Starting phenix.real_space_refine
on Sun Oct 13 11:12:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/10_2024/8wy4_37915.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/10_2024/8wy4_37915.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/10_2024/8wy4_37915.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/10_2024/8wy4_37915.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/10_2024/8wy4_37915.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wy4_37915/10_2024/8wy4_37915.cif"
  }
  resolution = 2.81
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001 sd=   0.031
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
     P      12      5.49       5
     S      48      5.16       5
     C    9504      2.51       5
     N    2448      2.21       5
     O    2852      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib"
  Total number of atoms: 14864
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3685
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 451, 3685
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 8, 'TRANS': 442}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 9.09, per 1000 atoms: 0.61
  Number of scatterers: 14864
  At special positions: 0
  Unit cell: (115.08, 190.68, 68.04, 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)
     S      48     16.00
     P      12     15.00
     O    2852      8.00
     N    2448      7.00
     C    9504      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.31
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3416

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 16 sheets defined
      42.8% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 47
      removed outlier: 3.960A  pdb=" N   LEU A  39 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 83 through 91
      removed outlier: 3.860A  pdb=" N   LYS A  87 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 308
    Processing helix  chain 'A' and resid 321 through 326
      removed outlier: 3.612A  pdb=" N   LEU A 324 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   TYR A 326 " --> pdb=" O   GLU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 370
      removed outlier: 3.784A  pdb=" N   SER A 368 " --> pdb=" O   LYS A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 395
      removed outlier: 3.558A  pdb=" N   LYS A 384 " --> pdb=" O   GLY A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 402
    Processing helix  chain 'A' and resid 413 through 423
      removed outlier: 3.630A  pdb=" N   THR A 419 " --> pdb=" O   HIS A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 457
      removed outlier: 4.019A  pdb=" N   CYS A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 493
    Processing helix  chain 'A' and resid 493 through 503
      removed outlier: 3.671A  pdb=" N   GLU A 503 " --> pdb=" O   GLU A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 528
      removed outlier: 3.592A  pdb=" N   SER A 518 " --> pdb=" O   ASN A 514 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA A 519 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   GLU A 522 " --> pdb=" O   SER A 518 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   SER A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE A 528 " --> pdb=" O   MET A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 540
      removed outlier: 3.662A  pdb=" N   TYR A 536 " --> pdb=" O   ASP A 532 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER A 540 " --> pdb=" O   TYR A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 551
      removed outlier: 3.632A  pdb=" N   ASN A 544 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN A 551 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 562
      removed outlier: 3.564A  pdb=" N   CYS A 557 " --> pdb=" O   SER A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 574
    Processing helix  chain 'B' and resid 31 through 47
      removed outlier: 3.960A  pdb=" N   LEU B  39 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'B' and resid 83 through 91
      removed outlier: 3.861A  pdb=" N   LYS B  87 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 308
    Processing helix  chain 'B' and resid 321 through 326
      removed outlier: 3.612A  pdb=" N   LEU B 324 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   TYR B 326 " --> pdb=" O   GLU B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 370
      removed outlier: 3.784A  pdb=" N   SER B 368 " --> pdb=" O   LYS B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 395
      removed outlier: 3.558A  pdb=" N   LYS B 384 " --> pdb=" O   GLY B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 402
    Processing helix  chain 'B' and resid 413 through 423
      removed outlier: 3.630A  pdb=" N   THR B 419 " --> pdb=" O   HIS B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 457
      removed outlier: 4.019A  pdb=" N   CYS B 453 " --> pdb=" O   GLY B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 493
    Processing helix  chain 'B' and resid 493 through 503
      removed outlier: 3.671A  pdb=" N   GLU B 503 " --> pdb=" O   GLU B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 528
      removed outlier: 3.592A  pdb=" N   SER B 518 " --> pdb=" O   ASN B 514 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA B 519 " --> pdb=" O   ASP B 515 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   GLU B 522 " --> pdb=" O   SER B 518 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   SER B 523 " --> pdb=" O   ALA B 519 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE B 528 " --> pdb=" O   MET B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 540
      removed outlier: 3.662A  pdb=" N   TYR B 536 " --> pdb=" O   ASP B 532 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   SER B 540 " --> pdb=" O   TYR B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 551
      removed outlier: 3.632A  pdb=" N   ASN B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN B 551 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 562
      removed outlier: 3.564A  pdb=" N   CYS B 557 " --> pdb=" O   SER B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 574
    Processing helix  chain 'D' and resid 31 through 47
      removed outlier: 3.960A  pdb=" N   LEU D  39 " --> pdb=" O   LYS D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 47 through 52
    Processing helix  chain 'D' and resid 83 through 91
      removed outlier: 3.859A  pdb=" N   LYS D  87 " --> pdb=" O   ASP D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 295 through 308
    Processing helix  chain 'D' and resid 321 through 326
      removed outlier: 3.612A  pdb=" N   LEU D 324 " --> pdb=" O   SER D 321 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   TYR D 326 " --> pdb=" O   GLU D 323 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 358 through 370
      removed outlier: 3.784A  pdb=" N   SER D 368 " --> pdb=" O   LYS D 364 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 380 through 395
      removed outlier: 3.558A  pdb=" N   LYS D 384 " --> pdb=" O   GLY D 380 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 397 through 402
    Processing helix  chain 'D' and resid 413 through 423
      removed outlier: 3.629A  pdb=" N   THR D 419 " --> pdb=" O   HIS D 415 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 448 through 457
      removed outlier: 4.020A  pdb=" N   CYS D 453 " --> pdb=" O   GLY D 449 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 476 through 493
    Processing helix  chain 'D' and resid 493 through 503
      removed outlier: 3.671A  pdb=" N   GLU D 503 " --> pdb=" O   GLU D 499 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 512 through 528
      removed outlier: 3.592A  pdb=" N   SER D 518 " --> pdb=" O   ASN D 514 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA D 519 " --> pdb=" O   ASP D 515 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   GLU D 522 " --> pdb=" O   SER D 518 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   SER D 523 " --> pdb=" O   ALA D 519 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE D 528 " --> pdb=" O   MET D 524 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 532 through 540
      removed outlier: 3.662A  pdb=" N   TYR D 536 " --> pdb=" O   ASP D 532 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   SER D 540 " --> pdb=" O   TYR D 536 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 540 through 551
      removed outlier: 3.632A  pdb=" N   ASN D 544 " --> pdb=" O   SER D 540 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN D 551 " --> pdb=" O   GLU D 547 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 553 through 562
      removed outlier: 3.564A  pdb=" N   CYS D 557 " --> pdb=" O   SER D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 567 through 574
    Processing helix  chain 'C' and resid 31 through 47
      removed outlier: 3.959A  pdb=" N   LEU C  39 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 52
    Processing helix  chain 'C' and resid 83 through 91
      removed outlier: 3.860A  pdb=" N   LYS C  87 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 308
    Processing helix  chain 'C' and resid 321 through 326
      removed outlier: 3.612A  pdb=" N   LEU C 324 " --> pdb=" O   SER C 321 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   TYR C 326 " --> pdb=" O   GLU C 323 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 358 through 370
      removed outlier: 3.784A  pdb=" N   SER C 368 " --> pdb=" O   LYS C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 380 through 395
      removed outlier: 3.558A  pdb=" N   LYS C 384 " --> pdb=" O   GLY C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 397 through 402
    Processing helix  chain 'C' and resid 413 through 423
      removed outlier: 3.630A  pdb=" N   THR C 419 " --> pdb=" O   HIS C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 448 through 457
      removed outlier: 4.019A  pdb=" N   CYS C 453 " --> pdb=" O   GLY C 449 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 476 through 493
    Processing helix  chain 'C' and resid 493 through 503
      removed outlier: 3.671A  pdb=" N   GLU C 503 " --> pdb=" O   GLU C 499 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 512 through 528
      removed outlier: 3.592A  pdb=" N   SER C 518 " --> pdb=" O   ASN C 514 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA C 519 " --> pdb=" O   ASP C 515 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   GLU C 522 " --> pdb=" O   SER C 518 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   SER C 523 " --> pdb=" O   ALA C 519 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE C 528 " --> pdb=" O   MET C 524 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 532 through 540
      removed outlier: 3.662A  pdb=" N   TYR C 536 " --> pdb=" O   ASP C 532 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER C 540 " --> pdb=" O   TYR C 536 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 540 through 551
      removed outlier: 3.633A  pdb=" N   ASN C 544 " --> pdb=" O   SER C 540 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ASN C 551 " --> pdb=" O   GLU C 547 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 553 through 562
      removed outlier: 3.565A  pdb=" N   CYS C 557 " --> pdb=" O   SER C 553 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 567 through 574
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20
      removed outlier: 3.533A  pdb=" N   ILE A   8 " --> pdb=" O   VAL A  17 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ASN A   5 " --> pdb=" O   THR A  74 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLY A 127 " --> pdb=" O   TYR A 106 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154
      removed outlier: 6.726A  pdb=" N   VAL A 283 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   PHE A 316 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   TYR A 285 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
      removed outlier: 8.366A  pdb=" N   SER A 318 " --> pdb=" O   TYR A 285 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ILE A 287 " --> pdb=" O   SER A 318 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL A  26 " --> pdb=" O   ILE A 334 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   VAL A 336 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   PHE A  28 " --> pdb=" O   VAL A 336 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 403 through 407
      removed outlier: 6.723A  pdb=" N   ARG A 374 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LEU A 406 " --> pdb=" O   ARG A 374 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   LEU A 376 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437
    Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 20
      removed outlier: 3.533A  pdb=" N   ILE B   8 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ASN B   5 " --> pdb=" O   THR B  74 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLY B 127 " --> pdb=" O   TYR B 106 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 154
      removed outlier: 6.727A  pdb=" N   VAL B 283 " --> pdb=" O   TYR B 314 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   PHE B 316 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   TYR B 285 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   SER B 318 " --> pdb=" O   TYR B 285 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ILE B 287 " --> pdb=" O   SER B 318 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL B  26 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   VAL B 336 " --> pdb=" O   VAL B  26 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   PHE B  28 " --> pdb=" O   VAL B 336 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 403 through 407
      removed outlier: 6.724A  pdb=" N   ARG B 374 " --> pdb=" O   PHE B 404 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LEU B 406 " --> pdb=" O   ARG B 374 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   LEU B 376 " --> pdb=" O   LEU B 406 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 435 through 437
    Processing sheet with id=AA9, first strand: chain 'D' and resid 17 through 20
      removed outlier: 3.532A  pdb=" N   ILE D   8 " --> pdb=" O   VAL D  17 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ASN D   5 " --> pdb=" O   THR D  74 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLY D 127 " --> pdb=" O   TYR D 106 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 149 through 154
      removed outlier: 6.726A  pdb=" N   VAL D 283 " --> pdb=" O   TYR D 314 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   PHE D 316 " --> pdb=" O   VAL D 283 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   TYR D 285 " --> pdb=" O   PHE D 316 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   SER D 318 " --> pdb=" O   TYR D 285 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ILE D 287 " --> pdb=" O   SER D 318 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   VAL D  26 " --> pdb=" O   ILE D 334 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   VAL D 336 " --> pdb=" O   VAL D  26 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   PHE D  28 " --> pdb=" O   VAL D 336 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 403 through 407
      removed outlier: 6.723A  pdb=" N   ARG D 374 " --> pdb=" O   PHE D 404 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LEU D 406 " --> pdb=" O   ARG D 374 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LEU D 376 " --> pdb=" O   LEU D 406 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 435 through 437
    Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 20
      removed outlier: 3.534A  pdb=" N   ILE C   8 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ASN C   5 " --> pdb=" O   THR C  74 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLY C 127 " --> pdb=" O   TYR C 106 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 149 through 154
      removed outlier: 4.299A  pdb=" N   TYR C 314 " --> pdb=" O   VAL C 283 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   VAL C  26 " --> pdb=" O   ILE C 334 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   VAL C 336 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   PHE C  28 " --> pdb=" O   VAL C 336 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 403 through 407
      removed outlier: 6.723A  pdb=" N   ARG C 374 " --> pdb=" O   PHE C 404 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LEU C 406 " --> pdb=" O   ARG C 374 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LEU C 376 " --> pdb=" O   LEU C 406 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 435 through 437

    600 hydrogen bonds defined for protein.
    1716 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: 4.82

  Time building geometry restraints manager: 3.91 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: 4400
        1.34 -     1.46: 2405
        1.46 -     1.57: 8223
        1.57 -     1.69: 20
        1.69 -     1.81: 76
  Bond restraints: 15124
  Sorted by residual:
  bond pdb=" N   GLU B 503 "
       pdb=" CA  GLU B 503 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 6.40e-03 2.44e+04 2.06e+01
  bond pdb=" N   GLU A 503 "
       pdb=" CA  GLU A 503 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 6.40e-03 2.44e+04 2.06e+01
  bond pdb=" N   GLU C 503 "
       pdb=" CA  GLU C 503 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 6.40e-03 2.44e+04 2.06e+01
  bond pdb=" N   GLU D 503 "
       pdb=" CA  GLU D 503 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 6.40e-03 2.44e+04 1.94e+01
  bond pdb=" N   VAL A 497 "
       pdb=" CA  VAL A 497 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.19e-02 7.06e+03 8.75e+00
  ... (remaining 15119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 19535
        2.41 -     4.82: 665
        4.82 -     7.23: 124
        7.23 -     9.64: 12
        9.64 -    12.06: 8
  Bond angle restraints: 20344
  Sorted by residual:
  angle pdb=" C   LYS A 116 "
        pdb=" N   GLU A 117 "
        pdb=" CA  GLU A 117 "
      ideal   model   delta    sigma   weight residual
     121.54  130.91   -9.37 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" C   LYS D 116 "
        pdb=" N   GLU D 117 "
        pdb=" CA  GLU D 117 "
      ideal   model   delta    sigma   weight residual
     121.54  130.87   -9.33 1.91e+00 2.74e-01 2.39e+01
  angle pdb=" C   LYS B 116 "
        pdb=" N   GLU B 117 "
        pdb=" CA  GLU B 117 "
      ideal   model   delta    sigma   weight residual
     121.54  130.87   -9.33 1.91e+00 2.74e-01 2.39e+01
  angle pdb=" C   LYS C 116 "
        pdb=" N   GLU C 117 "
        pdb=" CA  GLU C 117 "
      ideal   model   delta    sigma   weight residual
     121.54  130.85   -9.31 1.91e+00 2.74e-01 2.38e+01
  angle pdb=" N   ASP B  22 "
        pdb=" CA  ASP B  22 "
        pdb=" C   ASP B  22 "
      ideal   model   delta    sigma   weight residual
     108.45  102.61    5.84 1.26e+00 6.30e-01 2.15e+01
  ... (remaining 20339 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.18: 8132
       17.18 -    34.36: 900
       34.36 -    51.55: 200
       51.55 -    68.73: 36
       68.73 -    85.91: 20
  Dihedral angle restraints: 9288
    sinusoidal: 3992
      harmonic: 5296
  Sorted by residual:
  dihedral pdb=" CA  ASP B  76 "
           pdb=" C   ASP B  76 "
           pdb=" N   LEU B  77 "
           pdb=" CA  LEU B  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.37  -26.63     0      5.00e+00 4.00e-02 2.84e+01
  dihedral pdb=" CA  ASP C  76 "
           pdb=" C   ASP C  76 "
           pdb=" N   LEU C  77 "
           pdb=" CA  LEU C  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.39  -26.61     0      5.00e+00 4.00e-02 2.83e+01
  dihedral pdb=" CA  ASP D  76 "
           pdb=" C   ASP D  76 "
           pdb=" N   LEU D  77 "
           pdb=" CA  LEU D  77 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.41  -26.59     0      5.00e+00 4.00e-02 2.83e+01
  ... (remaining 9285 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1641
       0.057 -    0.114: 416
       0.114 -    0.171: 168
       0.171 -    0.228: 23
       0.228 -    0.285: 8
  Chirality restraints: 2256
  Sorted by residual:
  chirality pdb=" CB  ILE C   6 "
            pdb=" CA  ILE C   6 "
            pdb=" CG1 ILE C   6 "
            pdb=" CG2 ILE C   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CB  ILE D   6 "
            pdb=" CA  ILE D   6 "
            pdb=" CG1 ILE D   6 "
            pdb=" CG2 ILE D   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CB  ILE B   6 "
            pdb=" CA  ILE B   6 "
            pdb=" CG1 ILE B   6 "
            pdb=" CG2 ILE B   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 2253 not shown)

  Planarity restraints: 2564
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B   9 "   -0.011 2.00e-02 2.50e+03   2.11e-02 4.47e+00
        pdb=" C   LYS B   9 "    0.037 2.00e-02 2.50e+03
        pdb=" O   LYS B   9 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASN B  10 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C   9 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.30e+00
        pdb=" C   LYS C   9 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   LYS C   9 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ASN C  10 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A   9 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.28e+00
        pdb=" C   LYS A   9 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   LYS A   9 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ASN A  10 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2561 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 4842
        2.87 -     3.38: 12020
        3.38 -     3.89: 24467
        3.89 -     4.39: 27338
        4.39 -     4.90: 47837
  Nonbonded interactions: 116504
  Sorted by model distance:
  nonbonded pdb=" OG  SER D   4 "
            pdb=" OD2 ASP D  76 "
     model   vdw
     2.368 3.040
  nonbonded pdb=" OG  SER B   4 "
            pdb=" OD2 ASP B  76 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OG  SER C   4 "
            pdb=" OD2 ASP C  76 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" OG  SER A   4 "
            pdb=" OD2 ASP A  76 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OG1 THR A 339 "
            pdb=" O   LYS A 341 "
     model   vdw
     2.378 3.040
  ... (remaining 116499 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.520
  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:             0.020
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.090
  Set scattering table:                    0.150
  Process input model:                     34.550
  Find NCS groups from input model:        0.700
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  15124  Z= 0.389
  Angle     :  1.057  12.055  20344  Z= 0.595
  Chirality :  0.061   0.285   2256
  Planarity :  0.006   0.045   2564
  Dihedral  : 15.320  85.911   5872
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.16), residues: 1788
  helix: -3.71 (0.09), residues: 732
  sheet:  0.05 (0.27), residues: 392
  loop : -1.83 (0.20), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.006   TRP D 126 
 HIS   0.006   0.002   HIS A 415 
 PHE   0.031   0.002   PHE A 315 
 TYR   0.022   0.002   TYR A 326 
 ARG   0.016   0.001   ARG A 332 

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

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

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 1.629 
Fit side-chains
REVERT: A  141 ASN cc_start: 0.6872 (m-40) cc_final: 0.6356 (m-40)
REVERT: A  422 ASP cc_start: 0.7603 (m-30) cc_final: 0.7394 (t0)
REVERT: A  474 LYS cc_start: 0.7773 (mttt) cc_final: 0.7516 (mttt)
REVERT: B  141 ASN cc_start: 0.6822 (m-40) cc_final: 0.6322 (m-40)
REVERT: B  422 ASP cc_start: 0.7606 (m-30) cc_final: 0.7400 (t0)
REVERT: D  141 ASN cc_start: 0.6873 (m-40) cc_final: 0.6357 (m-40)
REVERT: D  422 ASP cc_start: 0.7605 (m-30) cc_final: 0.7395 (t0)
REVERT: D  474 LYS cc_start: 0.7753 (mttt) cc_final: 0.7523 (mttt)
REVERT: C  141 ASN cc_start: 0.6874 (m-40) cc_final: 0.6357 (m-40)
REVERT: C  422 ASP cc_start: 0.7604 (m-30) cc_final: 0.7387 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 1.4362
  time to fit residues: 424.5217
Evaluate side-chains
  167 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 151 optimal weight:    0.7980
   chunk 136 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0060
   chunk 92 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0970
   chunk 141 optimal weight:    0.0870
   chunk 54 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 163 optimal weight:    0.9980
   overall best weight:    0.3372

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  15124  Z= 0.159
  Angle     :  0.574   8.467  20344  Z= 0.312
  Chirality :  0.045   0.170   2256
  Planarity :  0.003   0.022   2564
  Dihedral  :  8.599  50.416   2076
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  :  8.39 %
    Favored  : 90.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.18), residues: 1788
  helix: -1.18 (0.16), residues: 700
  sheet:  0.09 (0.28), residues: 408
  loop : -1.32 (0.22), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 126 
 HIS   0.004   0.001   HIS D 415 
 PHE   0.009   0.001   PHE A 316 
 TYR   0.013   0.001   TYR C 314 
 ARG   0.005   0.000   ARG D 332 

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

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

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 175
  time to evaluate  : 1.795 
Fit side-chains
REVERT: A  141 ASN cc_start: 0.6820 (m-40) cc_final: 0.6426 (m-40)
REVERT: A  474 LYS cc_start: 0.7764 (mttt) cc_final: 0.7490 (mtmt)
REVERT: B  141 ASN cc_start: 0.6817 (m-40) cc_final: 0.6432 (m-40)
REVERT: D  141 ASN cc_start: 0.6824 (m-40) cc_final: 0.6432 (m-40)
REVERT: D  474 LYS cc_start: 0.7769 (mttt) cc_final: 0.7497 (mtmt)
REVERT: C  141 ASN cc_start: 0.6820 (m-40) cc_final: 0.6424 (m-40)
  outliers start: 21
  outliers final: 5
  residues processed: 187
  average time/residue: 1.4296
  time to fit residues: 293.5851
Evaluate side-chains
  165 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 160
  time to evaluate  : 1.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain D residue  455 ASN
Chi-restraints excluded: chain C residue  455 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 136 optimal weight:    0.2980
   chunk 111 optimal weight:    0.0370
   chunk 45 optimal weight:    3.9990
   chunk 163 optimal weight:    0.9980
   chunk 176 optimal weight:    4.9990
   chunk 145 optimal weight:    1.9990
   chunk 162 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   chunk 131 optimal weight:    0.0870
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
A 415 HIS
B 415 HIS
D 415 HIS
C 415 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  15124  Z= 0.143
  Angle     :  0.538   9.927  20344  Z= 0.285
  Chirality :  0.044   0.148   2256
  Planarity :  0.003   0.021   2564
  Dihedral  :  7.591  50.408   2076
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  9.96 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.20), residues: 1788
  helix:  0.02 (0.19), residues: 700
  sheet:  0.13 (0.27), residues: 408
  loop : -1.13 (0.23), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP A 126 
 HIS   0.005   0.001   HIS A 415 
 PHE   0.009   0.001   PHE C 315 
 TYR   0.014   0.001   TYR C 314 
 ARG   0.005   0.000   ARG C 332 

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

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

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 188
  time to evaluate  : 1.703 
Fit side-chains
REVERT: A  139 ARG cc_start: 0.6506 (mmm160) cc_final: 0.6053 (mmm160)
REVERT: A  141 ASN cc_start: 0.6744 (m-40) cc_final: 0.6355 (m-40)
REVERT: A  474 LYS cc_start: 0.7704 (mttt) cc_final: 0.7303 (mttt)
REVERT: A  573 VAL cc_start: 0.5323 (t) cc_final: 0.5061 (m)
REVERT: B  139 ARG cc_start: 0.6509 (mmm160) cc_final: 0.6057 (mmm160)
REVERT: B  141 ASN cc_start: 0.6812 (m-40) cc_final: 0.6407 (m-40)
REVERT: B  392 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.7011 (p0)
REVERT: B  478 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7415 (ttpp)
REVERT: D  139 ARG cc_start: 0.6511 (mmm160) cc_final: 0.6050 (mmm160)
REVERT: D  141 ASN cc_start: 0.6756 (m-40) cc_final: 0.6362 (m-40)
REVERT: D  392 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7023 (p0)
REVERT: D  474 LYS cc_start: 0.7706 (mttt) cc_final: 0.7307 (mttt)
REVERT: C  139 ARG cc_start: 0.6502 (mmm160) cc_final: 0.6059 (mmm160)
REVERT: C  141 ASN cc_start: 0.6756 (m-40) cc_final: 0.6362 (m-40)
REVERT: C  573 VAL cc_start: 0.5367 (t) cc_final: 0.5095 (m)
  outliers start: 25
  outliers final: 6
  residues processed: 199
  average time/residue: 1.4948
  time to fit residues: 325.7591
Evaluate side-chains
  174 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 1.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue  392 ASP
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  478 LYS
Chi-restraints excluded: chain D residue  392 ASP
Chi-restraints excluded: chain D residue  455 ASN
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain C residue  455 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 161 optimal weight:    2.9990
   chunk 123 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 109 optimal weight:    0.6980
   chunk 164 optimal weight:    4.9990
   chunk 173 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 155 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 551 ASN
B 551 ASN
D 551 ASN
C 551 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.062  15124  Z= 0.511
  Angle     :  0.876  10.945  20344  Z= 0.456
  Chirality :  0.053   0.176   2256
  Planarity :  0.006   0.091   2564
  Dihedral  :  8.399  58.595   2076
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 13.29 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.19), residues: 1788
  helix:  0.07 (0.19), residues: 688
  sheet: -0.17 (0.26), residues: 396
  loop : -1.38 (0.22), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP B 126 
 HIS   0.005   0.002   HIS C  63 
 PHE   0.022   0.003   PHE B 371 
 TYR   0.031   0.003   TYR C 314 
 ARG   0.013   0.001   ARG C 332 

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

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

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 54
    poor density    : 179
  time to evaluate  : 1.613 
Fit side-chains
REVERT: A   59 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7562 (p0)
REVERT: A  474 LYS cc_start: 0.7607 (mttt) cc_final: 0.7396 (mmpt)
REVERT: B   59 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7134 (p0)
REVERT: D   59 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7606 (p0)
REVERT: D  474 LYS cc_start: 0.7584 (mttt) cc_final: 0.7293 (mttt)
REVERT: C   59 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7693 (p0)
  outliers start: 54
  outliers final: 18
  residues processed: 224
  average time/residue: 1.5201
  time to fit residues: 372.2845
Evaluate side-chains
  173 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 2.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue  116 LYS
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  460 GLU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue  116 LYS
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain D residue  142 ILE
Chi-restraints excluded: chain D residue  324 LEU
Chi-restraints excluded: chain D residue  460 GLU
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  116 LYS
Chi-restraints excluded: chain C residue  142 ILE
Chi-restraints excluded: chain C residue  324 LEU
Chi-restraints excluded: chain C residue  426 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 144 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 129 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 148 optimal weight:    5.9990
   chunk 120 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 156 optimal weight:    0.6980
   chunk 43 optimal weight:    0.4980
   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 414 ASN
A 455 ASN
B 414 ASN
B 455 ASN
D 414 ASN
D 455 ASN
C 414 ASN
C 455 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15124  Z= 0.192
  Angle     :  0.608  10.230  20344  Z= 0.321
  Chirality :  0.046   0.154   2256
  Planarity :  0.003   0.046   2564
  Dihedral  :  7.635  58.483   2076
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.09 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.20), residues: 1788
  helix:  0.82 (0.20), residues: 680
  sheet: -0.12 (0.27), residues: 396
  loop : -1.20 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 126 
 HIS   0.003   0.001   HIS D 415 
 PHE   0.012   0.001   PHE C 315 
 TYR   0.013   0.001   TYR A 314 
 ARG   0.006   0.001   ARG D 459 

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

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

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 1.682 
Fit side-chains
REVERT: A  474 LYS cc_start: 0.7483 (mttt) cc_final: 0.7236 (mttt)
REVERT: B  392 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7210 (p0)
REVERT: B  478 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7587 (ttpp)
REVERT: D  392 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7216 (p0)
REVERT: D  474 LYS cc_start: 0.7465 (mttt) cc_final: 0.7225 (mttt)
  outliers start: 42
  outliers final: 12
  residues processed: 196
  average time/residue: 1.4776
  time to fit residues: 318.2798
Evaluate side-chains
  170 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 155
  time to evaluate  : 1.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LYS
Chi-restraints excluded: chain A residue  523 SER
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue   16 LYS
Chi-restraints excluded: chain B residue  392 ASP
Chi-restraints excluded: chain B residue  478 LYS
Chi-restraints excluded: chain B residue  523 SER
Chi-restraints excluded: chain D residue   16 LYS
Chi-restraints excluded: chain D residue   74 THR
Chi-restraints excluded: chain D residue  392 ASP
Chi-restraints excluded: chain D residue  523 SER
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain C residue   16 LYS
Chi-restraints excluded: chain C residue   74 THR
Chi-restraints excluded: chain C residue  523 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 156 optimal weight:    0.9990
   chunk 34 optimal weight:    0.4980
   chunk 102 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 174 optimal weight:    2.9990
   chunk 144 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9990
   chunk 14 optimal weight:    0.3980
   chunk 57 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
B 414 ASN
C 414 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15124  Z= 0.178
  Angle     :  0.586  10.543  20344  Z= 0.306
  Chirality :  0.045   0.147   2256
  Planarity :  0.003   0.050   2564
  Dihedral  :  7.362  59.295   2076
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.21 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.20), residues: 1788
  helix:  1.24 (0.20), residues: 680
  sheet: -0.14 (0.27), residues: 396
  loop : -1.05 (0.23), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 126 
 HIS   0.004   0.001   HIS A 415 
 PHE   0.012   0.001   PHE C 315 
 TYR   0.014   0.001   TYR C 314 
 ARG   0.005   0.000   ARG A 481 

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

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

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 161
  time to evaluate  : 1.920 
Fit side-chains
REVERT: A  285 TYR cc_start: 0.7941 (m-80) cc_final: 0.7505 (m-80)
REVERT: A  474 LYS cc_start: 0.7438 (mttt) cc_final: 0.7218 (mttt)
REVERT: B  285 TYR cc_start: 0.7938 (m-80) cc_final: 0.7503 (m-80)
REVERT: B  392 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7204 (p0)
REVERT: D  285 TYR cc_start: 0.7938 (m-80) cc_final: 0.7504 (m-80)
REVERT: D  392 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7213 (p0)
REVERT: D  474 LYS cc_start: 0.7415 (mttt) cc_final: 0.7079 (mmtt)
  outliers start: 42
  outliers final: 16
  residues processed: 190
  average time/residue: 1.3841
  time to fit residues: 290.9654
Evaluate side-chains
  176 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 1.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LYS
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  523 SER
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain B residue   16 LYS
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue  392 ASP
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  523 SER
Chi-restraints excluded: chain D residue   16 LYS
Chi-restraints excluded: chain D residue  392 ASP
Chi-restraints excluded: chain D residue  455 ASN
Chi-restraints excluded: chain D residue  523 SER
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain C residue   16 LYS
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  455 ASN
Chi-restraints excluded: chain C residue  523 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 167 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0870
   chunk 99 optimal weight:    0.3980
   chunk 127 optimal weight:    0.9980
   chunk 98 optimal weight:    0.2980
   chunk 146 optimal weight:    3.9990
   chunk 97 optimal weight:    0.8980
   chunk 173 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
D 414 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  15124  Z= 0.163
  Angle     :  0.574  10.804  20344  Z= 0.298
  Chirality :  0.044   0.149   2256
  Planarity :  0.003   0.045   2564
  Dihedral  :  7.230  59.930   2076
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.39 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.21), residues: 1788
  helix:  1.49 (0.20), residues: 692
  sheet: -0.10 (0.27), residues: 396
  loop : -0.85 (0.24), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 126 
 HIS   0.004   0.001   HIS C 415 
 PHE   0.012   0.001   PHE C 315 
 TYR   0.012   0.001   TYR C 314 
 ARG   0.007   0.001   ARG A 481 

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

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

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 42
    poor density    : 170
  time to evaluate  : 1.622 
Fit side-chains
REVERT: A  285 TYR cc_start: 0.7947 (m-80) cc_final: 0.7494 (m-80)
REVERT: A  474 LYS cc_start: 0.7430 (mttt) cc_final: 0.7210 (mttt)
REVERT: B  139 ARG cc_start: 0.6735 (mmm160) cc_final: 0.6185 (mmm160)
REVERT: B  285 TYR cc_start: 0.7945 (m-80) cc_final: 0.7492 (m-80)
REVERT: B  392 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.7146 (p0)
REVERT: D  285 TYR cc_start: 0.7943 (m-80) cc_final: 0.7491 (m-80)
REVERT: D  392 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7113 (p0)
REVERT: D  474 LYS cc_start: 0.7406 (mttt) cc_final: 0.7186 (mttt)
REVERT: C  285 TYR cc_start: 0.7903 (m-80) cc_final: 0.7448 (m-80)
  outliers start: 42
  outliers final: 16
  residues processed: 197
  average time/residue: 1.3613
  time to fit residues: 298.0725
Evaluate side-chains
  168 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 150
  time to evaluate  : 1.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LYS
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  455 ASN
Chi-restraints excluded: chain A residue  523 SER
Chi-restraints excluded: chain B residue   16 LYS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  392 ASP
Chi-restraints excluded: chain B residue  455 ASN
Chi-restraints excluded: chain B residue  523 SER
Chi-restraints excluded: chain D residue   16 LYS
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue  392 ASP
Chi-restraints excluded: chain D residue  455 ASN
Chi-restraints excluded: chain D residue  523 SER
Chi-restraints excluded: chain C residue   16 LYS
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue  455 ASN
Chi-restraints excluded: chain C residue  523 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 118 optimal weight:    0.7980
   chunk 85 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 136 optimal weight:    2.9990
   overall best weight:    1.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  15124  Z= 0.355
  Angle     :  0.741  10.729  20344  Z= 0.384
  Chirality :  0.049   0.182   2256
  Planarity :  0.005   0.082   2564
  Dihedral  :  7.677  59.742   2076
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.60 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.20), residues: 1788
  helix:  1.05 (0.20), residues: 680
  sheet: -0.39 (0.26), residues: 396
  loop : -1.00 (0.24), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 126 
 HIS   0.004   0.001   HIS D 415 
 PHE   0.016   0.002   PHE B 315 
 TYR   0.023   0.002   TYR C 314 
 ARG   0.009   0.001   ARG C 332 

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

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

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 34
    poor density    : 158
  time to evaluate  : 1.756 
Fit side-chains
REVERT: A   59 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7788 (p0)
REVERT: A  152 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7916 (mp)
REVERT: B   59 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7836 (p0)
REVERT: B  152 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7918 (mp)
REVERT: B  392 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7340 (p0)
REVERT: D  152 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7921 (mp)
REVERT: D  392 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7368 (p0)
REVERT: C  152 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7853 (mp)
REVERT: C  334 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8142 (mt)
  outliers start: 34
  outliers final: 6
  residues processed: 183
  average time/residue: 1.5366
  time to fit residues: 308.1854
Evaluate side-chains
  176 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 2.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 ASP
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  523 SER
Chi-restraints excluded: chain B residue   59 ASP
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  392 ASP
Chi-restraints excluded: chain B residue  523 SER
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  392 ASP
Chi-restraints excluded: chain D residue  523 SER
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  334 ILE
Chi-restraints excluded: chain C residue  523 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 157 optimal weight:    2.9990
   chunk 166 optimal weight:    9.9990
   chunk 151 optimal weight:    0.9980
   chunk 161 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 70 optimal weight:    0.9980
   chunk 126 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 146 optimal weight:    6.9990
   chunk 152 optimal weight:    0.7980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN
B 330 ASN
D 330 ASN
C 330 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  15124  Z= 0.231
  Angle     :  0.658  11.449  20344  Z= 0.341
  Chirality :  0.047   0.149   2256
  Planarity :  0.004   0.062   2564
  Dihedral  :  7.249  59.095   2076
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.78 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.20), residues: 1788
  helix:  1.28 (0.20), residues: 680
  sheet: -0.00 (0.26), residues: 380
  loop : -1.11 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 126 
 HIS   0.004   0.001   HIS C 415 
 PHE   0.014   0.001   PHE C 315 
 TYR   0.015   0.001   TYR A 314 
 ARG   0.008   0.001   ARG D 481 

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

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

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3576 Ramachandran restraints generated.
    1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 150
  time to evaluate  : 1.654 
Fit side-chains
REVERT: B  392 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7305 (p0)
REVERT: D  392 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7299 (p0)
  outliers start: 36
  outliers final: 12
  residues processed: 178
  average time/residue: 1.4089
  time to fit residues: 278.6045
Evaluate side-chains
  168 residues out of total 1656 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 2.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LYS
Chi-restraints excluded: chain A residue   74 THR
Chi-restraints excluded: chain A residue  422 ASP
Chi-restraints excluded: chain A residue  523 SER
Chi-restraints excluded: chain B residue   16 LYS
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain B residue  392 ASP
Chi-restraints excluded: chain B residue  523 SER
Chi-restraints excluded: chain D residue   16 LYS
Chi-restraints excluded: chain D residue  392 ASP
Chi-restraints excluded: chain D residue  523 SER
Chi-restraints excluded: chain C residue   16 LYS
Chi-restraints excluded: chain C residue  422 ASP
Chi-restraints excluded: chain C residue  523 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 180
   random chunks:
   chunk 170 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 118 optimal weight:    0.7980
   chunk 179 optimal weight:    0.8980
   chunk 165 optimal weight:    2.9990
   chunk 142 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3187
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_fail.pdb'.
Return code: -15
Dumping stderr: