Starting phenix.real_space_refine
on Thu Feb 13 16:41:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ffc_4256/02_2025/6ffc_4256.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ffc_4256/02_2025/6ffc_4256.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ffc_4256/02_2025/6ffc_4256.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ffc_4256/02_2025/6ffc_4256.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ffc_4256/02_2025/6ffc_4256.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ffc_4256/02_2025/6ffc_4256.cif"
  }
  resolution = 3.56
  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=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5836      2.51       5
     N    1472      2.21       5
     O    1608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8974
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4449
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 19, 'TRANS': 552}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4449
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 19, 'TRANS': 552}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 38
          Unusual residues: {'BWQ': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 38
          Unusual residues: {'BWQ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.71, per 1000 atoms: 0.64
  Number of scatterers: 8974
  At special positions: 0
  Unit cell: (96.628, 84.448, 126.672, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1608      8.00
     N    1472      7.00
     C    5836      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 592 " - pdb=" SG  CYS A 608 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 603 " - pdb=" SG  CYS B 603 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 592 " - pdb=" SG  CYS B 608 " distance=2.04

  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: 2.42
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 4 sheets defined
      62.8% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 85 through 94
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 135 through 148
      removed outlier: 3.577A  pdb=" N   LEU A 148 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 169
      removed outlier: 3.663A  pdb=" N   GLY A 169 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 200
      removed outlier: 3.927A  pdb=" N   GLU A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 233
    Processing helix  chain 'A' and resid 246 through 251
    Processing helix  chain 'A' and resid 271 through 281
      removed outlier: 4.415A  pdb=" N   GLY A 275 " --> pdb=" O   GLN A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 329 through 338
      removed outlier: 3.788A  pdb=" N   GLU A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   TYR A 336 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 354
      removed outlier: 3.984A  pdb=" N   LYS A 343 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU A 344 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR A 345 " --> pdb=" O   PHE A 341 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLN A 351 " --> pdb=" O   ALA A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'A' and resid 392 through 413
      removed outlier: 4.519A  pdb=" N   GLN A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ILE A 399 " --> pdb=" O   SER A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 441
    Processing helix  chain 'A' and resid 446 through 451
      removed outlier: 3.863A  pdb=" N   GLU A 451 " --> pdb=" O   LEU A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 461
    Processing helix  chain 'A' and resid 465 through 478
    Processing helix  chain 'A' and resid 479 through 498
      Proline residue:  A 485  - end of helix
      removed outlier: 4.722A  pdb=" N   PHE A 495 " --> pdb=" O   CYS A 491 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   MET A 496 " --> pdb=" O   ILE A 492 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 497 " --> pdb=" O   VAL A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 529
      removed outlier: 3.734A  pdb=" N   PHE A 507 " --> pdb=" O   ALA A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 549
    Processing helix  chain 'A' and resid 557 through 561
      removed outlier: 3.678A  pdb=" N   ILE A 561 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 571
      removed outlier: 3.660A  pdb=" N   GLN A 569 " --> pdb=" O   SER A 566 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   TYR A 570 " --> pdb=" O   TRP A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 586
      removed outlier: 3.570A  pdb=" N   TYR A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 601 through 605
      removed outlier: 3.785A  pdb=" N   ASN A 604 " --> pdb=" O   ASN A 601 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   TYR A 605 " --> pdb=" O   PRO A 602 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 601 through 605'
    Processing helix  chain 'A' and resid 609 through 617
      removed outlier: 3.534A  pdb=" N   TYR A 613 " --> pdb=" O   THR A 609 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS A 616 " --> pdb=" O   GLU A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 650
      removed outlier: 4.974A  pdb=" N   ASN A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   HIS A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 94
    Processing helix  chain 'B' and resid 116 through 121
    Processing helix  chain 'B' and resid 135 through 148
      removed outlier: 3.577A  pdb=" N   LEU B 148 " --> pdb=" O   ALA B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 169
      removed outlier: 3.663A  pdb=" N   GLY B 169 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 200
      removed outlier: 3.928A  pdb=" N   GLU B 199 " --> pdb=" O   SER B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 233
    Processing helix  chain 'B' and resid 246 through 251
    Processing helix  chain 'B' and resid 271 through 281
      removed outlier: 4.414A  pdb=" N   GLY B 275 " --> pdb=" O   GLN B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 300
    Processing helix  chain 'B' and resid 329 through 338
      removed outlier: 3.788A  pdb=" N   GLU B 334 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ILE B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   TYR B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 354
      removed outlier: 3.984A  pdb=" N   LYS B 343 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU B 344 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR B 345 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLN B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 391
    Processing helix  chain 'B' and resid 392 through 413
      removed outlier: 4.520A  pdb=" N   GLN B 398 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ILE B 399 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 441
    Processing helix  chain 'B' and resid 446 through 451
      removed outlier: 3.863A  pdb=" N   GLU B 451 " --> pdb=" O   LEU B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 461
    Processing helix  chain 'B' and resid 465 through 478
    Processing helix  chain 'B' and resid 479 through 498
      Proline residue:  B 485  - end of helix
      removed outlier: 4.721A  pdb=" N   PHE B 495 " --> pdb=" O   CYS B 491 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   MET B 496 " --> pdb=" O   ILE B 492 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU B 497 " --> pdb=" O   VAL B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 529
      removed outlier: 3.734A  pdb=" N   PHE B 507 " --> pdb=" O   ALA B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 549
    Processing helix  chain 'B' and resid 557 through 561
      removed outlier: 3.677A  pdb=" N   ILE B 561 " --> pdb=" O   LEU B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 571
      removed outlier: 3.659A  pdb=" N   GLN B 569 " --> pdb=" O   SER B 566 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   TYR B 570 " --> pdb=" O   TRP B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 586
      removed outlier: 3.570A  pdb=" N   TYR B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 605
      removed outlier: 3.786A  pdb=" N   ASN B 604 " --> pdb=" O   ASN B 601 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR B 605 " --> pdb=" O   PRO B 602 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 601 through 605'
    Processing helix  chain 'B' and resid 609 through 617
      removed outlier: 3.535A  pdb=" N   TYR B 613 " --> pdb=" O   THR B 609 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LYS B 616 " --> pdb=" O   GLU B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 650
      removed outlier: 4.974A  pdb=" N   ASN B 629 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   HIS B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 71
      removed outlier: 7.087A  pdb=" N   LYS A  61 " --> pdb=" O   LYS A  47 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   LYS A  47 " --> pdb=" O   LYS A  61 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE A  63 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   ARG A  45 " --> pdb=" O   ILE A  63 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   SER A  65 " --> pdb=" O   CYS A  43 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   CYS A  43 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   ILE A  67 " --> pdb=" O   ASN A  41 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASP A 105 " --> pdb=" O   HIS A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 124
      removed outlier: 6.442A  pdb=" N   GLY A 122 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   ASP A 210 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   VAL A 124 " --> pdb=" O   ASP A 210 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE A 266 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ALA A 260 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 5.194A  pdb=" N   LEU A 264 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 71
      removed outlier: 7.087A  pdb=" N   LYS B  61 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   LYS B  47 " --> pdb=" O   LYS B  61 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ILE B  63 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   ARG B  45 " --> pdb=" O   ILE B  63 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   SER B  65 " --> pdb=" O   CYS B  43 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   CYS B  43 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   ILE B  67 " --> pdb=" O   ASN B  41 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ASP B 105 " --> pdb=" O   HIS B  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 122 through 124
      removed outlier: 6.441A  pdb=" N   GLY B 122 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   ASP B 210 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   VAL B 124 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE B 266 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ALA B 260 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 5.193A  pdb=" N   LEU B 264 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)

    504 hydrogen bonds defined for protein.
    1476 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.62

  Time building geometry restraints manager: 2.79 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1406
        1.31 -     1.45: 2506
        1.45 -     1.58: 5162
        1.58 -     1.71: 0
        1.71 -     1.84: 94
  Bond restraints: 9168
  Sorted by residual:
  bond pdb=" C36 BWQ B 701 "
       pdb=" O37 BWQ B 701 "
    ideal  model  delta    sigma   weight residual
    1.220  1.393 -0.173 2.00e-02 2.50e+03 7.44e+01
  bond pdb=" C36 BWQ A 701 "
       pdb=" O37 BWQ A 701 "
    ideal  model  delta    sigma   weight residual
    1.220  1.393 -0.173 2.00e-02 2.50e+03 7.44e+01
  bond pdb=" C23 BWQ B 701 "
       pdb=" O24 BWQ B 701 "
    ideal  model  delta    sigma   weight residual
    1.222  1.390 -0.168 2.00e-02 2.50e+03 7.04e+01
  bond pdb=" C23 BWQ A 701 "
       pdb=" O24 BWQ A 701 "
    ideal  model  delta    sigma   weight residual
    1.222  1.389 -0.167 2.00e-02 2.50e+03 7.00e+01
  bond pdb=" C19 BWQ A 701 "
       pdb=" C20 BWQ A 701 "
    ideal  model  delta    sigma   weight residual
    1.431  1.566 -0.135 2.00e-02 2.50e+03 4.54e+01
  ... (remaining 9163 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.89: 12109
        2.89 -     5.78: 242
        5.78 -     8.67: 56
        8.67 -    11.56: 7
       11.56 -    14.45: 2
  Bond angle restraints: 12416
  Sorted by residual:
  angle pdb=" C   SER B 572 "
        pdb=" N   ILE B 573 "
        pdb=" CA  ILE B 573 "
      ideal   model   delta    sigma   weight residual
     120.24  126.49   -6.25 6.30e-01 2.52e+00 9.84e+01
  angle pdb=" C   SER A 572 "
        pdb=" N   ILE A 573 "
        pdb=" CA  ILE A 573 "
      ideal   model   delta    sigma   weight residual
     120.24  126.47   -6.23 6.30e-01 2.52e+00 9.77e+01
  angle pdb=" C   VAL A 445 "
        pdb=" N   GLU A 446 "
        pdb=" CA  GLU A 446 "
      ideal   model   delta    sigma   weight residual
     120.38  127.88   -7.50 1.46e+00 4.69e-01 2.64e+01
  angle pdb=" C   VAL B 445 "
        pdb=" N   GLU B 446 "
        pdb=" CA  GLU B 446 "
      ideal   model   delta    sigma   weight residual
     120.38  127.81   -7.43 1.46e+00 4.69e-01 2.59e+01
  angle pdb=" C06 BWQ A 701 "
        pdb=" N07 BWQ A 701 "
        pdb=" C08 BWQ A 701 "
      ideal   model   delta    sigma   weight residual
     109.00  123.45  -14.45 3.00e+00 1.11e-01 2.32e+01
  ... (remaining 12411 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.16: 5389
       27.16 -    54.33: 72
       54.33 -    81.49: 6
       81.49 -   108.65: 2
      108.65 -   135.82: 6
  Dihedral angle restraints: 5475
    sinusoidal: 2183
      harmonic: 3292
  Sorted by residual:
  dihedral pdb=" CA  ASN A 601 "
           pdb=" C   ASN A 601 "
           pdb=" N   PRO A 602 "
           pdb=" CA  PRO A 602 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.70  -49.30     0      5.00e+00 4.00e-02 9.72e+01
  dihedral pdb=" CA  ASN B 601 "
           pdb=" C   ASN B 601 "
           pdb=" N   PRO B 602 "
           pdb=" CA  PRO B 602 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.74  -49.26     0      5.00e+00 4.00e-02 9.71e+01
  dihedral pdb=" CA  PRO B 602 "
           pdb=" C   PRO B 602 "
           pdb=" N   CYS B 603 "
           pdb=" CA  CYS B 603 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.55   24.45     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 5472 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.075: 1238
       0.075 -    0.150: 164
       0.150 -    0.226: 22
       0.226 -    0.301: 6
       0.301 -    0.376: 2
  Chirality restraints: 1432
  Sorted by residual:
  chirality pdb=" CB  VAL B 173 "
            pdb=" CA  VAL B 173 "
            pdb=" CG1 VAL B 173 "
            pdb=" CG2 VAL B 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.25   -0.38 2.00e-01 2.50e+01 3.54e+00
  chirality pdb=" CB  VAL A 173 "
            pdb=" CA  VAL A 173 "
            pdb=" CG1 VAL A 173 "
            pdb=" CG2 VAL A 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.25   -0.37 2.00e-01 2.50e+01 3.51e+00
  chirality pdb=" C22 BWQ A 701 "
            pdb=" C21 BWQ A 701 "
            pdb=" C23 BWQ A 701 "
            pdb=" N38 BWQ A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.59    0.27 2.00e-01 2.50e+01 1.79e+00
  ... (remaining 1429 not shown)

  Planarity restraints: 1540
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C05 BWQ B 701 "   -0.184 2.00e-02 2.50e+03   2.20e-01 7.24e+02
        pdb=" C22 BWQ B 701 "    0.309 2.00e-02 2.50e+03
        pdb=" C26 BWQ B 701 "   -0.200 2.00e-02 2.50e+03
        pdb=" C36 BWQ B 701 "   -0.026 2.00e-02 2.50e+03
        pdb=" N38 BWQ B 701 "   -0.189 2.00e-02 2.50e+03
        pdb=" O37 BWQ B 701 "    0.290 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C22 BWQ B 701 "    0.032 2.00e-02 2.50e+03   2.14e-01 5.74e+02
        pdb=" C23 BWQ B 701 "    0.063 2.00e-02 2.50e+03
        pdb=" C26 BWQ B 701 "   -0.264 2.00e-02 2.50e+03
        pdb=" N25 BWQ B 701 "    0.349 2.00e-02 2.50e+03
        pdb=" O24 BWQ B 701 "   -0.181 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C05 BWQ A 701 "   -0.046 2.00e-02 2.50e+03   8.93e-02 1.20e+02
        pdb=" C22 BWQ A 701 "   -0.097 2.00e-02 2.50e+03
        pdb=" C26 BWQ A 701 "   -0.010 2.00e-02 2.50e+03
        pdb=" C36 BWQ A 701 "    0.038 2.00e-02 2.50e+03
        pdb=" N38 BWQ A 701 "    0.176 2.00e-02 2.50e+03
        pdb=" O37 BWQ A 701 "   -0.060 2.00e-02 2.50e+03
  ... (remaining 1537 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1823
        2.77 -     3.30: 8297
        3.30 -     3.83: 14537
        3.83 -     4.37: 16989
        4.37 -     4.90: 30383
  Nonbonded interactions: 72029
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 494 "
            pdb=" O   LYS A 500 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OH  TYR B 494 "
            pdb=" O   LYS B 500 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" NH1 ARG B 426 "
            pdb=" OE2 GLU B 585 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" NH1 ARG A 426 "
            pdb=" OE2 GLU A 585 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" OG  SER A 218 "
            pdb=" ND2 ASN B 299 "
     model   vdw
     2.360 3.120
  ... (remaining 72024 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: 0.04
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     23.270
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
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      :  0.009   0.173   9168  Z= 0.614
  Angle     :  1.091  14.446  12416  Z= 0.585
  Chirality :  0.057   0.376   1432
  Planarity :  0.010   0.220   1540
  Dihedral  : 11.436 135.815   3354
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.90 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    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: -3.27 (0.20), residues: 1128
  helix: -1.94 (0.16), residues: 658
  sheet: -0.72 (0.66), residues: 48
  loop : -2.52 (0.25), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP A 624 
 HIS   0.015   0.002   HIS A 583 
 PHE   0.031   0.004   PHE A 489 
 TYR   0.021   0.002   TYR B 342 
 ARG   0.012   0.001   ARG B 383 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 GLU cc_start: 0.7797 (tp30) cc_final: 0.7404 (tm-30)
REVERT: A  385 PHE cc_start: 0.8823 (t80) cc_final: 0.8528 (t80)
REVERT: B  331 LYS cc_start: 0.8247 (tttm) cc_final: 0.7986 (mptt)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.2354
  time to fit residues: 69.5917
Evaluate side-chains
  112 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 86 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    8.9990
   chunk 46 optimal weight:    0.5980
   chunk 89 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 103 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  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 116 ASN
A 425 ASN
A 437 GLN
** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  76 ASN
B 299 ASN
B 425 ASN
B 437 GLN
B 582 GLN
** B 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.153794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.120937 restraints weight = 10620.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.124257 restraints weight = 6407.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.126389 restraints weight = 4674.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9168  Z= 0.204
  Angle     :  0.639   8.542  12416  Z= 0.320
  Chirality :  0.041   0.164   1432
  Planarity :  0.004   0.046   1540
  Dihedral  : 11.621 140.441   1310
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  :  8.52 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    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: -1.30 (0.24), residues: 1128
  helix: -0.13 (0.19), residues: 674
  sheet: -0.37 (0.69), residues: 48
  loop : -2.09 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 379 
 HIS   0.006   0.001   HIS A 583 
 PHE   0.022   0.002   PHE B 293 
 TYR   0.013   0.001   TYR A 342 
 ARG   0.004   0.001   ARG A 246 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 1.631 
Fit side-chains
   revert: symmetry clash
REVERT: A  296 ASP cc_start: 0.7937 (t70) cc_final: 0.7605 (t0)
REVERT: B  331 LYS cc_start: 0.8081 (tttm) cc_final: 0.7876 (mptt)
  outliers start: 21
  outliers final: 13
  residues processed: 146
  average time/residue: 0.1895
  time to fit residues: 40.5789
Evaluate side-chains
  122 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  127 ASP
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 86 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
A 120 ASN
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 583 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.146241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.113015 restraints weight = 11150.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.116156 restraints weight = 6793.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.117985 restraints weight = 4995.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9168  Z= 0.380
  Angle     :  0.690   9.253  12416  Z= 0.344
  Chirality :  0.046   0.190   1432
  Planarity :  0.004   0.039   1540
  Dihedral  : 11.410 139.779   1310
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 11.40 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    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: -0.47 (0.25), residues: 1128
  helix:  0.58 (0.20), residues: 672
  sheet: -0.05 (0.75), residues: 48
  loop : -1.83 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 379 
 HIS   0.007   0.002   HIS A 583 
 PHE   0.017   0.002   PHE B 240 
 TYR   0.015   0.002   TYR A 342 
 ARG   0.003   0.001   ARG A 163 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 THR cc_start: 0.8424 (m) cc_final: 0.7660 (m)
REVERT: A  296 ASP cc_start: 0.8004 (t70) cc_final: 0.7672 (t0)
REVERT: B  331 LYS cc_start: 0.8168 (tttm) cc_final: 0.7910 (mptt)
  outliers start: 27
  outliers final: 22
  residues processed: 144
  average time/residue: 0.1728
  time to fit residues: 37.2143
Evaluate side-chains
  134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  127 ASP
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  514 MET
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  127 ASP
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 THR
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 83 optimal weight:    0.0070
   chunk 81 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 76 optimal weight:    0.6980
   chunk 105 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 112 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 424 GLN
A 583 HIS
A 617 GLN
B 424 GLN
B 617 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.152628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.123424 restraints weight = 10839.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.124507 restraints weight = 7471.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.126019 restraints weight = 6310.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9168  Z= 0.174
  Angle     :  0.572   6.753  12416  Z= 0.287
  Chirality :  0.041   0.186   1432
  Planarity :  0.003   0.036   1540
  Dihedral  : 11.069 142.739   1310
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.76 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    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:  0.24 (0.26), residues: 1128
  helix:  1.26 (0.21), residues: 666
  sheet:  0.28 (0.74), residues: 48
  loop : -1.73 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 379 
 HIS   0.004   0.001   HIS A 583 
 PHE   0.010   0.001   PHE A 591 
 TYR   0.008   0.001   TYR A 463 
 ARG   0.002   0.000   ARG A  96 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.061 
Fit side-chains
   revert: symmetry clash
REVERT: A  296 ASP cc_start: 0.7904 (t70) cc_final: 0.7660 (t0)
REVERT: B   71 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6941 (mmt)
REVERT: B  331 LYS cc_start: 0.8105 (tttm) cc_final: 0.7848 (mptt)
  outliers start: 19
  outliers final: 12
  residues processed: 139
  average time/residue: 0.1722
  time to fit residues: 35.9814
Evaluate side-chains
  124 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  330 GLU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 108 optimal weight:   20.0000
   chunk 98 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 81 optimal weight:    8.9990
   chunk 113 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 28 optimal weight:   10.0000
   chunk 88 optimal weight:    0.4980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 424 GLN
B 120 ASN
B 424 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.150062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.118399 restraints weight = 10956.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.121554 restraints weight = 6558.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.123721 restraints weight = 4750.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9168  Z= 0.241
  Angle     :  0.601   7.816  12416  Z= 0.300
  Chirality :  0.042   0.192   1432
  Planarity :  0.003   0.035   1540
  Dihedral  : 10.796 141.121   1310
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.37 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    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:  0.46 (0.26), residues: 1128
  helix:  1.41 (0.21), residues: 666
  sheet:  0.52 (0.77), residues: 48
  loop : -1.60 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A  40 
 PHE   0.026   0.001   PHE A 293 
 TYR   0.010   0.001   TYR A 463 
 ARG   0.003   0.000   ARG B 246 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 1.008 
Fit side-chains
REVERT: A  296 ASP cc_start: 0.7884 (t70) cc_final: 0.7651 (t0)
REVERT: A  339 SER cc_start: 0.8192 (p) cc_final: 0.7988 (m)
REVERT: B   71 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7219 (mmt)
REVERT: B  331 LYS cc_start: 0.8062 (tttm) cc_final: 0.7849 (mptt)
  outliers start: 21
  outliers final: 15
  residues processed: 133
  average time/residue: 0.1871
  time to fit residues: 36.4162
Evaluate side-chains
  118 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  483 MET
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 96 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0000
   chunk 49 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0570
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.4502

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.153574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.121892 restraints weight = 10829.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.125260 restraints weight = 6486.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.127126 restraints weight = 4710.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
moved from start:          0.3677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9168  Z= 0.161
  Angle     :  0.562   7.173  12416  Z= 0.281
  Chirality :  0.041   0.183   1432
  Planarity :  0.003   0.037   1540
  Dihedral  : 10.532 144.313   1310
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 14.89 %
    Favored  : 83.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    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:  0.75 (0.26), residues: 1128
  helix:  1.63 (0.21), residues: 666
  sheet:  0.55 (0.62), residues: 66
  loop : -1.52 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 267 
 PHE   0.017   0.001   PHE B 578 
 TYR   0.009   0.001   TYR B 463 
 ARG   0.002   0.000   ARG B 246 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.934 
Fit side-chains
REVERT: B   71 MET cc_start: 0.7431 (mtt) cc_final: 0.7157 (mmt)
REVERT: B  331 LYS cc_start: 0.8080 (tttm) cc_final: 0.7870 (mptt)
  outliers start: 16
  outliers final: 13
  residues processed: 124
  average time/residue: 0.1756
  time to fit residues: 32.6602
Evaluate side-chains
  115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  483 MET
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 112 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.155508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.123858 restraints weight = 10923.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.127353 restraints weight = 6350.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.129501 restraints weight = 4525.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.3800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9168  Z= 0.201
  Angle     :  0.594  10.024  12416  Z= 0.291
  Chirality :  0.041   0.161   1432
  Planarity :  0.003   0.036   1540
  Dihedral  : 10.271 145.623   1310
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.89 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.56 %
    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:  0.87 (0.26), residues: 1128
  helix:  1.68 (0.21), residues: 670
  sheet:  0.72 (0.63), residues: 66
  loop : -1.45 (0.33), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A  40 
 PHE   0.015   0.001   PHE B 578 
 TYR   0.010   0.001   TYR A 463 
 ARG   0.002   0.000   ARG B 246 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  585 GLU cc_start: 0.7699 (tp30) cc_final: 0.7423 (tp30)
  outliers start: 20
  outliers final: 15
  residues processed: 122
  average time/residue: 0.1747
  time to fit residues: 32.0723
Evaluate side-chains
  115 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 0 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 102 optimal weight:    3.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A  40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.150953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.118947 restraints weight = 11278.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.122314 restraints weight = 6621.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.124497 restraints weight = 4764.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.3886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9168  Z= 0.331
  Angle     :  0.665  11.387  12416  Z= 0.323
  Chirality :  0.044   0.156   1432
  Planarity :  0.003   0.034   1540
  Dihedral  : 10.312 146.760   1310
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.78 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    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:  0.67 (0.26), residues: 1128
  helix:  1.62 (0.20), residues: 658
  sheet:  0.64 (0.66), residues: 64
  loop : -1.62 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 379 
 HIS   0.004   0.001   HIS A  40 
 PHE   0.022   0.002   PHE A 293 
 TYR   0.014   0.002   TYR B 463 
 ARG   0.002   0.000   ARG B 147 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.963 
Fit side-chains
REVERT: B   71 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7227 (mmt)
REVERT: B  585 GLU cc_start: 0.7707 (tp30) cc_final: 0.7307 (tp30)
  outliers start: 21
  outliers final: 19
  residues processed: 123
  average time/residue: 0.1846
  time to fit residues: 33.4546
Evaluate side-chains
  121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue   71 MET
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 91 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.155261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.126678 restraints weight = 10932.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.128143 restraints weight = 7446.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.128884 restraints weight = 6807.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9168  Z= 0.190
  Angle     :  0.598   9.549  12416  Z= 0.291
  Chirality :  0.041   0.149   1432
  Planarity :  0.003   0.035   1540
  Dihedral  : 10.342 147.667   1310
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.40 %
    Favored  : 82.55 %
  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:  0.91 (0.26), residues: 1128
  helix:  1.82 (0.21), residues: 658
  sheet:  0.82 (0.66), residues: 64
  loop : -1.56 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 379 
 HIS   0.002   0.001   HIS B 267 
 PHE   0.020   0.001   PHE A 293 
 TYR   0.008   0.001   TYR B 463 
 ARG   0.002   0.000   ARG B 246 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A  585 GLU cc_start: 0.7674 (tp30) cc_final: 0.7441 (tp30)
REVERT: B  585 GLU cc_start: 0.7627 (tp30) cc_final: 0.7278 (tp30)
  outliers start: 20
  outliers final: 17
  residues processed: 124
  average time/residue: 0.1826
  time to fit residues: 33.2678
Evaluate side-chains
  119 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue   38 SER
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 28 optimal weight:    7.9990
   chunk 95 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 582 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.154840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.126125 restraints weight = 11010.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.126310 restraints weight = 7796.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.126805 restraints weight = 6803.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.4073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9168  Z= 0.209
  Angle     :  0.614  10.619  12416  Z= 0.300
  Chirality :  0.041   0.148   1432
  Planarity :  0.003   0.035   1540
  Dihedral  : 10.242 145.420   1310
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 14.99 %
    Favored  : 83.06 %
  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:  0.97 (0.26), residues: 1128
  helix:  1.87 (0.20), residues: 658
  sheet:  0.89 (0.66), residues: 64
  loop : -1.54 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 379 
 HIS   0.002   0.001   HIS A  40 
 PHE   0.019   0.001   PHE A 578 
 TYR   0.007   0.001   TYR B 463 
 ARG   0.002   0.000   ARG B 246 

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 1.008 
Fit side-chains
REVERT: B  585 GLU cc_start: 0.7682 (tp30) cc_final: 0.7308 (tp30)
  outliers start: 19
  outliers final: 18
  residues processed: 117
  average time/residue: 0.1838
  time to fit residues: 31.7980
Evaluate side-chains
  116 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLU
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  214 THR
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  486 SER
Chi-restraints excluded: chain A residue  489 PHE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue   38 SER
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  176 SER
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  285 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  486 SER
Chi-restraints excluded: chain B residue  489 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 25 optimal weight:    0.4980
   chunk 77 optimal weight:    0.3980
   chunk 88 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   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 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.156308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.127794 restraints weight = 10978.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.128052 restraints weight = 7729.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.128483 restraints weight = 6809.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9168  Z= 0.189
  Angle     :  0.608  11.205  12416  Z= 0.294
  Chirality :  0.041   0.144   1432
  Planarity :  0.003   0.036   1540
  Dihedral  : 10.231 144.849   1310
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 15.61 %
    Favored  : 82.96 %
  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:  1.08 (0.26), residues: 1128
  helix:  1.96 (0.20), residues: 658
  sheet:  0.89 (0.66), residues: 64
  loop : -1.49 (0.33), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 379 
 HIS   0.002   0.001   HIS B 267 
 PHE   0.043   0.001   PHE B 293 
 TYR   0.007   0.001   TYR B 463 
 ARG   0.002   0.000   ARG B 246 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2468.90 seconds
wall clock time: 45 minutes 32.49 seconds (2732.49 seconds total)