Starting phenix.real_space_refine
on Sun May  3 04:39:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xve_67287/05_2026/9xve_67287.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xve_67287/05_2026/9xve_67287.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xve_67287/05_2026/9xve_67287.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xve_67287/05_2026/9xve_67287.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xve_67287/05_2026/9xve_67287.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xve_67287/05_2026/9xve_67287.map"
  }
  resolution = 2.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.059
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    6636      2.51       5
     N    1774      2.21       5
     O    1924      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10400
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 640, 5200
          Classifications: {'peptide': 640}
          Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 608}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 5200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 640, 5200
          Classifications: {'peptide': 640}
          Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 608}
          Chain breaks: 4
  Time building chain proxies: 2.40, per 1000 atoms: 0.23
  Number of scatterers: 10400
  At special positions: 0
  Unit cell: (195.84, 70.08, 69.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1924      8.00
     N    1774      7.00
     C    6636      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: 1.08
  Conformation dependent library (CDL) restraints added in 436.2 milliseconds
  

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2384

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 12 sheets defined
      29.8% alpha, 15.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 181 through 186
      removed outlier: 4.526A  pdb=" N   THR A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 192
      removed outlier: 3.607A  pdb=" N   LYS A 192 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.567A  pdb=" N   LYS A 205 " --> pdb=" O   GLY A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 213
      removed outlier: 3.994A  pdb=" N   LEU A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 260
    Processing helix  chain 'A' and resid 269 through 286
      removed outlier: 3.810A  pdb=" N   ASN A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 319
      removed outlier: 3.533A  pdb=" N   ASN A 315 " --> pdb=" O   ARG A 311 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   SER A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   VAL A 317 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 360
      removed outlier: 3.611A  pdb=" N   ARG A 345 " --> pdb=" O   HIS A 341 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 411
    Processing helix  chain 'A' and resid 446 through 458
      removed outlier: 4.074A  pdb=" N   ARG A 450 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASP A 451 " --> pdb=" O   GLY A 447 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLN A 455 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 472
      removed outlier: 3.794A  pdb=" N   PHE A 467 " --> pdb=" O   PHE A 463 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ALA A 468 " --> pdb=" O   SER A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 485
      No H-bonds generated for 'chain 'A' and resid 483 through 485'
    Processing helix  chain 'A' and resid 498 through 503
      removed outlier: 3.967A  pdb=" N   VAL A 503 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 557
      removed outlier: 3.953A  pdb=" N   ARG A 549 " --> pdb=" O   LYS A 545 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASN A 550 " --> pdb=" O   ARG A 546 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE A 551 " --> pdb=" O   GLN A 547 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   PHE A 552 " --> pdb=" O   MET A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 589
    Processing helix  chain 'A' and resid 591 through 598
      removed outlier: 3.559A  pdb=" N   GLU A 597 " --> pdb=" O   ASP A 593 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 616
    Processing helix  chain 'A' and resid 705 through 712
      removed outlier: 3.641A  pdb=" N   GLN A 712 " --> pdb=" O   THR A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 718
    Processing helix  chain 'B' and resid 62 through 66
    Processing helix  chain 'B' and resid 110 through 113
    Processing helix  chain 'B' and resid 181 through 186
      removed outlier: 4.521A  pdb=" N   THR B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 192
      removed outlier: 3.562A  pdb=" N   LYS B 192 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 205
    Processing helix  chain 'B' and resid 206 through 213
    Processing helix  chain 'B' and resid 256 through 260
    Processing helix  chain 'B' and resid 269 through 285
      removed outlier: 3.854A  pdb=" N   ASN B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ARG B 285 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 319
      removed outlier: 3.514A  pdb=" N   ASN B 315 " --> pdb=" O   ARG B 311 " (cutoff:3.500A)
      removed outlier: 8.629A  pdb=" N   SER B 316 " --> pdb=" O   GLY B 312 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   VAL B 317 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   TYR B 319 " --> pdb=" O   ASN B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 360
      removed outlier: 3.581A  pdb=" N   LEU B 349 " --> pdb=" O   ARG B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 446 through 458
      removed outlier: 3.969A  pdb=" N   ARG B 450 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASP B 451 " --> pdb=" O   GLY B 447 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLN B 455 " --> pdb=" O   ASP B 451 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS B 458 " --> pdb=" O   ARG B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 472
      removed outlier: 3.624A  pdb=" N   PHE B 467 " --> pdb=" O   PHE B 463 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLU B 469 " --> pdb=" O   GLY B 465 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS B 472 " --> pdb=" O   ALA B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 485
      No H-bonds generated for 'chain 'B' and resid 483 through 485'
    Processing helix  chain 'B' and resid 498 through 503
      removed outlier: 3.966A  pdb=" N   VAL B 503 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 557
      removed outlier: 3.902A  pdb=" N   ARG B 549 " --> pdb=" O   LYS B 545 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASN B 550 " --> pdb=" O   ARG B 546 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE B 551 " --> pdb=" O   GLN B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 589
    Processing helix  chain 'B' and resid 591 through 598
      removed outlier: 3.545A  pdb=" N   GLU B 597 " --> pdb=" O   ASP B 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 616
    Processing helix  chain 'B' and resid 705 through 712
      removed outlier: 3.759A  pdb=" N   GLN B 712 " --> pdb=" O   THR B 708 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 718
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27
    Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 76
      removed outlier: 4.756A  pdb=" N   ALA A  55 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER A  54 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109
    Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 180
      removed outlier: 6.300A  pdb=" N   TYR A 178 " --> pdb=" O   GLU A 218 " (cutoff:3.500A)
      removed outlier: 6.948A  pdb=" N   VAL A 289 " --> pdb=" O   GLY A 363 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ARG A 365 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   MET A 291 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   LEU A 420 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
      removed outlier: 7.893A  pdb=" N   TRP A 445 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   ALA A 422 " --> pdb=" O   TRP A 445 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   GLU A 444 " --> pdb=" O   ILE A 488 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   SER A 487 " --> pdb=" O   VAL A 561 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   MET A 563 " --> pdb=" O   SER A 487 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   ASN A 489 " --> pdb=" O   MET A 563 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   TYR A 565 " --> pdb=" O   ASN A 489 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 631 through 633
      removed outlier: 4.047A  pdb=" N   ALA A 650 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLU A 660 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   SER A 729 " --> pdb=" O   ASP A 689 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ASP A 689 " --> pdb=" O   SER A 729 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE A 731 " --> pdb=" O   PHE A 687 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 672 through 675
    Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 27
    Processing sheet with id=AA8, first strand: chain 'B' and resid 72 through 76
      removed outlier: 4.758A  pdb=" N   ALA B  55 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER B  54 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 109
    Processing sheet with id=AB1, first strand: chain 'B' and resid 177 through 180
      removed outlier: 6.304A  pdb=" N   TYR B 178 " --> pdb=" O   GLU B 218 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   VAL B 289 " --> pdb=" O   GLY B 363 " (cutoff:3.500A)
      removed outlier: 8.111A  pdb=" N   ARG B 365 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   MET B 291 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LEU B 420 " --> pdb=" O   SER B 443 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   TRP B 445 " --> pdb=" O   LEU B 420 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   ALA B 422 " --> pdb=" O   TRP B 445 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   GLU B 444 " --> pdb=" O   ILE B 488 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   SER B 487 " --> pdb=" O   VAL B 561 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   MET B 563 " --> pdb=" O   SER B 487 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ASN B 489 " --> pdb=" O   MET B 563 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   TYR B 565 " --> pdb=" O   ASN B 489 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 630 through 633
      removed outlier: 4.085A  pdb=" N   ALA B 650 " --> pdb=" O   HIS B 633 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   GLU B 660 " --> pdb=" O   LEU B 734 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   SER B 729 " --> pdb=" O   ASP B 689 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   ASP B 689 " --> pdb=" O   SER B 729 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE B 731 " --> pdb=" O   PHE B 687 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 672 through 675

    305 hydrogen bonds defined for protein.
    825 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: 1.57

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1732
        1.30 -     1.42: 3052
        1.42 -     1.55: 5800
        1.55 -     1.68: 4
        1.68 -     1.81: 102
  Bond restraints: 10690
  Sorted by residual:
  bond pdb=" CA  HIS A 341 "
       pdb=" C   HIS A 341 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 1.18e-02 7.18e+03 4.41e+01
  bond pdb=" CA  HIS B 341 "
       pdb=" C   HIS B 341 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 1.18e-02 7.18e+03 4.37e+01
  bond pdb=" CA  CYS A 339 "
       pdb=" C   CYS A 339 "
    ideal  model  delta    sigma   weight residual
    1.524  1.432  0.092 1.48e-02 4.57e+03 3.90e+01
  bond pdb=" CA  CYS B 339 "
       pdb=" C   CYS B 339 "
    ideal  model  delta    sigma   weight residual
    1.524  1.432  0.092 1.48e-02 4.57e+03 3.87e+01
  bond pdb=" C   HIS A 341 "
       pdb=" O   HIS A 341 "
    ideal  model  delta    sigma   weight residual
    1.240  1.170  0.070 1.14e-02 7.69e+03 3.78e+01
  ... (remaining 10685 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 14259
        2.22 -     4.45: 184
        4.45 -     6.67: 12
        6.67 -     8.89: 7
        8.89 -    11.12: 6
  Bond angle restraints: 14468
  Sorted by residual:
  angle pdb=" N   VAL A 344 "
        pdb=" CA  VAL A 344 "
        pdb=" C   VAL A 344 "
      ideal   model   delta    sigma   weight residual
     110.72  117.86   -7.14 1.01e+00 9.80e-01 4.99e+01
  angle pdb=" N   ASN A 338 "
        pdb=" CA  ASN A 338 "
        pdb=" C   ASN A 338 "
      ideal   model   delta    sigma   weight residual
     107.20  117.43  -10.23 1.70e+00 3.46e-01 3.62e+01
  angle pdb=" N   ASN B 338 "
        pdb=" CA  ASN B 338 "
        pdb=" C   ASN B 338 "
      ideal   model   delta    sigma   weight residual
     107.20  116.95   -9.75 1.70e+00 3.46e-01 3.29e+01
  angle pdb=" N   CYS A 339 "
        pdb=" CA  CYS A 339 "
        pdb=" C   CYS A 339 "
      ideal   model   delta    sigma   weight residual
     112.72  119.04   -6.32 1.14e+00 7.69e-01 3.07e+01
  angle pdb=" N   CYS B 339 "
        pdb=" CA  CYS B 339 "
        pdb=" C   CYS B 339 "
      ideal   model   delta    sigma   weight residual
     112.72  118.63   -5.91 1.14e+00 7.69e-01 2.69e+01
  ... (remaining 14463 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 5255
       17.50 -    34.99: 705
       34.99 -    52.49: 250
       52.49 -    69.98: 51
       69.98 -    87.48: 17
  Dihedral angle restraints: 6278
    sinusoidal: 2566
      harmonic: 3712
  Sorted by residual:
  dihedral pdb=" CA  VAL A 503 "
           pdb=" C   VAL A 503 "
           pdb=" N   THR A 504 "
           pdb=" CA  THR A 504 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.75   17.25     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  VAL B 503 "
           pdb=" C   VAL B 503 "
           pdb=" N   THR B 504 "
           pdb=" CA  THR B 504 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.86   17.14     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CA  ASP B 412 "
           pdb=" CB  ASP B 412 "
           pdb=" CG  ASP B 412 "
           pdb=" OD1 ASP B 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.04   57.04     1      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 6275 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1214
       0.056 -    0.112: 235
       0.112 -    0.169: 25
       0.169 -    0.225: 7
       0.225 -    0.281: 5
  Chirality restraints: 1486
  Sorted by residual:
  chirality pdb=" CA  PRO A 342 "
            pdb=" N   PRO A 342 "
            pdb=" C   PRO A 342 "
            pdb=" CB  PRO A 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  PRO B 342 "
            pdb=" N   PRO B 342 "
            pdb=" C   PRO B 342 "
            pdb=" CB  PRO B 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.27 2.00e-01 2.50e+01 1.88e+00
  chirality pdb=" CA  CYS A 339 "
            pdb=" N   CYS A 339 "
            pdb=" C   CYS A 339 "
            pdb=" CB  CYS A 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.43e+00
  ... (remaining 1483 not shown)

  Planarity restraints: 1892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 344 "    0.012 2.00e-02 2.50e+03   2.27e-02 5.16e+00
        pdb=" C   VAL A 344 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   VAL A 344 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ARG A 345 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 338 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.42e+00
        pdb=" C   ASN A 338 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ASN A 338 "    0.012 2.00e-02 2.50e+03
        pdb=" N   CYS A 339 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 338 "    0.009 2.00e-02 2.50e+03   1.80e-02 3.23e+00
        pdb=" C   ASN B 338 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   ASN B 338 "    0.012 2.00e-02 2.50e+03
        pdb=" N   CYS B 339 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1889 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.97: 4683
        2.97 -     3.45: 9190
        3.45 -     3.93: 16610
        3.93 -     4.42: 19384
        4.42 -     4.90: 32346
  Nonbonded interactions: 82213
  Sorted by model distance:
  nonbonded pdb=" CB  PHE A 337 "
            pdb=" N   ASN A 338 "
     model   vdw
     2.483 2.816
  nonbonded pdb=" CB  PHE B 337 "
            pdb=" N   ASN B 338 "
     model   vdw
     2.510 2.816
  nonbonded pdb=" O   VAL B 344 "
            pdb=" CA  ARG B 345 "
     model   vdw
     2.526 2.776
  nonbonded pdb=" O   GLN A 346 "
            pdb=" OD1 ASP A 350 "
     model   vdw
     2.539 3.040
  nonbonded pdb=" N   ASP A  77 "
            pdb=" OD1 ASP A  77 "
     model   vdw
     2.540 3.120
  ... (remaining 82208 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:             5.010
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.440
  Find NCS groups from input model:        0.140
  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:6.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
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      :  0.005   0.092  10690  Z= 0.334
  Angle     :  0.654  11.117  14468  Z= 0.380
  Chirality :  0.049   0.281   1486
  Planarity :  0.004   0.047   1892
  Dihedral  : 18.482  87.475   3894
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.76 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 27.55 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.22), residues: 1260
  helix: -0.84 (0.28), residues: 306
  sheet:  0.19 (0.32), residues: 266
  loop : -1.46 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 683 
 TYR   0.009   0.001   TYR A 102 
 PHE   0.030   0.001   PHE A 337 
 TRP   0.009   0.001   TRP A 485 
 HIS   0.004   0.001   HIS A 341 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 (10690)
  covalent geometry    : angle       0.65366 (14468)
  hydrogen bonds       : bond        0.25059 (  305)
  hydrogen bonds       : angle       8.90957 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 170
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 THR cc_start: 0.7027 (m) cc_final: 0.6667 (p)
REVERT: A   75 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7297 (mm-40)
REVERT: A  161 ASP cc_start: 0.6290 (t70) cc_final: 0.6006 (t70)
REVERT: A  166 MET cc_start: 0.6982 (pmm) cc_final: 0.5923 (ptt)
REVERT: A  220 MET cc_start: 0.7902 (mtt) cc_final: 0.7527 (mmm)
REVERT: A  230 TYR cc_start: 0.5522 (OUTLIER) cc_final: 0.4905 (p90)
REVERT: A  292 ASP cc_start: 0.7795 (t70) cc_final: 0.7459 (m-30)
REVERT: A  339 CYS cc_start: 0.6374 (OUTLIER) cc_final: 0.6100 (m)
REVERT: A  341 HIS cc_start: 0.7264 (t-90) cc_final: 0.7063 (t-90)
REVERT: A  359 MET cc_start: 0.7500 (mmm) cc_final: 0.7185 (mmt)
REVERT: A  464 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7307 (t)
REVERT: A  538 ILE cc_start: 0.6992 (tt) cc_final: 0.6757 (tp)
REVERT: A  659 LYS cc_start: 0.7256 (mmtt) cc_final: 0.6525 (mptt)
REVERT: A  683 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7576 (ttp-110)
REVERT: A  685 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7971 (mp0)
REVERT: A  707 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7274 (mp0)
REVERT: A  714 ARG cc_start: 0.8468 (ttp-170) cc_final: 0.8196 (ttm170)
REVERT: B   37 THR cc_start: 0.7052 (m) cc_final: 0.6708 (p)
REVERT: B   75 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7225 (mm-40)
REVERT: B   80 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.5465 (ttp-110)
REVERT: B  161 ASP cc_start: 0.6249 (t70) cc_final: 0.5926 (t70)
REVERT: B  166 MET cc_start: 0.6808 (ptm) cc_final: 0.6205 (ptt)
REVERT: B  204 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7449 (mt-10)
REVERT: B  230 TYR cc_start: 0.5483 (OUTLIER) cc_final: 0.4903 (p90)
REVERT: B  281 GLU cc_start: 0.6682 (tt0) cc_final: 0.5312 (tm-30)
REVERT: B  341 HIS cc_start: 0.7096 (t-90) cc_final: 0.6880 (t-90)
REVERT: B  455 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6849 (mt0)
REVERT: B  464 SER cc_start: 0.7751 (OUTLIER) cc_final: 0.7315 (t)
REVERT: B  538 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7313 (tp)
REVERT: B  556 MET cc_start: 0.8954 (mmt) cc_final: 0.8746 (mmt)
REVERT: B  659 LYS cc_start: 0.6963 (mmmt) cc_final: 0.6328 (mptt)
  outliers start: 40
  outliers final: 10
  residues processed: 201
  average time/residue: 0.5362
  time to fit residues: 116.4659
Evaluate side-chains
  152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  464 SER
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue   80 ARG
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  538 ILE
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  674 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.4980
   chunk 66 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A  44 ASN
A 338 ASN
A 631 GLN
B 338 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.192685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.160154 restraints weight = 10915.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 1.67
r_work: 0.3714 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10690  Z= 0.123
  Angle     :  0.552   7.291  14468  Z= 0.292
  Chirality :  0.045   0.141   1486
  Planarity :  0.004   0.036   1892
  Dihedral  :  5.705  57.501   1426
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 25.62 %
    Favored  : 69.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.23), residues: 1260
  helix: -0.23 (0.28), residues: 308
  sheet:  0.38 (0.31), residues: 262
  loop : -1.32 (0.22), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 683 
 TYR   0.010   0.001   TYR A 696 
 PHE   0.012   0.001   PHE A 456 
 TRP   0.009   0.001   TRP A 485 
 HIS   0.005   0.001   HIS B 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10690)
  covalent geometry    : angle       0.55159 (14468)
  hydrogen bonds       : bond        0.05060 (  305)
  hydrogen bonds       : angle       6.15178 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 141
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7527 (mm-40)
REVERT: A  161 ASP cc_start: 0.6663 (t70) cc_final: 0.6445 (t0)
REVERT: A  166 MET cc_start: 0.7224 (OUTLIER) cc_final: 0.6298 (ptt)
REVERT: A  189 GLU cc_start: 0.6787 (pt0) cc_final: 0.6577 (pt0)
REVERT: A  230 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.5300 (p90)
REVERT: A  359 MET cc_start: 0.7713 (mmm) cc_final: 0.7253 (mmt)
REVERT: A  659 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6669 (mptt)
REVERT: A  685 GLU cc_start: 0.8247 (mt-10) cc_final: 0.8038 (tp30)
REVERT: A  714 ARG cc_start: 0.8580 (ttp-170) cc_final: 0.8372 (tpp80)
REVERT: B   75 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7527 (mm-40)
REVERT: B  166 MET cc_start: 0.6871 (ptm) cc_final: 0.6336 (ptt)
REVERT: B  230 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.5237 (p90)
REVERT: B  292 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7820 (m-30)
REVERT: B  353 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7275 (ttm110)
REVERT: B  359 MET cc_start: 0.7679 (mmm) cc_final: 0.7208 (mmt)
REVERT: B  531 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6863 (mt-10)
REVERT: B  659 LYS cc_start: 0.7002 (mmmt) cc_final: 0.6587 (mptt)
REVERT: B  714 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8123 (tpp80)
  outliers start: 53
  outliers final: 18
  residues processed: 182
  average time/residue: 0.5672
  time to fit residues: 111.1682
Evaluate side-chains
  145 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  337 PHE
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  292 ASP
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  531 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  706 ARG
Chi-restraints excluded: chain B residue  714 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0060
   chunk 114 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 105 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 113 optimal weight:    2.9990
   chunk 104 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    1.5402

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

Flipped N/Q/H residues before XYZ refinement:
A 341 HIS
A 489 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.189517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.155667 restraints weight = 10969.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 1.76
r_work: 0.3681 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3576 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10690  Z= 0.172
  Angle     :  0.620   7.322  14468  Z= 0.331
  Chirality :  0.048   0.151   1486
  Planarity :  0.005   0.040   1892
  Dihedral  :  5.482  58.001   1410
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 22.80 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.22), residues: 1260
  helix: -0.23 (0.28), residues: 306
  sheet:  0.30 (0.32), residues: 260
  loop : -1.32 (0.22), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 629 
 TYR   0.012   0.002   TYR A 696 
 PHE   0.013   0.002   PHE B 651 
 TRP   0.010   0.001   TRP A 485 
 HIS   0.007   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (10690)
  covalent geometry    : angle       0.61998 (14468)
  hydrogen bonds       : bond        0.06025 (  305)
  hydrogen bonds       : angle       6.05758 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 116
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  161 ASP cc_start: 0.6433 (t70) cc_final: 0.6137 (t0)
REVERT: A  166 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6081 (ptt)
REVERT: A  295 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7690 (pp)
REVERT: A  348 ILE cc_start: 0.8390 (mt) cc_final: 0.8046 (mm)
REVERT: A  365 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.6921 (ttm170)
REVERT: A  408 MET cc_start: 0.4908 (tpp) cc_final: 0.4284 (ptp)
REVERT: A  659 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6595 (mptt)
REVERT: A  685 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7909 (tp30)
REVERT: A  714 ARG cc_start: 0.8410 (ttp-170) cc_final: 0.8195 (tpp-160)
REVERT: B   75 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7442 (mm-40)
REVERT: B  166 MET cc_start: 0.6775 (OUTLIER) cc_final: 0.6162 (ptt)
REVERT: B  189 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5539 (pp20)
REVERT: B  285 ARG cc_start: 0.7450 (mtp180) cc_final: 0.7139 (mtp85)
REVERT: B  292 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7710 (m-30)
REVERT: B  295 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7820 (pp)
REVERT: B  365 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7090 (ttm170)
REVERT: B  408 MET cc_start: 0.4804 (tpp) cc_final: 0.4286 (ptp)
REVERT: B  659 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6635 (mppt)
REVERT: B  705 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7887 (mm-30)
  outliers start: 59
  outliers final: 29
  residues processed: 160
  average time/residue: 0.6083
  time to fit residues: 104.2399
Evaluate side-chains
  148 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 109
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  166 MET
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  292 ASP
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain B residue  339 CYS
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  705 GLU
Chi-restraints excluded: chain B residue  706 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 58 optimal weight:    0.6980
   chunk 68 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 70 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 98 optimal weight:    7.9990
   chunk 42 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 104 optimal weight:    0.6980
   overall best weight:    1.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 341 HIS
A 631 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.187741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.153206 restraints weight = 10990.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 1.88
r_work: 0.3653 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10690  Z= 0.188
  Angle     :  0.644   8.244  14468  Z= 0.344
  Chirality :  0.048   0.157   1486
  Planarity :  0.005   0.044   1892
  Dihedral  :  5.623  59.445   1410
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 21.74 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.22), residues: 1260
  helix: -0.28 (0.28), residues: 308
  sheet:  0.18 (0.31), residues: 256
  loop : -1.33 (0.22), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 629 
 TYR   0.012   0.002   TYR A 696 
 PHE   0.014   0.002   PHE B 651 
 TRP   0.011   0.002   TRP B 485 
 HIS   0.006   0.001   HIS B 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (10690)
  covalent geometry    : angle       0.64437 (14468)
  hydrogen bonds       : bond        0.06082 (  305)
  hydrogen bonds       : angle       6.01115 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 122
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7693 (mm-40) cc_final: 0.7447 (mm-40)
REVERT: A  161 ASP cc_start: 0.6468 (OUTLIER) cc_final: 0.5781 (t0)
REVERT: A  166 MET cc_start: 0.7051 (OUTLIER) cc_final: 0.6024 (ptt)
REVERT: A  295 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7627 (pp)
REVERT: A  348 ILE cc_start: 0.8414 (mt) cc_final: 0.8064 (mm)
REVERT: A  365 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.6991 (ttm170)
REVERT: A  367 ASP cc_start: 0.7256 (t70) cc_final: 0.6750 (t0)
REVERT: A  631 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7064 (tt0)
REVERT: A  659 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6830 (mppt)
REVERT: A  685 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8008 (mp0)
REVERT: B   75 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7458 (mm-40)
REVERT: B  166 MET cc_start: 0.6764 (ptm) cc_final: 0.6127 (ptt)
REVERT: B  189 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.5620 (pp20)
REVERT: B  292 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7725 (m-30)
REVERT: B  295 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7678 (pp)
REVERT: B  345 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7765 (mtm-85)
REVERT: B  359 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.6131 (mmm)
REVERT: B  365 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7039 (ttm170)
REVERT: B  367 ASP cc_start: 0.7247 (t70) cc_final: 0.6738 (t0)
REVERT: B  455 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.7081 (mt0)
  outliers start: 58
  outliers final: 31
  residues processed: 156
  average time/residue: 0.5991
  time to fit residues: 100.3154
Evaluate side-chains
  161 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 118
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  292 ASP
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  339 CYS
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  359 MET
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  674 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 109 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0570
   chunk 3 optimal weight:   10.0000
   overall best weight:    0.9900

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

Flipped N/Q/H residues before XYZ refinement:
A 518 ASN
B 518 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.189655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.155479 restraints weight = 10917.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 1.88
r_work: 0.3680 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10690  Z= 0.129
  Angle     :  0.559   7.270  14468  Z= 0.296
  Chirality :  0.045   0.140   1486
  Planarity :  0.004   0.041   1892
  Dihedral  :  5.361  59.159   1410
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 22.01 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.23), residues: 1260
  helix:  0.08 (0.28), residues: 308
  sheet:  0.12 (0.31), residues: 264
  loop : -1.25 (0.23), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 258 
 TYR   0.009   0.001   TYR A 696 
 PHE   0.013   0.002   PHE A 651 
 TRP   0.011   0.001   TRP A 485 
 HIS   0.004   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10690)
  covalent geometry    : angle       0.55853 (14468)
  hydrogen bonds       : bond        0.04973 (  305)
  hydrogen bonds       : angle       5.71358 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 122
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7316 (mm-40)
REVERT: A  161 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.5784 (t0)
REVERT: A  166 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6044 (ptt)
REVERT: A  295 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7590 (pp)
REVERT: A  346 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6948 (tt0)
REVERT: A  348 ILE cc_start: 0.8419 (mt) cc_final: 0.8053 (mm)
REVERT: A  367 ASP cc_start: 0.7205 (t70) cc_final: 0.6650 (t0)
REVERT: A  628 LYS cc_start: 0.7396 (mtmm) cc_final: 0.6763 (mttm)
REVERT: A  659 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6760 (mppt)
REVERT: A  685 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7939 (mp0)
REVERT: B   75 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7446 (mm-40)
REVERT: B  166 MET cc_start: 0.6797 (ptm) cc_final: 0.6165 (ptt)
REVERT: B  189 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.5594 (pp20)
REVERT: B  295 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7668 (pp)
REVERT: B  346 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6840 (tt0)
REVERT: B  359 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6131 (mmm)
REVERT: B  367 ASP cc_start: 0.7229 (t70) cc_final: 0.6700 (t0)
REVERT: B  455 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7116 (mt0)
REVERT: B  705 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7823 (mm-30)
  outliers start: 48
  outliers final: 29
  residues processed: 152
  average time/residue: 0.5821
  time to fit residues: 95.2818
Evaluate side-chains
  161 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 121
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  314 ASP
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  359 MET
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  683 ARG
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  705 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 76 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 88 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 34 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 116 optimal weight:    1.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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 = 0.4152 r_free = 0.4152 target = 0.186665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.152053 restraints weight = 10957.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3788 rms_B_bonded: 1.87
r_work: 0.3639 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3533 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10690  Z= 0.210
  Angle     :  0.675   8.457  14468  Z= 0.359
  Chirality :  0.049   0.177   1486
  Planarity :  0.005   0.046   1892
  Dihedral  :  5.771  59.409   1410
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 19.89 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.22), residues: 1260
  helix: -0.16 (0.28), residues: 308
  sheet: -0.05 (0.30), residues: 260
  loop : -1.33 (0.22), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 629 
 TYR   0.013   0.002   TYR A 696 
 PHE   0.015   0.002   PHE B 651 
 TRP   0.012   0.002   TRP B 485 
 HIS   0.006   0.001   HIS B 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (10690)
  covalent geometry    : angle       0.67471 (14468)
  hydrogen bonds       : bond        0.06463 (  305)
  hydrogen bonds       : angle       6.02419 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 118
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7394 (mm-40)
REVERT: A  161 ASP cc_start: 0.6485 (OUTLIER) cc_final: 0.5798 (t0)
REVERT: A  166 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6072 (ptt)
REVERT: A  220 MET cc_start: 0.8104 (mtt) cc_final: 0.7551 (mmm)
REVERT: A  288 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7866 (mt-10)
REVERT: A  295 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7799 (pp)
REVERT: A  346 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6897 (tt0)
REVERT: A  348 ILE cc_start: 0.8449 (mt) cc_final: 0.8089 (mm)
REVERT: A  365 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7078 (ttm170)
REVERT: A  367 ASP cc_start: 0.7335 (t70) cc_final: 0.6833 (t0)
REVERT: A  659 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6838 (mppt)
REVERT: A  685 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7999 (mp0)
REVERT: B   75 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7435 (mm-40)
REVERT: B  166 MET cc_start: 0.6794 (ptm) cc_final: 0.5632 (pp-130)
REVERT: B  189 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.5681 (pp20)
REVERT: B  220 MET cc_start: 0.8134 (mtt) cc_final: 0.7560 (mmm)
REVERT: B  288 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7897 (mt-10)
REVERT: B  295 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7816 (pp)
REVERT: B  346 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6861 (tt0)
REVERT: B  365 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7041 (ttm170)
REVERT: B  367 ASP cc_start: 0.7352 (t70) cc_final: 0.6889 (t0)
REVERT: B  455 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7123 (mt0)
REVERT: B  705 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7785 (mm-30)
  outliers start: 62
  outliers final: 34
  residues processed: 157
  average time/residue: 0.5720
  time to fit residues: 96.8421
Evaluate side-chains
  162 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 114
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  288 GLU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  339 CYS
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  365 ARG
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  474 SER
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  683 ARG
Chi-restraints excluded: chain B residue  705 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 11 optimal weight:    0.0570
   chunk 123 optimal weight:    0.7980
   chunk 91 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 80 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    1.1702

-------------------------------------------------------------------------------
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 = 0.4171 r_free = 0.4171 target = 0.188634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.154667 restraints weight = 10883.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3817 rms_B_bonded: 1.83
r_work: 0.3671 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3567 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10690  Z= 0.140
  Angle     :  0.579   7.549  14468  Z= 0.306
  Chirality :  0.046   0.142   1486
  Planarity :  0.004   0.044   1892
  Dihedral  :  5.469  59.061   1410
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 20.86 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.22), residues: 1260
  helix:  0.05 (0.28), residues: 310
  sheet:  0.07 (0.31), residues: 264
  loop : -1.29 (0.22), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 258 
 TYR   0.011   0.001   TYR A 696 
 PHE   0.014   0.002   PHE A 651 
 TRP   0.012   0.001   TRP A 485 
 HIS   0.003   0.001   HIS B 715 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (10690)
  covalent geometry    : angle       0.57893 (14468)
  hydrogen bonds       : bond        0.05139 (  305)
  hydrogen bonds       : angle       5.71594 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 117
  time to evaluate  : 0.397 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7554 (mm-40) cc_final: 0.6928 (tm-30)
REVERT: A  161 ASP cc_start: 0.6468 (OUTLIER) cc_final: 0.6091 (t0)
REVERT: A  166 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6060 (ptt)
REVERT: A  295 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7702 (pp)
REVERT: A  348 ILE cc_start: 0.8425 (mt) cc_final: 0.8067 (mm)
REVERT: A  367 ASP cc_start: 0.7288 (t70) cc_final: 0.6816 (t0)
REVERT: A  659 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6777 (mppt)
REVERT: A  685 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7933 (mp0)
REVERT: A  714 ARG cc_start: 0.8246 (tpp-160) cc_final: 0.8006 (tpp80)
REVERT: B   75 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7401 (mm-40)
REVERT: B  166 MET cc_start: 0.6714 (ptm) cc_final: 0.5594 (pp-130)
REVERT: B  189 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.5619 (pp20)
REVERT: B  288 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7921 (mt-10)
REVERT: B  295 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7760 (pp)
REVERT: B  346 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6838 (tt0)
REVERT: B  367 ASP cc_start: 0.7295 (t70) cc_final: 0.6807 (t0)
REVERT: B  444 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6696 (pt0)
REVERT: B  455 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7093 (mt0)
REVERT: B  705 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7803 (mm-30)
  outliers start: 53
  outliers final: 30
  residues processed: 151
  average time/residue: 0.5764
  time to fit residues: 93.7200
Evaluate side-chains
  156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 115
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  444 GLU
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  683 ARG
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  705 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 40 optimal weight:    0.2980
   chunk 36 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 102 optimal weight:    0.1980
   chunk 112 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0030
   chunk 121 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 127 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.2994

-------------------------------------------------------------------------------
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 = 0.4163 r_free = 0.4163 target = 0.187789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.153953 restraints weight = 10930.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 1.82
r_work: 0.3662 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3558 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10690  Z= 0.150
  Angle     :  0.591   7.994  14468  Z= 0.313
  Chirality :  0.046   0.149   1486
  Planarity :  0.004   0.044   1892
  Dihedral  :  5.467  59.091   1410
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 20.33 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.22), residues: 1260
  helix:  0.03 (0.28), residues: 312
  sheet:  0.07 (0.31), residues: 264
  loop : -1.33 (0.22), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 629 
 TYR   0.011   0.001   TYR A 696 
 PHE   0.013   0.002   PHE A 651 
 TRP   0.011   0.001   TRP B 485 
 HIS   0.003   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10690)
  covalent geometry    : angle       0.59124 (14468)
  hydrogen bonds       : bond        0.05374 (  305)
  hydrogen bonds       : angle       5.73370 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 116
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7425 (mm-40) cc_final: 0.6823 (tm-30)
REVERT: A  161 ASP cc_start: 0.6526 (OUTLIER) cc_final: 0.5828 (t0)
REVERT: A  166 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6037 (ptt)
REVERT: A  295 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7668 (pp)
REVERT: A  348 ILE cc_start: 0.8420 (mt) cc_final: 0.8054 (mm)
REVERT: A  365 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.6975 (ttm170)
REVERT: A  367 ASP cc_start: 0.7364 (t70) cc_final: 0.6951 (t70)
REVERT: A  659 LYS cc_start: 0.7322 (OUTLIER) cc_final: 0.6810 (mppt)
REVERT: A  685 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7909 (mp0)
REVERT: A  714 ARG cc_start: 0.8248 (tpp-160) cc_final: 0.7996 (tpp80)
REVERT: B   75 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7379 (mm-40)
REVERT: B  166 MET cc_start: 0.6779 (ptm) cc_final: 0.5637 (pp-130)
REVERT: B  189 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.5611 (pp20)
REVERT: B  220 MET cc_start: 0.8071 (mtt) cc_final: 0.7508 (mmm)
REVERT: B  288 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7908 (mt-10)
REVERT: B  295 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7780 (pp)
REVERT: B  346 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6830 (tt0)
REVERT: B  359 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.6169 (mmm)
REVERT: B  367 ASP cc_start: 0.7371 (t70) cc_final: 0.6950 (t70)
REVERT: B  444 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6730 (pt0)
REVERT: B  455 GLN cc_start: 0.7390 (OUTLIER) cc_final: 0.7094 (mt0)
REVERT: B  705 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7794 (mm-30)
  outliers start: 54
  outliers final: 33
  residues processed: 150
  average time/residue: 0.5911
  time to fit residues: 95.4345
Evaluate side-chains
  160 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 114
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  474 SER
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  339 CYS
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  359 MET
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  444 GLU
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  683 ARG
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  705 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 87 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 82 optimal weight:    0.9980
   chunk 120 optimal weight:    0.6980
   chunk 2 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4179 r_free = 0.4179 target = 0.189694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.155926 restraints weight = 11015.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 1.84
r_work: 0.3686 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3582 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10690  Z= 0.117
  Angle     :  0.539   7.102  14468  Z= 0.285
  Chirality :  0.044   0.139   1486
  Planarity :  0.004   0.042   1892
  Dihedral  :  5.273  58.609   1410
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 3.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 21.21 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.23), residues: 1260
  helix:  0.21 (0.29), residues: 312
  sheet:  0.09 (0.31), residues: 264
  loop : -1.25 (0.23), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 613 
 TYR   0.009   0.001   TYR A 696 
 PHE   0.012   0.001   PHE B 456 
 TRP   0.012   0.001   TRP A 485 
 HIS   0.003   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10690)
  covalent geometry    : angle       0.53944 (14468)
  hydrogen bonds       : bond        0.04605 (  305)
  hydrogen bonds       : angle       5.51852 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 120
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7294 (mm-40) cc_final: 0.6772 (tm-30)
REVERT: A  161 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.5823 (t0)
REVERT: A  166 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6038 (ptt)
REVERT: A  295 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7663 (pp)
REVERT: A  348 ILE cc_start: 0.8411 (mt) cc_final: 0.8042 (mm)
REVERT: A  367 ASP cc_start: 0.7306 (t70) cc_final: 0.6891 (t70)
REVERT: A  659 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6765 (mppt)
REVERT: A  685 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7914 (mp0)
REVERT: A  714 ARG cc_start: 0.8243 (tpp-160) cc_final: 0.8015 (tpp80)
REVERT: B   75 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7290 (mm-40)
REVERT: B  166 MET cc_start: 0.6794 (ptm) cc_final: 0.5634 (pp-130)
REVERT: B  168 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7611 (mp)
REVERT: B  189 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.5593 (pp20)
REVERT: B  285 ARG cc_start: 0.7422 (mtp180) cc_final: 0.7159 (mtp85)
REVERT: B  288 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7923 (mt-10)
REVERT: B  295 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7796 (pp)
REVERT: B  346 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6826 (tt0)
REVERT: B  359 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.6219 (mmm)
REVERT: B  367 ASP cc_start: 0.7317 (t70) cc_final: 0.6914 (t70)
REVERT: B  444 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7552 (tp30)
REVERT: B  455 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7139 (mt0)
REVERT: B  705 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7813 (mm-30)
  outliers start: 45
  outliers final: 25
  residues processed: 150
  average time/residue: 0.5579
  time to fit residues: 90.3776
Evaluate side-chains
  156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 118
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  359 MET
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  444 GLU
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  683 ARG
Chi-restraints excluded: chain B residue  685 GLU
Chi-restraints excluded: chain B residue  705 GLU
Chi-restraints excluded: chain B residue  706 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 110 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 127 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0030
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.5594

-------------------------------------------------------------------------------
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 = 0.4159 r_free = 0.4159 target = 0.187586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.153481 restraints weight = 10813.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 1.81
r_work: 0.3657 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3553 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10690  Z= 0.167
  Angle     :  0.614   7.967  14468  Z= 0.325
  Chirality :  0.047   0.155   1486
  Planarity :  0.005   0.043   1892
  Dihedral  :  5.530  58.993   1410
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.48 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.22), residues: 1260
  helix:  0.06 (0.28), residues: 312
  sheet:  0.06 (0.30), residues: 260
  loop : -1.32 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 629 
 TYR   0.012   0.002   TYR A 696 
 PHE   0.013   0.002   PHE B 651 
 TRP   0.011   0.001   TRP A 485 
 HIS   0.004   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (10690)
  covalent geometry    : angle       0.61363 (14468)
  hydrogen bonds       : bond        0.05685 (  305)
  hydrogen bonds       : angle       5.77584 (  825)

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

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

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2520 Ramachandran restraints generated.
    1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 113
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A   75 GLN cc_start: 0.7401 (mm-40) cc_final: 0.6780 (tm-30)
REVERT: A  161 ASP cc_start: 0.6590 (OUTLIER) cc_final: 0.5872 (t0)
REVERT: A  166 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6067 (ptt)
REVERT: A  220 MET cc_start: 0.8063 (mtt) cc_final: 0.7538 (mmm)
REVERT: A  295 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7705 (pp)
REVERT: A  348 ILE cc_start: 0.8425 (mt) cc_final: 0.8058 (mm)
REVERT: A  365 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7029 (ttm170)
REVERT: A  367 ASP cc_start: 0.7279 (t70) cc_final: 0.6990 (t70)
REVERT: A  659 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6822 (mppt)
REVERT: A  685 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7927 (mp0)
REVERT: B   75 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7359 (mm-40)
REVERT: B  166 MET cc_start: 0.6806 (ptm) cc_final: 0.5637 (pp-130)
REVERT: B  168 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7627 (mp)
REVERT: B  189 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.5620 (pp20)
REVERT: B  220 MET cc_start: 0.8088 (mtt) cc_final: 0.7533 (mmm)
REVERT: B  288 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7902 (mt-10)
REVERT: B  295 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7755 (pp)
REVERT: B  346 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6799 (tt0)
REVERT: B  359 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6197 (mmm)
REVERT: B  367 ASP cc_start: 0.7397 (t70) cc_final: 0.7114 (t70)
REVERT: B  444 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7638 (tt0)
REVERT: B  455 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7122 (mt0)
REVERT: B  705 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7805 (mm-30)
  outliers start: 41
  outliers final: 26
  residues processed: 137
  average time/residue: 0.5717
  time to fit residues: 84.5459
Evaluate side-chains
  154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 114
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  166 MET
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  365 ARG
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  659 LYS
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  189 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  261 SER
Chi-restraints excluded: chain B residue  288 GLU
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  359 MET
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  444 GLU
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  460 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  587 MET
Chi-restraints excluded: chain B residue  657 VAL
Chi-restraints excluded: chain B residue  674 VAL
Chi-restraints excluded: chain B residue  683 ARG
Chi-restraints excluded: chain B residue  705 GLU
Chi-restraints excluded: chain B residue  706 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 126 optimal weight:    0.4980
   chunk 71 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0010
   chunk 0 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.8992

-------------------------------------------------------------------------------
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 = 0.4176 r_free = 0.4176 target = 0.189293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.155728 restraints weight = 11005.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3829 rms_B_bonded: 1.81
r_work: 0.3682 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3578 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10690  Z= 0.121
  Angle     :  0.548   7.037  14468  Z= 0.288
  Chirality :  0.045   0.142   1486
  Planarity :  0.004   0.042   1892
  Dihedral  :  5.307  58.969   1410
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.74 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.22), residues: 1260
  helix:  0.26 (0.28), residues: 312
  sheet:  0.11 (0.30), residues: 260
  loop : -1.22 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 613 
 TYR   0.009   0.001   TYR A 696 
 PHE   0.012   0.001   PHE B 456 
 TRP   0.011   0.001   TRP A 485 
 HIS   0.003   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10690)
  covalent geometry    : angle       0.54767 (14468)
  hydrogen bonds       : bond        0.04675 (  305)
  hydrogen bonds       : angle       5.52620 (  825)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4278.44 seconds
wall clock time: 73 minutes 34.12 seconds (4414.12 seconds total)