERT: A  590 LYS cc_start: 0.4367 (OUTLIER) cc_final: 0.3613 (mppt)
REVERT: A  671 MET cc_start: 0.8217 (mmm) cc_final: 0.7676 (mmm)
REVERT: A  742 MET cc_start: 0.7116 (mmt) cc_final: 0.6810 (tpp)
REVERT: A  826 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4985 (pt)
REVERT: A  853 ILE cc_start: 0.8491 (mm) cc_final: 0.8249 (mt)
REVERT: B  275 HIS cc_start: 0.5514 (OUTLIER) cc_final: 0.4570 (t70)
REVERT: B  298 ILE cc_start: 0.8361 (tp) cc_final: 0.8095 (tt)
REVERT: B  403 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7410 (tm-30)
REVERT: B  590 LYS cc_start: 0.4209 (OUTLIER) cc_final: 0.3396 (mmtt)
REVERT: B  649 ARG cc_start: 0.6494 (pmt170) cc_final: 0.6141 (ptt-90)
REVERT: B  750 MET cc_start: 0.5962 (mmp) cc_final: 0.5059 (ttm)
  outliers start: 38
  outliers final: 9
  residues processed: 233
  average time/residue: 0.1031
  time to fit residues: 33.1158
Evaluate side-chains
  153 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  586 TYR
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  682 VAL
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  826 ILE
Chi-restraints excluded: chain A residue  862 LYS
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  586 TYR
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  682 VAL
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  862 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 117 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
A 129 HIS
A 275 HIS
A 283 GLN
A 620 ASN
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 710 GLN
A 726 GLN
A 740 ASN
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 ASN
B  99 GLN
B 129 HIS
B 275 HIS
B 620 ASN
** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 710 GLN
B 726 GLN
B 740 ASN
B 825 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4803 r_free = 0.4803 target = 0.231310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4506 r_free = 0.4506 target = 0.200330 restraints weight = 14793.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.4463 rms_B_bonded: 3.45
r_work: 0.4247 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6576
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10214  Z= 0.188
  Angle     :  0.821  13.592  13860  Z= 0.438
  Chirality :  0.047   0.188   1538
  Planarity :  0.007   0.063   1686
  Dihedral  :  8.740  59.908   1361
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  7.02 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 15.80 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -4.62 (0.20), residues: 1168
  helix: -2.87 (0.15), residues: 708
  sheet: -3.53 (0.76), residues: 26
  loop : -3.12 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 542 
 TYR   0.034   0.002   TYR A 323 
 PHE   0.020   0.002   PHE A 556 
 TRP   0.025   0.003   TRP B 629 
 HIS   0.005   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (10206)
  covalent geometry    : angle       0.81958 (13844)
  SS BOND              : bond        0.00286 (    8)
  SS BOND              : angle       1.42307 (   16)
  hydrogen bonds       : bond        0.07237 (  418)
  hydrogen bonds       : angle       7.33786 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 187
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 HIS cc_start: 0.5951 (OUTLIER) cc_final: 0.4789 (t-90)
REVERT: A  298 ILE cc_start: 0.8187 (tp) cc_final: 0.7861 (tt)
REVERT: A  403 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7672 (tm-30)
REVERT: A  588 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5825 (mm)
REVERT: A  742 MET cc_start: 0.7842 (mmt) cc_final: 0.7597 (tpp)
REVERT: A  842 MET cc_start: 0.6704 (mmt) cc_final: 0.6490 (mmt)
REVERT: B  101 TYR cc_start: 0.6376 (t80) cc_final: 0.6126 (t80)
REVERT: B  270 TYR cc_start: 0.5309 (t80) cc_final: 0.4882 (t80)
REVERT: B  275 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.5038 (t-90)
REVERT: B  298 ILE cc_start: 0.8215 (tp) cc_final: 0.7915 (tt)
REVERT: B  396 PHE cc_start: 0.6858 (t80) cc_final: 0.6606 (t80)
REVERT: B  403 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7580 (tm-30)
REVERT: B  461 PHE cc_start: 0.8341 (m-10) cc_final: 0.8083 (m-80)
REVERT: B  590 LYS cc_start: 0.4771 (OUTLIER) cc_final: 0.3688 (mmtt)
REVERT: B  649 ARG cc_start: 0.6823 (pmt170) cc_final: 0.6529 (ptt-90)
  outliers start: 49
  outliers final: 21
  residues processed: 226
  average time/residue: 0.0865
  time to fit residues: 28.4637
Evaluate side-chains
  172 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 147
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  587 LEU
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  516 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  711 PHE
Chi-restraints excluded: chain B residue  730 GLN
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  818 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 81 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 GLN
B 696 ASN
** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 830 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.230461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.198433 restraints weight = 14841.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.4460 rms_B_bonded: 3.35
r_work: 0.4229 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10214  Z= 0.190
  Angle     :  0.745   9.942  13860  Z= 0.399
  Chirality :  0.047   0.202   1538
  Planarity :  0.006   0.070   1686
  Dihedral  :  7.595  58.347   1340
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 15.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.30 %
    Favored  : 91.70 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 19.80 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.87 (0.22), residues: 1168
  helix: -2.25 (0.17), residues: 710
  sheet: -3.52 (0.75), residues: 26
  loop : -2.83 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 478 
 TYR   0.039   0.002   TYR B 323 
 PHE   0.030   0.002   PHE A 461 
 TRP   0.035   0.002   TRP B 629 
 HIS   0.007   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (10206)
  covalent geometry    : angle       0.74388 (13844)
  SS BOND              : bond        0.00292 (    8)
  SS BOND              : angle       1.44070 (   16)
  hydrogen bonds       : bond        0.06386 (  418)
  hydrogen bonds       : angle       6.85093 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 162
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 HIS cc_start: 0.6213 (OUTLIER) cc_final: 0.4976 (t-90)
REVERT: A  298 ILE cc_start: 0.8072 (tp) cc_final: 0.7743 (tt)
REVERT: A  403 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7561 (tm-30)
REVERT: A  586 TYR cc_start: 0.5282 (OUTLIER) cc_final: 0.3903 (t80)
REVERT: A  588 LEU cc_start: 0.5871 (OUTLIER) cc_final: 0.5642 (mm)
REVERT: A  590 LYS cc_start: 0.5186 (OUTLIER) cc_final: 0.3775 (mppt)
REVERT: A  595 GLU cc_start: 0.6739 (mp0) cc_final: 0.6285 (mp0)
REVERT: B  101 TYR cc_start: 0.6183 (t80) cc_final: 0.5864 (t80)
REVERT: B  275 HIS cc_start: 0.6685 (OUTLIER) cc_final: 0.4968 (t-90)
REVERT: B  298 ILE cc_start: 0.8112 (tp) cc_final: 0.7782 (tt)
REVERT: B  403 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7564 (tm-30)
REVERT: B  586 TYR cc_start: 0.5037 (OUTLIER) cc_final: 0.4053 (t80)
REVERT: B  590 LYS cc_start: 0.4841 (OUTLIER) cc_final: 0.3317 (mppt)
REVERT: B  649 ARG cc_start: 0.6800 (pmt170) cc_final: 0.6459 (ptt-90)
REVERT: B  666 TYR cc_start: 0.8725 (m-10) cc_final: 0.8515 (m-80)
REVERT: B  730 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7573 (mt0)
  outliers start: 43
  outliers final: 27
  residues processed: 195
  average time/residue: 0.0731
  time to fit residues: 21.5990
Evaluate side-chains
  176 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  586 TYR
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  586 TYR
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  698 LEU
Chi-restraints excluded: chain B residue  711 PHE
Chi-restraints excluded: chain B residue  729 MET
Chi-restraints excluded: chain B residue  730 GLN
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  818 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 109 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 GLN
** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.232462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.201103 restraints weight = 15034.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.4485 rms_B_bonded: 3.46
r_work: 0.4259 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6598
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10214  Z= 0.165
  Angle     :  0.683   8.679  13860  Z= 0.366
  Chirality :  0.045   0.166   1538
  Planarity :  0.006   0.072   1686
  Dihedral  :  7.240  59.175   1340
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 22.30 %
    Favored  : 72.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.32 (0.23), residues: 1168
  helix: -1.82 (0.18), residues: 718
  sheet: -3.52 (0.75), residues: 26
  loop : -2.57 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 753 
 TYR   0.047   0.001   TYR B 323 
 PHE   0.029   0.002   PHE B 461 
 TRP   0.036   0.002   TRP A 629 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10206)
  covalent geometry    : angle       0.68241 (13844)
  SS BOND              : bond        0.00240 (    8)
  SS BOND              : angle       1.29998 (   16)
  hydrogen bonds       : bond        0.05744 (  418)
  hydrogen bonds       : angle       6.49965 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 170
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 HIS cc_start: 0.6506 (OUTLIER) cc_final: 0.5116 (t-90)
REVERT: A  298 ILE cc_start: 0.8062 (tp) cc_final: 0.7745 (tt)
REVERT: A  377 PHE cc_start: 0.3551 (OUTLIER) cc_final: 0.3226 (t80)
REVERT: A  403 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: A  586 TYR cc_start: 0.5141 (OUTLIER) cc_final: 0.3860 (t80)
REVERT: A  588 LEU cc_start: 0.5812 (OUTLIER) cc_final: 0.5568 (mm)
REVERT: A  595 GLU cc_start: 0.6787 (mp0) cc_final: 0.6346 (mp0)
REVERT: B  101 TYR cc_start: 0.6204 (t80) cc_final: 0.5871 (t80)
REVERT: B  275 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.5253 (t-90)
REVERT: B  298 ILE cc_start: 0.8118 (tp) cc_final: 0.7768 (tt)
REVERT: B  394 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7561 (mm)
REVERT: B  403 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7480 (tm-30)
REVERT: B  404 LEU cc_start: 0.7623 (mt) cc_final: 0.7406 (mt)
REVERT: B  586 TYR cc_start: 0.5019 (OUTLIER) cc_final: 0.4018 (t80)
REVERT: B  730 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7625 (mt0)
REVERT: B  857 ILE cc_start: 0.7112 (tp) cc_final: 0.6904 (tt)
  outliers start: 58
  outliers final: 33
  residues processed: 216
  average time/residue: 0.0747
  time to fit residues: 24.5451
Evaluate side-chains
  185 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  586 TYR
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  601 CYS
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  586 TYR
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  698 LEU
Chi-restraints excluded: chain B residue  711 PHE
Chi-restraints excluded: chain B residue  729 MET
Chi-restraints excluded: chain B residue  730 GLN
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  818 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9980
   chunk 94 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 101 optimal weight:    0.8980
   chunk 60 optimal weight:    8.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 GLN
** B 818 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 = 0.4818 r_free = 0.4818 target = 0.232693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.201569 restraints weight = 15092.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.4491 rms_B_bonded: 3.48
r_work: 0.4267 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6587
moved from start:          0.3850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10214  Z= 0.156
  Angle     :  0.687  13.466  13860  Z= 0.360
  Chirality :  0.045   0.163   1538
  Planarity :  0.006   0.069   1686
  Dihedral  :  6.916  56.304   1332
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 23.61 %
    Favored  : 71.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -2.97 (0.23), residues: 1168
  helix: -1.49 (0.18), residues: 714
  sheet: -3.50 (0.74), residues: 26
  loop : -2.52 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 701 
 TYR   0.039   0.001   TYR B 323 
 PHE   0.020   0.002   PHE B 461 
 TRP   0.034   0.002   TRP B 629 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10206)
  covalent geometry    : angle       0.68627 (13844)
  SS BOND              : bond        0.00172 (    8)
  SS BOND              : angle       1.28792 (   16)
  hydrogen bonds       : bond        0.05516 (  418)
  hydrogen bonds       : angle       6.31959 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 167
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 HIS cc_start: 0.6460 (OUTLIER) cc_final: 0.5233 (t-90)
REVERT: A  298 ILE cc_start: 0.8025 (tp) cc_final: 0.7702 (tt)
REVERT: A  377 PHE cc_start: 0.3554 (OUTLIER) cc_final: 0.3301 (t80)
REVERT: A  394 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7702 (mm)
REVERT: A  403 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7518 (tm-30)
REVERT: A  586 TYR cc_start: 0.5166 (OUTLIER) cc_final: 0.3932 (t80)
REVERT: A  595 GLU cc_start: 0.6707 (mp0) cc_final: 0.6261 (mp0)
REVERT: B  101 TYR cc_start: 0.6257 (t80) cc_final: 0.5916 (t80)
REVERT: B  138 TYR cc_start: 0.5181 (m-80) cc_final: 0.4920 (m-80)
REVERT: B  275 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.5408 (t-90)
REVERT: B  298 ILE cc_start: 0.8071 (tp) cc_final: 0.7701 (tt)
REVERT: B  394 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7535 (mm)
REVERT: B  403 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7466 (tm-30)
REVERT: B  586 TYR cc_start: 0.4927 (OUTLIER) cc_final: 0.3903 (t80)
REVERT: B  730 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7553 (mt0)
REVERT: B  742 MET cc_start: 0.7979 (tpp) cc_final: 0.7526 (mmt)
REVERT: B  768 HIS cc_start: 0.4641 (t-90) cc_final: 0.4300 (t-90)
REVERT: B  857 ILE cc_start: 0.7077 (tp) cc_final: 0.6856 (tt)
  outliers start: 52
  outliers final: 34
  residues processed: 207
  average time/residue: 0.0751
  time to fit residues: 23.8154
Evaluate side-chains
  192 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 150
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  586 TYR
Chi-restraints excluded: chain A residue  601 CYS
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  586 TYR
Chi-restraints excluded: chain B residue  601 CYS
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  698 LEU
Chi-restraints excluded: chain B residue  711 PHE
Chi-restraints excluded: chain B residue  729 MET
Chi-restraints excluded: chain B residue  730 GLN
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  818 HIS
Chi-restraints excluded: chain B residue  831 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 52 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 71 optimal weight:    0.6980
   chunk 107 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 56 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 283 GLN
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 GLN
** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.228523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.196645 restraints weight = 15096.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.4445 rms_B_bonded: 3.36
r_work: 0.4219 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.4219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6670
moved from start:          0.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10214  Z= 0.211
  Angle     :  0.720  12.056  13860  Z= 0.380
  Chirality :  0.046   0.179   1538
  Planarity :  0.006   0.072   1686
  Dihedral  :  6.916  54.892   1330
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 24.16 %
    Favored  : 70.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -2.92 (0.24), residues: 1168
  helix: -1.38 (0.18), residues: 706
  sheet: -3.73 (0.71), residues: 26
  loop : -2.61 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 753 
 TYR   0.037   0.002   TYR B 323 
 PHE   0.027   0.002   PHE B 382 
 TRP   0.035   0.002   TRP B 629 
 HIS   0.004   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (10206)
  covalent geometry    : angle       0.71914 (13844)
  SS BOND              : bond        0.00587 (    8)
  SS BOND              : angle       1.38947 (   16)
  hydrogen bonds       : bond        0.05989 (  418)
  hydrogen bonds       : angle       6.38762 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 150
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  275 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.5409 (t-90)
REVERT: A  298 ILE cc_start: 0.8206 (tp) cc_final: 0.7905 (tt)
REVERT: A  377 PHE cc_start: 0.3960 (OUTLIER) cc_final: 0.3667 (t80)
REVERT: A  394 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7631 (mm)
REVERT: A  403 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7510 (tm-30)
REVERT: A  586 TYR cc_start: 0.5194 (OUTLIER) cc_final: 0.3990 (t80)
REVERT: A  595 GLU cc_start: 0.6799 (mp0) cc_final: 0.6363 (mp0)
REVERT: B  101 TYR cc_start: 0.6496 (t80) cc_final: 0.6047 (t80)
REVERT: B  138 TYR cc_start: 0.5404 (m-80) cc_final: 0.4943 (m-80)
REVERT: B  275 HIS cc_start: 0.6799 (OUTLIER) cc_final: 0.6111 (t-90)
REVERT: B  298 ILE cc_start: 0.8167 (tp) cc_final: 0.7857 (tt)
REVERT: B  394 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7636 (mm)
REVERT: B  403 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7474 (tm-30)
REVERT: B  553 MET cc_start: 0.7908 (tpp) cc_final: 0.7615 (tpp)
REVERT: B  565 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7268 (t)
REVERT: B  586 TYR cc_start: 0.5058 (OUTLIER) cc_final: 0.3893 (t80)
REVERT: B  742 MET cc_start: 0.8128 (tpp) cc_final: 0.7685 (mmt)
  outliers start: 62
  outliers final: 39
  residues processed: 199
  average time/residue: 0.0740
  time to fit residues: 22.5364
Evaluate side-chains
  191 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 144
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  586 TYR
Chi-restraints excluded: chain A residue  601 CYS
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  565 SER
Chi-restraints excluded: chain B residue  586 TYR
Chi-restraints excluded: chain B residue  601 CYS
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  698 LEU
Chi-restraints excluded: chain B residue  729 MET
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  818 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 60 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 26 optimal weight:   20.0000
   chunk 70 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0470
   chunk 71 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 GLN
** B 818 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 = 0.4831 r_free = 0.4831 target = 0.233669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.204266 restraints weight = 15078.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.4534 rms_B_bonded: 3.18
r_work: 0.4297 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10214  Z= 0.151
  Angle     :  0.676  10.640  13860  Z= 0.353
  Chirality :  0.044   0.165   1538
  Planarity :  0.006   0.069   1686
  Dihedral  :  6.658  53.206   1330
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 25.28 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -2.62 (0.24), residues: 1168
  helix: -1.18 (0.18), residues: 710
  sheet: -3.53 (0.75), residues: 26
  loop : -2.41 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 701 
 TYR   0.034   0.001   TYR B 323 
 PHE   0.021   0.002   PHE B 382 
 TRP   0.040   0.002   TRP B 629 
 HIS   0.004   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10206)
  covalent geometry    : angle       0.67467 (13844)
  SS BOND              : bond        0.00393 (    8)
  SS BOND              : angle       1.41891 (   16)
  hydrogen bonds       : bond        0.05314 (  418)
  hydrogen bonds       : angle       6.16925 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 161
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A  275 HIS cc_start: 0.6458 (OUTLIER) cc_final: 0.5667 (t-90)
REVERT: A  298 ILE cc_start: 0.8105 (tp) cc_final: 0.7806 (tt)
REVERT: A  377 PHE cc_start: 0.3435 (OUTLIER) cc_final: 0.3180 (t80)
REVERT: A  586 TYR cc_start: 0.5076 (OUTLIER) cc_final: 0.3933 (t80)
REVERT: A  595 GLU cc_start: 0.6619 (mp0) cc_final: 0.6292 (mp0)
REVERT: A  730 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7585 (mp10)
REVERT: B  101 TYR cc_start: 0.6439 (t80) cc_final: 0.5980 (t80)
REVERT: B  138 TYR cc_start: 0.5261 (m-80) cc_final: 0.4818 (m-80)
REVERT: B  275 HIS cc_start: 0.6667 (OUTLIER) cc_final: 0.5967 (t-90)
REVERT: B  298 ILE cc_start: 0.8050 (tp) cc_final: 0.7727 (tt)
REVERT: B  586 TYR cc_start: 0.4898 (OUTLIER) cc_final: 0.3852 (t80)
REVERT: B  629 TRP cc_start: 0.5754 (m-90) cc_final: 0.5424 (m-90)
REVERT: B  742 MET cc_start: 0.8199 (tpp) cc_final: 0.7808 (mmt)
  outliers start: 52
  outliers final: 39
  residues processed: 200
  average time/residue: 0.0795
  time to fit residues: 24.0298
Evaluate side-chains
  189 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 145
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  373 ILE
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  586 TYR
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  586 TYR
Chi-restraints excluded: chain B residue  601 CYS
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  698 LEU
Chi-restraints excluded: chain B residue  711 PHE
Chi-restraints excluded: chain B residue  729 MET
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  818 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0980
   chunk 46 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 730 GLN
** B 818 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 = 0.4822 r_free = 0.4822 target = 0.232674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.202748 restraints weight = 15107.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.4533 rms_B_bonded: 3.24
r_work: 0.4303 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10214  Z= 0.168
  Angle     :  0.700  10.776  13860  Z= 0.365
  Chirality :  0.045   0.163   1538
  Planarity :  0.006   0.069   1686
  Dihedral  :  6.600  51.980   1330
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.33 %
    Favored  : 90.67 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 25.84 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -2.50 (0.24), residues: 1168
  helix: -1.06 (0.19), residues: 698
  sheet: -3.50 (0.76), residues: 26
  loop : -2.40 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 701 
 TYR   0.034   0.002   TYR B 528 
 PHE   0.027   0.002   PHE B 382 
 TRP   0.035   0.002   TRP A 629 
 HIS   0.004   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (10206)
  covalent geometry    : angle       0.69835 (13844)
  SS BOND              : bond        0.00323 (    8)
  SS BOND              : angle       1.40489 (   16)
  hydrogen bonds       : bond        0.05430 (  418)
  hydrogen bonds       : angle       6.13718 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 152
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6206 (ptt180)
REVERT: A  275 HIS cc_start: 0.6443 (OUTLIER) cc_final: 0.5786 (t-90)
REVERT: A  298 ILE cc_start: 0.8066 (tp) cc_final: 0.7741 (tt)
REVERT: A  377 PHE cc_start: 0.3809 (OUTLIER) cc_final: 0.3484 (t80)
REVERT: A  586 TYR cc_start: 0.5114 (OUTLIER) cc_final: 0.4063 (t80)
REVERT: A  595 GLU cc_start: 0.6632 (mp0) cc_final: 0.6252 (mp0)
REVERT: A  730 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7545 (mp10)
REVERT: A  825 ASN cc_start: 0.6646 (OUTLIER) cc_final: 0.6242 (m-40)
REVERT: B  101 TYR cc_start: 0.6412 (t80) cc_final: 0.5991 (t80)
REVERT: B  138 TYR cc_start: 0.5291 (m-80) cc_final: 0.4835 (m-80)
REVERT: B  275 HIS cc_start: 0.6572 (OUTLIER) cc_final: 0.5985 (t-90)
REVERT: B  298 ILE cc_start: 0.8008 (tp) cc_final: 0.7697 (tt)
REVERT: B  399 ARG cc_start: 0.7543 (ttt180) cc_final: 0.6874 (tmt170)
REVERT: B  565 SER cc_start: 0.7312 (OUTLIER) cc_final: 0.7108 (t)
REVERT: B  586 TYR cc_start: 0.4931 (OUTLIER) cc_final: 0.3859 (t80)
REVERT: B  742 MET cc_start: 0.8179 (tpp) cc_final: 0.7792 (mmt)
  outliers start: 54
  outliers final: 40
  residues processed: 194
  average time/residue: 0.0847
  time to fit residues: 24.3506
Evaluate side-chains
  189 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 141
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  586 TYR
Chi-restraints excluded: chain A residue  601 CYS
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  698 LEU
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  565 SER
Chi-restraints excluded: chain B residue  586 TYR
Chi-restraints excluded: chain B residue  601 CYS
Chi-restraints excluded: chain B residue  612 ILE
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  698 LEU
Chi-restraints excluded: chain B residue  711 PHE
Chi-restraints excluded: chain B residue  729 MET
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  818 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 71 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 83 optimal weight:    7.9990
   chunk 105 optimal weight:    0.7980
   chunk 60 optimal weight:    8.9990
   chunk 4 optimal weight:    7.9990
   chunk 98 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 GLN
B 283 GLN
** B 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.230668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.199984 restraints weight = 15223.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.4494 rms_B_bonded: 3.19
r_work: 0.4267 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.4267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10214  Z= 0.202
  Angle     :  0.743  14.286  13860  Z= 0.387
  Chirality :  0.046   0.161   1538
  Planarity :  0.006   0.071   1686
  Dihedral  :  6.720  52.855   1330
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 15.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.27 %
    Favored  : 89.73 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 27.14 %
    Favored  : 68.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -2.62 (0.24), residues: 1168
  helix: -1.08 (0.19), residues: 694
  sheet: -3.62 (0.74), residues: 26
  loop : -2.57 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 753 
 TYR   0.035   0.002   TYR B 528 
 PHE   0.031   0.002   PHE B 382 
 TRP   0.051   0.003   TRP B 629 
 HIS   0.004   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (10206)
  covalent geometry    : angle       0.74235 (13844)
  SS BOND              : bond        0.00357 (    8)
  SS BOND              : angle       1.42272 (   16)
  hydrogen bonds       : bond        0.05806 (  418)
  hydrogen bonds       : angle       6.24789 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 150
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  101 TYR cc_start: 0.6792 (m-80) cc_final: 0.6485 (m-80)
REVERT: A  235 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6267 (ptt180)
REVERT: A  275 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.5970 (t-90)
REVERT: A  298 ILE cc_start: 0.8124 (tp) cc_final: 0.7789 (tt)
REVERT: A  586 TYR cc_start: 0.5227 (OUTLIER) cc_final: 0.4036 (t80)
REVERT: A  595 GLU cc_start: 0.6808 (mp0) cc_final: 0.6414 (mp0)
REVERT: A  730 GLN cc_start: 0.7801 (mm-40) cc_final: 0.7569 (mp10)
REVERT: A  825 ASN cc_start: 0.6590 (OUTLIER) cc_final: 0.6235 (m-40)
REVERT: B  101 TYR cc_start: 0.6514 (t80) cc_final: 0.6031 (t80)
REVERT: B  138 TYR cc_start: 0.5447 (m-80) cc_final: 0.5006 (m-80)
REVERT: B  275 HIS cc_start: 0.6675 (OUTLIER) cc_final: 0.6131 (t-90)
REVERT: B  298 ILE cc_start: 0.8140 (tp) cc_final: 0.7822 (tt)
REVERT: B  573 PHE cc_start: 0.7814 (t80) cc_final: 0.7558 (t80)
REVERT: B  586 TYR cc_start: 0.4870 (OUTLIER) cc_final: 0.3968 (t80)
REVERT: B  629 TRP cc_start: 0.5775 (m-90) cc_final: 0.5447 (m-90)
REVERT: B  742 MET cc_start: 0.8196 (tpp) cc_final: 0.7793 (mmt)
  outliers start: 51
  outliers final: 35
  residues processed: 188
  average time/residue: 0.0782
  time to fit residues: 22.2880
Evaluate side-chains
  185 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 144
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  586 TYR
Chi-restraints excluded: chain A residue  601 CYS
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  586 TYR
Chi-restraints excluded: chain B residue  601 CYS
Chi-restraints excluded: chain B residue  612 ILE
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  729 MET
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  818 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 100 optimal weight:    9.9990
   chunk 46 optimal weight:    0.4980
   chunk 91 optimal weight:    0.9990
   chunk 110 optimal weight:    0.4980
   chunk 112 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 818 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 = 0.4837 r_free = 0.4837 target = 0.234720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.204526 restraints weight = 15098.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.4538 rms_B_bonded: 3.29
r_work: 0.4317 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.4792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10214  Z= 0.153
  Angle     :  0.735  17.083  13860  Z= 0.373
  Chirality :  0.045   0.217   1538
  Planarity :  0.006   0.068   1686
  Dihedral  :  6.518  51.459   1330
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 28.35 %
    Favored  : 67.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -2.42 (0.24), residues: 1168
  helix: -0.95 (0.19), residues: 700
  sheet: -3.42 (0.78), residues: 26
  loop : -2.45 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 271 
 TYR   0.039   0.002   TYR A 528 
 PHE   0.024   0.002   PHE B 382 
 TRP   0.050   0.003   TRP A 629 
 HIS   0.004   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (10206)
  covalent geometry    : angle       0.73374 (13844)
  SS BOND              : bond        0.00322 (    8)
  SS BOND              : angle       1.41027 (   16)
  hydrogen bonds       : bond        0.05242 (  418)
  hydrogen bonds       : angle       6.05092 ( 1248)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 158
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 TYR cc_start: 0.6679 (m-80) cc_final: 0.6378 (m-80)
REVERT: A  235 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6117 (ptt90)
REVERT: A  275 HIS cc_start: 0.6293 (OUTLIER) cc_final: 0.6019 (t-90)
REVERT: A  298 ILE cc_start: 0.8018 (tp) cc_final: 0.7688 (tt)
REVERT: A  524 LEU cc_start: 0.8019 (tt) cc_final: 0.7782 (pp)
REVERT: A  586 TYR cc_start: 0.5105 (OUTLIER) cc_final: 0.4025 (t80)
REVERT: A  595 GLU cc_start: 0.6691 (mp0) cc_final: 0.6354 (mp0)
REVERT: A  629 TRP cc_start: 0.5785 (m-90) cc_final: 0.5419 (m-90)
REVERT: A  730 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7502 (mp10)
REVERT: A  825 ASN cc_start: 0.6523 (OUTLIER) cc_final: 0.6205 (m-40)
REVERT: B  101 TYR cc_start: 0.6573 (t80) cc_final: 0.6135 (t80)
REVERT: B  138 TYR cc_start: 0.5422 (m-80) cc_final: 0.5048 (m-80)
REVERT: B  275 HIS cc_start: 0.6501 (OUTLIER) cc_final: 0.6149 (t-90)
REVERT: B  298 ILE cc_start: 0.8045 (tp) cc_final: 0.7734 (tt)
REVERT: B  478 ARG cc_start: 0.4942 (mpt-90) cc_final: 0.4089 (mmp80)
REVERT: B  573 PHE cc_start: 0.7774 (t80) cc_final: 0.7526 (t80)
REVERT: B  586 TYR cc_start: 0.4700 (OUTLIER) cc_final: 0.3877 (t80)
REVERT: B  629 TRP cc_start: 0.5918 (m-90) cc_final: 0.5595 (m-90)
REVERT: B  714 MET cc_start: 0.6089 (mmt) cc_final: 0.5739 (mmm)
REVERT: B  742 MET cc_start: 0.8148 (tpp) cc_final: 0.7764 (mmt)
  outliers start: 43
  outliers final: 34
  residues processed: 190
  average time/residue: 0.0752
  time to fit residues: 21.3331
Evaluate side-chains
  191 residues out of total 1078 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 151
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  235 ARG
Chi-restraints excluded: chain A residue  275 HIS
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  379 THR
Chi-restraints excluded: chain A residue  381 ILE
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  504 THR
Chi-restraints excluded: chain A residue  586 TYR
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain A residue  825 ASN
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  204 PHE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  275 HIS
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  373 ILE
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  381 ILE
Chi-restraints excluded: chain B residue  504 THR
Chi-restraints excluded: chain B residue  586 TYR
Chi-restraints excluded: chain B residue  601 CYS
Chi-restraints excluded: chain B residue  612 ILE
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  729 MET
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  818 HIS
Chi-restraints excluded: chain B residue  857 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 12 optimal weight:    0.2980
   chunk 46 optimal weight:    0.6980
   chunk 83 optimal weight:    8.9990
   chunk 110 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 559 GLN
** A 818 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  99 GLN
B 559 GLN
** B 818 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 = 0.4825 r_free = 0.4825 target = 0.233702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.204277 restraints weight = 15184.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.4542 rms_B_bonded: 3.46
r_work: 0.4305 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start:          0.4932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10214  Z= 0.156
  Angle     :  0.718  15.553  13860  Z= 0.368
  Chirality :  0.045   0.224   1538
  Planarity :  0.006   0.067   1686
  Dihedral  :  6.416  49.828   1330
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.99 %
    Favored  : 91.01 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 28.62 %
    Favored  : 67.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    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: -2.29 (0.24), residues: 1168
  helix: -0.81 (0.19), residues: 694
  sheet: -3.38 (0.78), residues: 26
  loop : -2.46 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 271 
 TYR   0.031   0.001   TYR B 323 
 PHE   0.030   0.002   PHE B 556 
 TRP   0.046   0.003   TRP A 629 
 HIS   0.004   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10206)
  covalent geometry    : angle       0.71735 (13844)
  SS BOND              : bond        0.00307 (    8)
  SS BOND              : angle       1.35920 (   16)
  hydrogen bonds       : bond        0.05250 (  418)
  hydrogen bonds       : angle       5.96347 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2622.73 seconds
wall clock time: 45 minutes 30.69 seconds (2730.69 seconds total)