Starting phenix.real_space_refine
on Sat Aug 23 05:24:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8opq_17085/08_2025/8opq_17085.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8opq_17085/08_2025/8opq_17085.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8opq_17085/08_2025/8opq_17085.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8opq_17085/08_2025/8opq_17085.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8opq_17085/08_2025/8opq_17085.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8opq_17085/08_2025/8opq_17085.map"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
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
     S      38      5.16       5
     Cl      2      4.86       5
     C    6532      2.51       5
     N    1668      2.21       5
     O    1766      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10006
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 648, 5002
          Classifications: {'peptide': 648}
          Link IDs: {'PTRANS': 28, 'TRANS': 619}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 648, 5002
          Classifications: {'peptide': 648}
          Link IDs: {'PTRANS': 28, 'TRANS': 619}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.98, per 1000 atoms: 0.20
  Number of scatterers: 10006
  At special positions: 0
  Unit cell: (100.905, 121.737, 106.764, 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)
     Cl      2     17.00
     S      38     16.00
     O    1766      8.00
     N    1668      7.00
     C    6532      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 239.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2412

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 4 sheets defined
      72.7% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 46
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 76 through 81
    Processing helix  chain 'A' and resid 85 through 116
      removed outlier: 5.327A  pdb=" N   LEU A  91 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   GLY A  92 " --> pdb=" O   ASP A  88 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
      removed outlier: 3.715A  pdb=" N   LEU A 109 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 126
      removed outlier: 4.212A  pdb=" N   GLY A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   LEU A 123 " --> pdb=" O   PRO A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 137
      removed outlier: 4.103A  pdb=" N   PHE A 131 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A 135 " --> pdb=" O   PHE A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 162
    Processing helix  chain 'A' and resid 170 through 201
    Processing helix  chain 'A' and resid 205 through 210
    Processing helix  chain 'A' and resid 211 through 236
      removed outlier: 4.024A  pdb=" N   LYS A 232 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   TYR A 233 " --> pdb=" O   SER A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 258
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 263 through 287
    Processing helix  chain 'A' and resid 296 through 313
    Processing helix  chain 'A' and resid 337 through 339
      No H-bonds generated for 'chain 'A' and resid 337 through 339'
    Processing helix  chain 'A' and resid 340 through 371
      removed outlier: 4.798A  pdb=" N   GLY A 346 " --> pdb=" O   SER A 342 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   SER A 347 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   THR A 350 " --> pdb=" O   GLY A 346 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE A 351 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 393
    Processing helix  chain 'A' and resid 401 through 412
      removed outlier: 3.598A  pdb=" N   GLY A 412 " --> pdb=" O   GLN A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 432
      removed outlier: 4.436A  pdb=" N   GLY A 419 " --> pdb=" O   SER A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 438
      removed outlier: 3.691A  pdb=" N   PHE A 437 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 452
      removed outlier: 4.058A  pdb=" N   LEU A 445 " --> pdb=" O   PRO A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 470
      removed outlier: 4.428A  pdb=" N   LEU A 460 " --> pdb=" O   MET A 456 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   SER A 461 " --> pdb=" O   LEU A 457 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ASP A 462 " --> pdb=" O   ARG A 458 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   TRP A 467 " --> pdb=" O   MET A 463 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   LYS A 468 " --> pdb=" O   ARG A 464 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 487
    Processing helix  chain 'A' and resid 487 through 509
      removed outlier: 3.946A  pdb=" N   LEU A 491 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL A 494 " --> pdb=" O   ASP A 490 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR A 508 " --> pdb=" O   VAL A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 565
    Processing helix  chain 'A' and resid 568 through 594
    Processing helix  chain 'A' and resid 656 through 661
    Processing helix  chain 'A' and resid 681 through 698
    Processing helix  chain 'A' and resid 708 through 718
      removed outlier: 3.619A  pdb=" N   VAL A 712 " --> pdb=" O   HIS A 708 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER A 713 " --> pdb=" O   SER A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 728
      No H-bonds generated for 'chain 'A' and resid 726 through 728'
    Processing helix  chain 'A' and resid 733 through 744
    Processing helix  chain 'B' and resid 37 through 46
    Processing helix  chain 'B' and resid 63 through 75
    Processing helix  chain 'B' and resid 76 through 81
    Processing helix  chain 'B' and resid 85 through 116
      removed outlier: 5.328A  pdb=" N   LEU B  91 " --> pdb=" O   ARG B  87 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   GLY B  92 " --> pdb=" O   ASP B  88 " (cutoff:3.500A)
      Proline residue:  B 106  - end of helix
      removed outlier: 3.716A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 126
      removed outlier: 4.212A  pdb=" N   GLY B 122 " --> pdb=" O   PRO B 118 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   LEU B 123 " --> pdb=" O   PRO B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 137
      removed outlier: 4.103A  pdb=" N   PHE B 131 " --> pdb=" O   PHE B 127 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU B 135 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 162
    Processing helix  chain 'B' and resid 170 through 201
    Processing helix  chain 'B' and resid 205 through 210
    Processing helix  chain 'B' and resid 211 through 236
      removed outlier: 4.023A  pdb=" N   LYS B 232 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   TYR B 233 " --> pdb=" O   SER B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 258
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 263 through 287
    Processing helix  chain 'B' and resid 296 through 313
    Processing helix  chain 'B' and resid 337 through 339
      No H-bonds generated for 'chain 'B' and resid 337 through 339'
    Processing helix  chain 'B' and resid 340 through 371
      removed outlier: 4.797A  pdb=" N   GLY B 346 " --> pdb=" O   SER B 342 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   SER B 347 " --> pdb=" O   LYS B 343 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   THR B 350 " --> pdb=" O   GLY B 346 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE B 351 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 393
    Processing helix  chain 'B' and resid 401 through 412
      removed outlier: 3.599A  pdb=" N   GLY B 412 " --> pdb=" O   GLN B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 415 through 432
      removed outlier: 4.436A  pdb=" N   GLY B 419 " --> pdb=" O   SER B 415 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 438
      removed outlier: 3.691A  pdb=" N   PHE B 437 " --> pdb=" O   GLY B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 452
      removed outlier: 4.057A  pdb=" N   LEU B 445 " --> pdb=" O   PRO B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 470
      removed outlier: 4.427A  pdb=" N   LEU B 460 " --> pdb=" O   MET B 456 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   SER B 461 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ASP B 462 " --> pdb=" O   ARG B 458 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   TRP B 467 " --> pdb=" O   MET B 463 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   LYS B 468 " --> pdb=" O   ARG B 464 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ALA B 469 " --> pdb=" O   SER B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 487
    Processing helix  chain 'B' and resid 487 through 509
      removed outlier: 3.946A  pdb=" N   LEU B 491 " --> pdb=" O   LEU B 487 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL B 494 " --> pdb=" O   ASP B 490 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   THR B 508 " --> pdb=" O   VAL B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 553 through 565
    Processing helix  chain 'B' and resid 568 through 594
    Processing helix  chain 'B' and resid 656 through 661
    Processing helix  chain 'B' and resid 681 through 698
    Processing helix  chain 'B' and resid 708 through 718
      removed outlier: 3.619A  pdb=" N   VAL B 712 " --> pdb=" O   HIS B 708 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER B 713 " --> pdb=" O   SER B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 726 through 728
      No H-bonds generated for 'chain 'B' and resid 726 through 728'
    Processing helix  chain 'B' and resid 733 through 744
    Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 145
    Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 527
      removed outlier: 4.430A  pdb=" N   VAL A 542 " --> pdb=" O   LEU A 516 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   GLN A 518 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
      removed outlier: 12.076A  pdb=" N   VAL A 540 " --> pdb=" O   GLN A 518 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   LYS A 541 " --> pdb=" O   ILE A 671 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   ASP A 673 " --> pdb=" O   LYS A 541 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   PHE A 543 " --> pdb=" O   ASP A 673 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   PHE A 731 " --> pdb=" O   VAL A 702 " (cutoff:3.500A)
      removed outlier: 6.046A  pdb=" N   MET A 704 " --> pdb=" O   PHE A 731 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 144 through 145
    Processing sheet with id=AA4, first strand: chain 'B' and resid 525 through 527
      removed outlier: 4.431A  pdb=" N   VAL B 542 " --> pdb=" O   LEU B 516 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   GLN B 518 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
      removed outlier: 12.076A  pdb=" N   VAL B 540 " --> pdb=" O   GLN B 518 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LYS B 541 " --> pdb=" O   ILE B 671 " (cutoff:3.500A)
      removed outlier: 7.400A  pdb=" N   ASP B 673 " --> pdb=" O   LYS B 541 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   PHE B 543 " --> pdb=" O   ASP B 673 " (cutoff:3.500A)
      removed outlier: 8.063A  pdb=" N   PHE B 731 " --> pdb=" O   VAL B 702 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   MET B 704 " --> pdb=" O   PHE B 731 " (cutoff:3.500A)

    664 hydrogen bonds defined for protein.
    1950 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 0.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3163
        1.34 -     1.46: 2037
        1.46 -     1.58: 4958
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 10220
  Sorted by residual:
  bond pdb=" N   VAL A  79 "
       pdb=" CA  VAL A  79 "
    ideal  model  delta    sigma   weight residual
    1.452  1.493 -0.041 1.18e-02 7.18e+03 1.20e+01
  bond pdb=" N   VAL B  79 "
       pdb=" CA  VAL B  79 "
    ideal  model  delta    sigma   weight residual
    1.452  1.492 -0.040 1.18e-02 7.18e+03 1.13e+01
  bond pdb=" N   LEU B  90 "
       pdb=" CA  LEU B  90 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.17e-02 7.31e+03 6.56e+00
  bond pdb=" N   CYS B 565 "
       pdb=" CA  CYS B 565 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.033 1.31e-02 5.83e+03 6.52e+00
  bond pdb=" N   ILE B 102 "
       pdb=" CA  ILE B 102 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.19e-02 7.06e+03 6.52e+00
  ... (remaining 10215 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 13459
        1.30 -     2.61: 318
        2.61 -     3.91: 99
        3.91 -     5.21: 16
        5.21 -     6.51: 4
  Bond angle restraints: 13896
  Sorted by residual:
  angle pdb=" N   VAL B 451 "
        pdb=" CA  VAL B 451 "
        pdb=" C   VAL B 451 "
      ideal   model   delta    sigma   weight residual
     112.80  108.60    4.20 1.15e+00 7.56e-01 1.33e+01
  angle pdb=" N   VAL A 451 "
        pdb=" CA  VAL A 451 "
        pdb=" C   VAL A 451 "
      ideal   model   delta    sigma   weight residual
     112.80  108.65    4.15 1.15e+00 7.56e-01 1.30e+01
  angle pdb=" N   ASP B 462 "
        pdb=" CA  ASP B 462 "
        pdb=" C   ASP B 462 "
      ideal   model   delta    sigma   weight residual
     111.36  107.46    3.90 1.09e+00 8.42e-01 1.28e+01
  angle pdb=" N   GLN A 575 "
        pdb=" CA  GLN A 575 "
        pdb=" C   GLN A 575 "
      ideal   model   delta    sigma   weight residual
     111.07  107.53    3.54 1.07e+00 8.73e-01 1.10e+01
  angle pdb=" N   VAL A  79 "
        pdb=" CA  VAL A  79 "
        pdb=" C   VAL A  79 "
      ideal   model   delta    sigma   weight residual
     112.96  109.83    3.13 1.00e+00 1.00e+00 9.80e+00
  ... (remaining 13891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.56: 5482
       11.56 -    23.11: 398
       23.11 -    34.67: 128
       34.67 -    46.23: 47
       46.23 -    57.79: 9
  Dihedral angle restraints: 6064
    sinusoidal: 2324
      harmonic: 3740
  Sorted by residual:
  dihedral pdb=" CA  ASP A 736 "
           pdb=" CB  ASP A 736 "
           pdb=" CG  ASP A 736 "
           pdb=" OD1 ASP A 736 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.79   57.79     1      2.00e+01 2.50e-03 1.12e+01
  dihedral pdb=" CA  ASP B 736 "
           pdb=" CB  ASP B 736 "
           pdb=" CG  ASP B 736 "
           pdb=" OD1 ASP B 736 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.49   57.49     1      2.00e+01 2.50e-03 1.11e+01
  dihedral pdb=" CA  ARG A 140 "
           pdb=" C   ARG A 140 "
           pdb=" N   HIS A 141 "
           pdb=" CA  HIS A 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.26  -15.74     0      5.00e+00 4.00e-02 9.90e+00
  ... (remaining 6061 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1243
       0.042 -    0.084: 314
       0.084 -    0.126: 93
       0.126 -    0.168: 15
       0.168 -    0.210: 3
  Chirality restraints: 1668
  Sorted by residual:
  chirality pdb=" CA  ILE A 102 "
            pdb=" N   ILE A 102 "
            pdb=" C   ILE A 102 "
            pdb=" CB  ILE A 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  ILE B 102 "
            pdb=" N   ILE B 102 "
            pdb=" C   ILE B 102 "
            pdb=" CB  ILE B 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CA  LEU A 491 "
            pdb=" N   LEU A 491 "
            pdb=" C   LEU A 491 "
            pdb=" CB  LEU A 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.16e-01
  ... (remaining 1665 not shown)

  Planarity restraints: 1730
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  64 "    0.017 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   ARG B  64 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   ARG B  64 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ALA B  65 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 537 "   -0.013 2.00e-02 2.50e+03   2.67e-02 7.13e+00
        pdb=" C   VAL A 537 "    0.046 2.00e-02 2.50e+03
        pdb=" O   VAL A 537 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG A 538 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 537 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.48e+00
        pdb=" C   VAL B 537 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   VAL B 537 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ARG B 538 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1727 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1941
        2.78 -     3.31: 10162
        3.31 -     3.84: 16914
        3.84 -     4.37: 18453
        4.37 -     4.90: 33014
  Nonbonded interactions: 80484
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 185 "
            pdb=" O   GLY A 391 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG  SER B 185 "
            pdb=" O   GLY B 391 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OG1 THR A 508 "
            pdb=" OH  TYR A 550 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" OG1 THR B 508 "
            pdb=" OH  TYR B 550 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   ALA B 420 "
            pdb=" OG  SER B 423 "
     model   vdw
     2.258 3.040
  ... (remaining 80479 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.290
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.850
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
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      :  0.003   0.041  10220  Z= 0.208
  Angle     :  0.524   6.514  13896  Z= 0.338
  Chirality :  0.041   0.210   1668
  Planarity :  0.005   0.070   1730
  Dihedral  :  9.908  57.785   3652
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.64 (0.25), residues: 1284
  helix:  1.55 (0.19), residues: 902
  sheet:  0.87 (0.74), residues: 54
  loop : -0.01 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 176 
 TYR   0.012   0.001   TYR A 550 
 PHE   0.011   0.001   PHE A 356 
 TRP   0.012   0.001   TRP A  80 
 HIS   0.004   0.000   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10220)
  covalent geometry    : angle       0.52372 (13896)
  hydrogen bonds       : bond        0.13595 (  664)
  hydrogen bonds       : angle       6.04010 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 269
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   68 TYR cc_start: 0.7383 (t80) cc_final: 0.7107 (t80)
REVERT: A  159 GLU cc_start: 0.7666 (mm-30) cc_final: 0.6855 (mm-30)
REVERT: A  240 SER cc_start: 0.8479 (m) cc_final: 0.8171 (t)
REVERT: A  334 VAL cc_start: 0.8213 (t) cc_final: 0.7954 (p)
REVERT: A  410 SER cc_start: 0.8677 (t) cc_final: 0.8398 (m)
REVERT: A  535 LYS cc_start: 0.8020 (mttp) cc_final: 0.7708 (mtpp)
REVERT: A  568 ASP cc_start: 0.6702 (t0) cc_final: 0.6461 (t0)
REVERT: A  728 LYS cc_start: 0.7454 (mttp) cc_final: 0.7177 (mttm)
REVERT: B  263 LYS cc_start: 0.7661 (mttt) cc_final: 0.7327 (mttt)
REVERT: B  308 ILE cc_start: 0.7923 (mt) cc_final: 0.7700 (mm)
REVERT: B  309 SER cc_start: 0.8020 (t) cc_final: 0.7711 (p)
REVERT: B  334 VAL cc_start: 0.8334 (t) cc_final: 0.8123 (m)
REVERT: B  369 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7737 (mtm-85)
REVERT: B  409 GLU cc_start: 0.6836 (tt0) cc_final: 0.6441 (tt0)
REVERT: B  410 SER cc_start: 0.8646 (t) cc_final: 0.8440 (p)
REVERT: B  521 ASP cc_start: 0.7408 (t0) cc_final: 0.7096 (t0)
REVERT: B  673 ASP cc_start: 0.7617 (t0) cc_final: 0.7393 (t0)
REVERT: B  728 LYS cc_start: 0.7287 (mttp) cc_final: 0.7023 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 269
  average time/residue: 0.1005
  time to fit residues: 36.4417
Evaluate side-chains
  214 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.2980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0980
   chunk 55 optimal weight:    0.2980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 182 GLN
A 230 GLN
A 394 GLN
A 488 ASN
A 563 GLN
B 104 GLN
B 182 GLN
B 230 GLN
B 563 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.137514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.120858 restraints weight = 13843.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.02
r_work: 0.3398 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10220  Z= 0.146
  Angle     :  0.559  10.516  13896  Z= 0.279
  Chirality :  0.041   0.144   1668
  Planarity :  0.004   0.040   1730
  Dihedral  :  3.687  15.735   1376
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.64 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.24), residues: 1284
  helix:  2.11 (0.18), residues: 892
  sheet:  0.67 (0.74), residues: 54
  loop :  0.15 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 404 
 TYR   0.016   0.001   TYR A 128 
 PHE   0.016   0.002   PHE A 356 
 TRP   0.008   0.001   TRP A  80 
 HIS   0.002   0.001   HIS B 735 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (10220)
  covalent geometry    : angle       0.55922 (13896)
  hydrogen bonds       : bond        0.04350 (  664)
  hydrogen bonds       : angle       4.13598 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 234
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6289 (tmm) cc_final: 0.6085 (tmm)
REVERT: A  209 TYR cc_start: 0.8052 (m-10) cc_final: 0.7840 (m-10)
REVERT: A  240 SER cc_start: 0.8668 (m) cc_final: 0.8300 (t)
REVERT: A  293 MET cc_start: 0.7052 (ptp) cc_final: 0.6806 (ptp)
REVERT: A  334 VAL cc_start: 0.8102 (t) cc_final: 0.7882 (p)
REVERT: A  358 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7516 (mt)
REVERT: A  409 GLU cc_start: 0.7338 (tt0) cc_final: 0.7083 (tt0)
REVERT: A  410 SER cc_start: 0.8733 (t) cc_final: 0.8425 (m)
REVERT: A  458 ARG cc_start: 0.7244 (tpt170) cc_final: 0.7039 (ttt180)
REVERT: A  568 ASP cc_start: 0.7095 (t0) cc_final: 0.6688 (t0)
REVERT: A  698 ILE cc_start: 0.8375 (tt) cc_final: 0.8162 (tt)
REVERT: A  699 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7136 (mm-30)
REVERT: A  728 LYS cc_start: 0.7700 (mttp) cc_final: 0.7329 (mttm)
REVERT: B  308 ILE cc_start: 0.8107 (mt) cc_final: 0.7862 (mm)
REVERT: B  309 SER cc_start: 0.8270 (t) cc_final: 0.8003 (m)
REVERT: B  334 VAL cc_start: 0.8323 (t) cc_final: 0.8035 (m)
REVERT: B  402 MET cc_start: 0.7691 (tpp) cc_final: 0.7473 (tpp)
REVERT: B  410 SER cc_start: 0.8624 (t) cc_final: 0.8383 (p)
REVERT: B  444 VAL cc_start: 0.8185 (t) cc_final: 0.7982 (p)
REVERT: B  521 ASP cc_start: 0.7531 (t0) cc_final: 0.7257 (t0)
REVERT: B  673 ASP cc_start: 0.7779 (t0) cc_final: 0.7501 (t70)
REVERT: B  699 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7394 (mm-30)
REVERT: B  728 LYS cc_start: 0.7622 (mttp) cc_final: 0.7121 (ttmm)
  outliers start: 20
  outliers final: 13
  residues processed: 247
  average time/residue: 0.0952
  time to fit residues: 32.0281
Evaluate side-chains
  232 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 218
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  415 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 124 optimal weight:    0.6980
   chunk 120 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 63 optimal weight:    0.4980
   chunk 88 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9990
   chunk 104 optimal weight:    0.2980
   chunk 97 optimal weight:    0.0770
   chunk 85 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 488 ASN
A 664 GLN
B 182 GLN
B 563 GLN
B 664 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.135685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.118889 restraints weight = 13934.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.03
r_work: 0.3389 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10220  Z= 0.136
  Angle     :  0.533  10.900  13896  Z= 0.262
  Chirality :  0.040   0.145   1668
  Planarity :  0.004   0.052   1730
  Dihedral  :  3.741  15.681   1376
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 14.09 %
    Favored  : 83.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.24), residues: 1284
  helix:  2.08 (0.18), residues: 908
  sheet:  0.31 (0.71), residues: 54
  loop :  0.14 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 180 
 TYR   0.011   0.001   TYR A 209 
 PHE   0.025   0.002   PHE B 731 
 TRP   0.013   0.001   TRP B  80 
 HIS   0.003   0.000   HIS B 735 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10220)
  covalent geometry    : angle       0.53325 (13896)
  hydrogen bonds       : bond        0.03930 (  664)
  hydrogen bonds       : angle       3.88479 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 246
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6237 (tmm) cc_final: 0.5961 (tmm)
REVERT: A   93 ASP cc_start: 0.7381 (m-30) cc_final: 0.7152 (t0)
REVERT: A  240 SER cc_start: 0.8671 (m) cc_final: 0.8311 (t)
REVERT: A  293 MET cc_start: 0.7044 (ptp) cc_final: 0.6772 (ptp)
REVERT: A  309 SER cc_start: 0.8162 (t) cc_final: 0.7911 (m)
REVERT: A  334 VAL cc_start: 0.8088 (t) cc_final: 0.7872 (p)
REVERT: A  358 ILE cc_start: 0.7754 (OUTLIER) cc_final: 0.7508 (mt)
REVERT: A  410 SER cc_start: 0.8721 (t) cc_final: 0.8408 (m)
REVERT: A  458 ARG cc_start: 0.7278 (tpt170) cc_final: 0.7047 (ttt180)
REVERT: A  535 LYS cc_start: 0.8358 (mttp) cc_final: 0.7958 (mtpp)
REVERT: A  568 ASP cc_start: 0.7082 (t0) cc_final: 0.6670 (t0)
REVERT: A  698 ILE cc_start: 0.8363 (tt) cc_final: 0.8121 (tt)
REVERT: A  699 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7206 (mm-30)
REVERT: A  728 LYS cc_start: 0.7788 (mttp) cc_final: 0.7510 (mttm)
REVERT: B  308 ILE cc_start: 0.8120 (mt) cc_final: 0.7864 (mm)
REVERT: B  309 SER cc_start: 0.8271 (t) cc_final: 0.7982 (m)
REVERT: B  334 VAL cc_start: 0.8301 (t) cc_final: 0.8001 (m)
REVERT: B  358 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7535 (mt)
REVERT: B  369 ARG cc_start: 0.8447 (ttm170) cc_final: 0.8232 (ttm170)
REVERT: B  444 VAL cc_start: 0.8162 (t) cc_final: 0.7889 (p)
REVERT: B  498 ILE cc_start: 0.7988 (mm) cc_final: 0.7541 (mt)
REVERT: B  673 ASP cc_start: 0.7866 (t0) cc_final: 0.7559 (t70)
REVERT: B  699 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7430 (mm-30)
REVERT: B  728 LYS cc_start: 0.7705 (mttp) cc_final: 0.7361 (ttmm)
  outliers start: 29
  outliers final: 14
  residues processed: 263
  average time/residue: 0.0961
  time to fit residues: 34.2257
Evaluate side-chains
  248 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 232
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 80 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 107 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 117 optimal weight:    1.9990
   chunk 96 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9980
   chunk 94 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 182 GLN
B 563 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.135579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.118670 restraints weight = 13990.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 2.04
r_work: 0.3361 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10220  Z= 0.174
  Angle     :  0.546  12.167  13896  Z= 0.272
  Chirality :  0.042   0.150   1668
  Planarity :  0.004   0.044   1730
  Dihedral  :  3.841  16.147   1376
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 14.27 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.24), residues: 1284
  helix:  1.98 (0.18), residues: 908
  sheet:  0.00 (0.68), residues: 54
  loop :  0.07 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 564 
 TYR   0.011   0.002   TYR A 209 
 PHE   0.019   0.002   PHE A 720 
 TRP   0.015   0.001   TRP B  80 
 HIS   0.004   0.001   HIS B 735 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (10220)
  covalent geometry    : angle       0.54575 (13896)
  hydrogen bonds       : bond        0.04020 (  664)
  hydrogen bonds       : angle       3.85556 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 239
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6241 (tmm) cc_final: 0.5372 (tmm)
REVERT: A   33 ARG cc_start: 0.7876 (ptt90) cc_final: 0.7619 (ptt-90)
REVERT: A   93 ASP cc_start: 0.7463 (m-30) cc_final: 0.7238 (t0)
REVERT: A  240 SER cc_start: 0.8691 (m) cc_final: 0.8335 (t)
REVERT: A  293 MET cc_start: 0.7095 (ptp) cc_final: 0.6807 (ptp)
REVERT: A  309 SER cc_start: 0.8229 (t) cc_final: 0.7964 (m)
REVERT: A  334 VAL cc_start: 0.8059 (t) cc_final: 0.7830 (p)
REVERT: A  358 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7546 (mt)
REVERT: A  410 SER cc_start: 0.8740 (t) cc_final: 0.8426 (m)
REVERT: A  458 ARG cc_start: 0.7318 (tpt170) cc_final: 0.7086 (ttt180)
REVERT: A  535 LYS cc_start: 0.8327 (mttp) cc_final: 0.7951 (mtpp)
REVERT: A  568 ASP cc_start: 0.7113 (t0) cc_final: 0.6699 (t0)
REVERT: A  662 LEU cc_start: 0.8736 (mt) cc_final: 0.8526 (mp)
REVERT: A  698 ILE cc_start: 0.8389 (tt) cc_final: 0.8143 (tt)
REVERT: A  699 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7290 (mm-30)
REVERT: A  728 LYS cc_start: 0.7769 (mttp) cc_final: 0.7539 (mttm)
REVERT: B  247 SER cc_start: 0.8178 (p) cc_final: 0.7924 (t)
REVERT: B  309 SER cc_start: 0.8293 (t) cc_final: 0.8052 (m)
REVERT: B  334 VAL cc_start: 0.8270 (t) cc_final: 0.7954 (m)
REVERT: B  358 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7564 (mt)
REVERT: B  498 ILE cc_start: 0.7972 (mm) cc_final: 0.7557 (mt)
REVERT: B  564 ARG cc_start: 0.8350 (mtt90) cc_final: 0.8038 (mtt90)
REVERT: B  673 ASP cc_start: 0.7892 (t0) cc_final: 0.7606 (t70)
REVERT: B  699 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7548 (mm-30)
REVERT: B  728 LYS cc_start: 0.7820 (mttp) cc_final: 0.7491 (ttmm)
  outliers start: 45
  outliers final: 31
  residues processed: 263
  average time/residue: 0.0959
  time to fit residues: 34.4089
Evaluate side-chains
  264 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 231
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 86 optimal weight:    0.6980
   chunk 57 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 87 optimal weight:    0.6980
   chunk 117 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 370 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.135257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.118393 restraints weight = 13896.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.02
r_work: 0.3357 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10220  Z= 0.170
  Angle     :  0.546  12.675  13896  Z= 0.271
  Chirality :  0.042   0.209   1668
  Planarity :  0.004   0.046   1730
  Dihedral  :  3.900  16.373   1376
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 16.00 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.24), residues: 1284
  helix:  1.94 (0.18), residues: 908
  sheet: -0.17 (0.67), residues: 54
  loop :  0.02 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 180 
 TYR   0.011   0.001   TYR B 550 
 PHE   0.033   0.002   PHE B 720 
 TRP   0.016   0.001   TRP B  80 
 HIS   0.003   0.001   HIS B 735 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (10220)
  covalent geometry    : angle       0.54572 (13896)
  hydrogen bonds       : bond        0.03926 (  664)
  hydrogen bonds       : angle       3.83404 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 240
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6211 (tmm) cc_final: 0.5477 (tmm)
REVERT: A   33 ARG cc_start: 0.7904 (ptt90) cc_final: 0.7664 (ptt-90)
REVERT: A  240 SER cc_start: 0.8705 (m) cc_final: 0.8421 (t)
REVERT: A  293 MET cc_start: 0.7136 (ptp) cc_final: 0.6832 (ptp)
REVERT: A  309 SER cc_start: 0.8260 (t) cc_final: 0.8004 (m)
REVERT: A  334 VAL cc_start: 0.8050 (t) cc_final: 0.7818 (p)
REVERT: A  358 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7561 (mt)
REVERT: A  458 ARG cc_start: 0.7333 (tpt170) cc_final: 0.7099 (ttt180)
REVERT: A  487 LEU cc_start: 0.7797 (mp) cc_final: 0.7581 (mt)
REVERT: A  535 LYS cc_start: 0.8313 (mttp) cc_final: 0.7930 (mtpp)
REVERT: A  568 ASP cc_start: 0.7124 (t0) cc_final: 0.6715 (t0)
REVERT: A  698 ILE cc_start: 0.8402 (tt) cc_final: 0.8153 (tt)
REVERT: A  699 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7357 (mm-30)
REVERT: A  728 LYS cc_start: 0.7815 (mttp) cc_final: 0.7523 (mttm)
REVERT: B  247 SER cc_start: 0.8152 (p) cc_final: 0.7920 (t)
REVERT: B  309 SER cc_start: 0.8312 (t) cc_final: 0.8059 (m)
REVERT: B  334 VAL cc_start: 0.8256 (t) cc_final: 0.7936 (m)
REVERT: B  358 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7562 (mt)
REVERT: B  498 ILE cc_start: 0.7957 (mm) cc_final: 0.7563 (mt)
REVERT: B  673 ASP cc_start: 0.7910 (t0) cc_final: 0.7628 (t70)
REVERT: B  699 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7618 (mm-30)
REVERT: B  728 LYS cc_start: 0.7810 (mttp) cc_final: 0.7488 (ttmm)
  outliers start: 43
  outliers final: 29
  residues processed: 268
  average time/residue: 0.0977
  time to fit residues: 36.2021
Evaluate side-chains
  262 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 231
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  409 GLU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  660 LEU
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 108 optimal weight:    0.6980
   chunk 127 optimal weight:    0.5980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 459 GLN
A 708 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.116042 restraints weight = 13953.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.10
r_work: 0.3338 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10220  Z= 0.195
  Angle     :  0.577  13.180  13896  Z= 0.285
  Chirality :  0.043   0.186   1668
  Planarity :  0.005   0.077   1730
  Dihedral  :  4.031  16.645   1376
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 16.18 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.24), residues: 1284
  helix:  1.89 (0.18), residues: 906
  sheet: -0.31 (0.66), residues: 54
  loop : -0.10 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 544 
 TYR   0.011   0.002   TYR A 557 
 PHE   0.025   0.002   PHE B 720 
 TRP   0.016   0.001   TRP B  80 
 HIS   0.020   0.001   HIS A 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (10220)
  covalent geometry    : angle       0.57677 (13896)
  hydrogen bonds       : bond        0.04038 (  664)
  hydrogen bonds       : angle       3.87701 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 240
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6195 (tmm) cc_final: 0.5490 (tmm)
REVERT: A   33 ARG cc_start: 0.7974 (ptt90) cc_final: 0.7756 (ptt-90)
REVERT: A  240 SER cc_start: 0.8719 (m) cc_final: 0.8423 (t)
REVERT: A  293 MET cc_start: 0.7204 (ptp) cc_final: 0.6875 (ptp)
REVERT: A  301 THR cc_start: 0.8285 (t) cc_final: 0.8070 (p)
REVERT: A  309 SER cc_start: 0.8254 (t) cc_final: 0.8002 (m)
REVERT: A  334 VAL cc_start: 0.8056 (t) cc_final: 0.7813 (p)
REVERT: A  358 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7495 (mt)
REVERT: A  458 ARG cc_start: 0.7373 (tpt170) cc_final: 0.7110 (ttt180)
REVERT: A  487 LEU cc_start: 0.7814 (mp) cc_final: 0.7606 (mt)
REVERT: A  498 ILE cc_start: 0.8108 (mm) cc_final: 0.7816 (mt)
REVERT: A  568 ASP cc_start: 0.7156 (t0) cc_final: 0.6756 (t0)
REVERT: A  698 ILE cc_start: 0.8356 (tt) cc_final: 0.8118 (tt)
REVERT: A  699 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7419 (mm-30)
REVERT: A  728 LYS cc_start: 0.7814 (mttp) cc_final: 0.7521 (mttm)
REVERT: B  247 SER cc_start: 0.8162 (p) cc_final: 0.7921 (t)
REVERT: B  309 SER cc_start: 0.8350 (t) cc_final: 0.7969 (p)
REVERT: B  334 VAL cc_start: 0.8217 (t) cc_final: 0.7882 (m)
REVERT: B  358 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7519 (mt)
REVERT: B  498 ILE cc_start: 0.7919 (mm) cc_final: 0.7537 (mt)
REVERT: B  673 ASP cc_start: 0.8025 (t0) cc_final: 0.7768 (t70)
REVERT: B  699 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7641 (mm-30)
REVERT: B  728 LYS cc_start: 0.7847 (mttp) cc_final: 0.7510 (ttmm)
  outliers start: 45
  outliers final: 32
  residues processed: 268
  average time/residue: 0.0963
  time to fit residues: 35.8471
Evaluate side-chains
  269 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 235
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  238 HIS
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 94 optimal weight:    0.3980
   chunk 81 optimal weight:    0.6980
   chunk 101 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.134255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.117486 restraints weight = 13974.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.01
r_work: 0.3342 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10220  Z= 0.185
  Angle     :  0.573  14.106  13896  Z= 0.281
  Chirality :  0.042   0.152   1668
  Planarity :  0.004   0.054   1730
  Dihedral  :  4.047  17.364   1376
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 16.91 %
    Favored  : 78.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.24), residues: 1284
  helix:  1.86 (0.18), residues: 908
  sheet: -0.48 (0.65), residues: 54
  loop : -0.13 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 404 
 TYR   0.011   0.001   TYR A 550 
 PHE   0.034   0.002   PHE B 720 
 TRP   0.016   0.001   TRP B  80 
 HIS   0.006   0.001   HIS A 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (10220)
  covalent geometry    : angle       0.57323 (13896)
  hydrogen bonds       : bond        0.03943 (  664)
  hydrogen bonds       : angle       3.89012 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 236
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6258 (tmm) cc_final: 0.5762 (tmm)
REVERT: A   93 ASP cc_start: 0.7430 (t70) cc_final: 0.7148 (t0)
REVERT: A  102 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8353 (tp)
REVERT: A  240 SER cc_start: 0.8731 (m) cc_final: 0.8445 (t)
REVERT: A  293 MET cc_start: 0.7212 (ptp) cc_final: 0.6871 (ptp)
REVERT: A  301 THR cc_start: 0.8322 (t) cc_final: 0.8080 (p)
REVERT: A  309 SER cc_start: 0.8269 (t) cc_final: 0.8026 (m)
REVERT: A  334 VAL cc_start: 0.8023 (t) cc_final: 0.7776 (p)
REVERT: A  358 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7520 (mt)
REVERT: A  458 ARG cc_start: 0.7339 (tpt170) cc_final: 0.7104 (ttt180)
REVERT: A  498 ILE cc_start: 0.8148 (mm) cc_final: 0.7848 (mt)
REVERT: A  568 ASP cc_start: 0.7133 (t0) cc_final: 0.6749 (t0)
REVERT: A  699 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7441 (mm-30)
REVERT: A  728 LYS cc_start: 0.7798 (mttp) cc_final: 0.7511 (mttm)
REVERT: B  247 SER cc_start: 0.8143 (p) cc_final: 0.7917 (t)
REVERT: B  309 SER cc_start: 0.8341 (t) cc_final: 0.7962 (p)
REVERT: B  334 VAL cc_start: 0.8195 (t) cc_final: 0.7866 (m)
REVERT: B  358 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7584 (mt)
REVERT: B  369 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8205 (ttm170)
REVERT: B  498 ILE cc_start: 0.7957 (mm) cc_final: 0.7571 (mt)
REVERT: B  673 ASP cc_start: 0.8011 (t0) cc_final: 0.7664 (t70)
REVERT: B  699 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7662 (mm-30)
REVERT: B  728 LYS cc_start: 0.7855 (mttp) cc_final: 0.7536 (ttmm)
  outliers start: 47
  outliers final: 34
  residues processed: 262
  average time/residue: 0.0986
  time to fit residues: 36.0711
Evaluate side-chains
  272 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 235
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  238 HIS
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  358 ILE
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  582 LYS
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 120 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 127 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 202 HIS
A 416 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.134582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.117424 restraints weight = 13888.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.13
r_work: 0.3333 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10220  Z= 0.165
  Angle     :  0.567  14.742  13896  Z= 0.278
  Chirality :  0.041   0.152   1668
  Planarity :  0.005   0.075   1730
  Dihedral  :  4.020  17.368   1376
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 17.64 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.92 (0.24), residues: 1284
  helix:  1.90 (0.18), residues: 908
  sheet: -0.63 (0.64), residues: 54
  loop : -0.09 (0.36), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 404 
 TYR   0.011   0.001   TYR A 550 
 PHE   0.026   0.001   PHE B 720 
 TRP   0.017   0.001   TRP B  80 
 HIS   0.004   0.001   HIS A 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (10220)
  covalent geometry    : angle       0.56675 (13896)
  hydrogen bonds       : bond        0.03831 (  664)
  hydrogen bonds       : angle       3.86167 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 236
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6261 (tmm) cc_final: 0.5435 (tmm)
REVERT: A   33 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7369 (pmt170)
REVERT: A   93 ASP cc_start: 0.7474 (t70) cc_final: 0.7163 (t0)
REVERT: A  102 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8273 (tp)
REVERT: A  240 SER cc_start: 0.8724 (m) cc_final: 0.8424 (t)
REVERT: A  293 MET cc_start: 0.7216 (ptp) cc_final: 0.6861 (ptp)
REVERT: A  309 SER cc_start: 0.8240 (t) cc_final: 0.7988 (m)
REVERT: A  334 VAL cc_start: 0.8059 (t) cc_final: 0.7804 (p)
REVERT: A  358 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7474 (mt)
REVERT: A  498 ILE cc_start: 0.8065 (mm) cc_final: 0.7786 (mt)
REVERT: A  699 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7455 (mm-30)
REVERT: A  728 LYS cc_start: 0.7810 (mttp) cc_final: 0.7527 (mttm)
REVERT: A  730 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7670 (mp)
REVERT: B  209 TYR cc_start: 0.8219 (m-10) cc_final: 0.8000 (m-10)
REVERT: B  247 SER cc_start: 0.8140 (p) cc_final: 0.7886 (t)
REVERT: B  293 MET cc_start: 0.6886 (ptp) cc_final: 0.6586 (ptp)
REVERT: B  309 SER cc_start: 0.8343 (t) cc_final: 0.7968 (p)
REVERT: B  334 VAL cc_start: 0.8213 (t) cc_final: 0.7876 (m)
REVERT: B  369 ARG cc_start: 0.8387 (ttm170) cc_final: 0.8146 (ttm170)
REVERT: B  498 ILE cc_start: 0.7891 (mm) cc_final: 0.7517 (mt)
REVERT: B  544 ARG cc_start: 0.8503 (ttt-90) cc_final: 0.8171 (ttt90)
REVERT: B  673 ASP cc_start: 0.8022 (t0) cc_final: 0.7786 (t70)
REVERT: B  699 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7642 (mm-30)
REVERT: B  728 LYS cc_start: 0.7858 (mttp) cc_final: 0.7500 (ttmm)
  outliers start: 46
  outliers final: 36
  residues processed: 265
  average time/residue: 0.0900
  time to fit residues: 33.1288
Evaluate side-chains
  269 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 229
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  238 HIS
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  401 SER
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 92 optimal weight:    0.4980
   chunk 66 optimal weight:    0.4980
   chunk 13 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 117 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 120 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 370 HIS
B 708 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.134438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.117283 restraints weight = 13941.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3465 rms_B_bonded: 2.13
r_work: 0.3334 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10220  Z= 0.167
  Angle     :  0.578  14.912  13896  Z= 0.282
  Chirality :  0.042   0.232   1668
  Planarity :  0.005   0.086   1730
  Dihedral  :  4.038  17.594   1376
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.18 %
    Favored  : 78.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.96 (0.24), residues: 1284
  helix:  1.91 (0.18), residues: 906
  sheet: -0.55 (0.65), residues: 54
  loop : -0.01 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 544 
 TYR   0.011   0.001   TYR A 550 
 PHE   0.026   0.001   PHE B 720 
 TRP   0.018   0.001   TRP B  80 
 HIS   0.021   0.001   HIS B 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (10220)
  covalent geometry    : angle       0.57814 (13896)
  hydrogen bonds       : bond        0.03830 (  664)
  hydrogen bonds       : angle       3.86544 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 235
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A   31 MET cc_start: 0.6327 (tmm) cc_final: 0.6021 (tmm)
REVERT: A   93 ASP cc_start: 0.7432 (t70) cc_final: 0.7133 (t0)
REVERT: A  102 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8270 (tp)
REVERT: A  240 SER cc_start: 0.8724 (m) cc_final: 0.8424 (t)
REVERT: A  293 MET cc_start: 0.7200 (ptp) cc_final: 0.6842 (ptp)
REVERT: A  309 SER cc_start: 0.8236 (t) cc_final: 0.8002 (m)
REVERT: A  334 VAL cc_start: 0.8053 (t) cc_final: 0.7805 (p)
REVERT: A  358 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7489 (mt)
REVERT: A  498 ILE cc_start: 0.8068 (mm) cc_final: 0.7786 (mt)
REVERT: A  699 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7444 (mm-30)
REVERT: A  728 LYS cc_start: 0.7806 (mttp) cc_final: 0.7526 (mttm)
REVERT: A  730 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7655 (mp)
REVERT: B  209 TYR cc_start: 0.8210 (m-10) cc_final: 0.7982 (m-10)
REVERT: B  247 SER cc_start: 0.8133 (p) cc_final: 0.7888 (t)
REVERT: B  293 MET cc_start: 0.6901 (ptp) cc_final: 0.6580 (ptp)
REVERT: B  309 SER cc_start: 0.8339 (t) cc_final: 0.8069 (m)
REVERT: B  334 VAL cc_start: 0.8207 (t) cc_final: 0.7871 (m)
REVERT: B  369 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8136 (ttm170)
REVERT: B  498 ILE cc_start: 0.7890 (mm) cc_final: 0.7510 (mt)
REVERT: B  544 ARG cc_start: 0.8490 (ttt-90) cc_final: 0.8132 (ttt-90)
REVERT: B  673 ASP cc_start: 0.8035 (t0) cc_final: 0.7789 (t70)
REVERT: B  699 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7611 (mm-30)
REVERT: B  728 LYS cc_start: 0.7883 (mttp) cc_final: 0.7525 (ttmm)
  outliers start: 41
  outliers final: 35
  residues processed: 258
  average time/residue: 0.0913
  time to fit residues: 32.9414
Evaluate side-chains
  271 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 233
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  582 LYS
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 2 optimal weight:    3.9990
   chunk 121 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 95 optimal weight:    0.8980
   chunk 4 optimal weight:    0.1980
   chunk 124 optimal weight:    0.6980
   chunk 78 optimal weight:    0.5980
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.134608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.117568 restraints weight = 13794.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.12
r_work: 0.3336 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10220  Z= 0.160
  Angle     :  0.582  15.391  13896  Z= 0.282
  Chirality :  0.042   0.248   1668
  Planarity :  0.005   0.058   1730
  Dihedral  :  4.017  18.302   1376
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.36 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.98 (0.24), residues: 1284
  helix:  1.92 (0.18), residues: 906
  sheet: -0.58 (0.65), residues: 54
  loop :  0.02 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 544 
 TYR   0.011   0.001   TYR A 550 
 PHE   0.032   0.002   PHE B 720 
 TRP   0.017   0.001   TRP B  80 
 HIS   0.003   0.001   HIS B 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (10220)
  covalent geometry    : angle       0.58166 (13896)
  hydrogen bonds       : bond        0.03779 (  664)
  hydrogen bonds       : angle       3.84894 ( 1950)

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

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

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2568 Ramachandran restraints generated.
    1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 236
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.6342 (tmm) cc_final: 0.6010 (tmm)
REVERT: A   93 ASP cc_start: 0.7425 (t70) cc_final: 0.6979 (t0)
REVERT: A  102 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8309 (tp)
REVERT: A  240 SER cc_start: 0.8720 (m) cc_final: 0.8421 (t)
REVERT: A  293 MET cc_start: 0.7196 (ptp) cc_final: 0.6848 (ptp)
REVERT: A  309 SER cc_start: 0.8224 (t) cc_final: 0.8014 (m)
REVERT: A  334 VAL cc_start: 0.8068 (t) cc_final: 0.7814 (p)
REVERT: A  358 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7503 (mt)
REVERT: A  458 ARG cc_start: 0.7354 (tpt170) cc_final: 0.7083 (ttt180)
REVERT: A  498 ILE cc_start: 0.8068 (mm) cc_final: 0.7784 (mt)
REVERT: A  699 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7395 (mm-30)
REVERT: A  728 LYS cc_start: 0.7782 (mttp) cc_final: 0.7480 (mttm)
REVERT: A  730 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7647 (mp)
REVERT: B  209 TYR cc_start: 0.8176 (m-10) cc_final: 0.7950 (m-10)
REVERT: B  293 MET cc_start: 0.6908 (ptp) cc_final: 0.6593 (ptp)
REVERT: B  309 SER cc_start: 0.8307 (t) cc_final: 0.8030 (m)
REVERT: B  334 VAL cc_start: 0.8196 (t) cc_final: 0.7864 (m)
REVERT: B  369 ARG cc_start: 0.8389 (ttm170) cc_final: 0.8164 (ttm170)
REVERT: B  498 ILE cc_start: 0.7897 (mm) cc_final: 0.7512 (mt)
REVERT: B  673 ASP cc_start: 0.8046 (t0) cc_final: 0.7768 (t70)
REVERT: B  699 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7603 (mm-30)
REVERT: B  728 LYS cc_start: 0.7889 (mttp) cc_final: 0.7532 (ttmm)
  outliers start: 41
  outliers final: 34
  residues processed: 262
  average time/residue: 0.0903
  time to fit residues: 33.1348
Evaluate side-chains
  268 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 231
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 LEU
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  277 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  360 ILE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  424 LEU
Chi-restraints excluded: chain A residue  426 ILE
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  532 SER
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  701 GLU
Chi-restraints excluded: chain A residue  719 HIS
Chi-restraints excluded: chain A residue  730 LEU
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  240 SER
Chi-restraints excluded: chain B residue  345 VAL
Chi-restraints excluded: chain B residue  360 ILE
Chi-restraints excluded: chain B residue  362 LEU
Chi-restraints excluded: chain B residue  398 VAL
Chi-restraints excluded: chain B residue  426 ILE
Chi-restraints excluded: chain B residue  427 LEU
Chi-restraints excluded: chain B residue  432 LYS
Chi-restraints excluded: chain B residue  485 ILE
Chi-restraints excluded: chain B residue  532 SER
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  582 LYS
Chi-restraints excluded: chain B residue  701 GLU
Chi-restraints excluded: chain B residue  719 HIS
Chi-restraints excluded: chain B residue  726 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 110 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 102 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0470
   chunk 119 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 111 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0050
   overall best weight:    0.4492

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.134781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.117680 restraints weight = 13932.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.12
r_work: 0.3348 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10220  Z= 0.137
  Angle     :  0.573  15.579  13896  Z= 0.277
  Chirality :  0.041   0.166   1668
  Planarity :  0.004   0.053   1730
  Dihedral  :  3.978  17.805   1376
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.55 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.24), residues: 1284
  helix:  1.97 (0.18), residues: 906
  sheet: -0.61 (0.64), residues: 54
  loop :  0.05 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  33 
 TYR   0.010   0.001   TYR A 550 
 PHE   0.031   0.001   PHE B 720 
 TRP   0.017   0.001   TRP B  80 
 HIS   0.002   0.000   HIS B 708 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (10220)
  covalent geometry    : angle       0.57254 (13896)
  hydrogen bonds       : bond        0.03591 (  664)
  hydrogen bonds       : angle       3.81406 ( 1950)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2361.91 seconds
wall clock time: 41 minutes 11.55 seconds (2471.55 seconds total)