Starting phenix.real_space_refine
on Wed Jul 30 07:32:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbf_61312/07_2025/9jbf_61312.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbf_61312/07_2025/9jbf_61312.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbf_61312/07_2025/9jbf_61312.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbf_61312/07_2025/9jbf_61312.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbf_61312/07_2025/9jbf_61312.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbf_61312/07_2025/9jbf_61312.cif"
  }
  resolution = 3.21
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      74      5.16       5
     C    7882      2.51       5
     N    1746      2.21       5
     O    2004      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11718
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 691, 5443
          Classifications: {'peptide': 691}
          Link IDs: {'PTRANS': 22, 'TRANS': 668}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 5443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 691, 5443
          Classifications: {'peptide': 691}
          Link IDs: {'PTRANS': 22, 'TRANS': 668}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 416
          Unusual residues: {'3PE': 2, 'CLR': 1, 'PC1': 2, 'Y01': 2}
          Classifications: {'peptide': 2, 'undetermined': 7}
          Link IDs: {None: 8}
    Chain: "B"
      Number of atoms: 416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 416
          Unusual residues: {'3PE': 2, 'CLR': 1, 'PC1': 2, 'Y01': 2}
          Classifications: {'peptide': 2, 'undetermined': 7}
          Link IDs: {None: 8}
  Time building chain proxies: 8.37, per 1000 atoms: 0.71
  Number of scatterers: 11718
  At special positions: 0
  Unit cell: (102.616, 130.088, 96.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      74     16.00
     P      12     15.00
     O    2004      8.00
     N    1746      7.00
     C    7882      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: 3.40
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2588

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 2 sheets defined
      79.9% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 62
      removed outlier: 3.800A  pdb=" N   ALA A  45 " --> pdb=" O   ARG A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 80
      removed outlier: 4.158A  pdb=" N   LEU A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 92
      removed outlier: 3.771A  pdb=" N   VAL A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 124
      removed outlier: 3.997A  pdb=" N   LEU A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
    Processing helix  chain 'A' and resid 136 through 141
    Processing helix  chain 'A' and resid 150 through 158
    Processing helix  chain 'A' and resid 162 through 167
    Processing helix  chain 'A' and resid 168 through 180
      removed outlier: 3.632A  pdb=" N   ALA A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
    Processing helix  chain 'A' and resid 180 through 197
    Processing helix  chain 'A' and resid 202 through 216
      removed outlier: 4.434A  pdb=" N   ILE A 206 " --> pdb=" O   ASN A 202 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   VAL A 207 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.557A  pdb=" N   PHE A 221 " --> pdb=" O   ASN A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 251
      removed outlier: 4.255A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   SER A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 264
    Processing helix  chain 'A' and resid 272 through 288
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 306 through 322
      removed outlier: 3.510A  pdb=" N   GLY A 321 " --> pdb=" O   ALA A 317 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A 322 " --> pdb=" O   PHE A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 337
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 3.517A  pdb=" N   PHE A 352 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ALA A 355 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 368 through 370
      No H-bonds generated for 'chain 'A' and resid 368 through 370'
    Processing helix  chain 'A' and resid 371 through 405
    Processing helix  chain 'A' and resid 409 through 434
      removed outlier: 3.536A  pdb=" N   MET A 430 " --> pdb=" O   CYS A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 474
      removed outlier: 4.116A  pdb=" N   ILE A 444 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   LEU A 445 " --> pdb=" O   VAL A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 502
      removed outlier: 4.372A  pdb=" N   ILE A 484 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
      Proline residue:  A 492  - end of helix
    Processing helix  chain 'A' and resid 511 through 515
      removed outlier: 3.689A  pdb=" N   PHE A 514 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 542
      removed outlier: 3.557A  pdb=" N   SER A 538 " --> pdb=" O   ILE A 534 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   CYS A 541 " --> pdb=" O   ILE A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 651
    Processing helix  chain 'A' and resid 654 through 682
      removed outlier: 3.760A  pdb=" N   GLY A 668 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 711
      removed outlier: 3.984A  pdb=" N   PHE A 701 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   GLY A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 5.345A  pdb=" N   PHE A 705 " --> pdb=" O   PHE A 701 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A 706 " --> pdb=" O   GLY A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 758
    Processing helix  chain 'A' and resid 762 through 767
    Processing helix  chain 'A' and resid 783 through 794
    Processing helix  chain 'A' and resid 798 through 812
    Processing helix  chain 'B' and resid 38 through 40
      No H-bonds generated for 'chain 'B' and resid 38 through 40'
    Processing helix  chain 'B' and resid 41 through 62
      removed outlier: 3.671A  pdb=" N   ALA B  45 " --> pdb=" O   ARG B  41 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA B  62 " --> pdb=" O   ILE B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 80
      removed outlier: 4.094A  pdb=" N   GLY B  72 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LEU B  73 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 92
      removed outlier: 3.526A  pdb=" N   ALA B  84 " --> pdb=" O   PHE B  80 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL B  92 " --> pdb=" O   LYS B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 124
      removed outlier: 3.887A  pdb=" N   LEU B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 141
      removed outlier: 3.704A  pdb=" N   PHE B 137 " --> pdb=" O   LYS B 133 " (cutoff:3.500A)
      Proline residue:  B 138  - end of helix
    Processing helix  chain 'B' and resid 150 through 158
    Processing helix  chain 'B' and resid 162 through 166
    Processing helix  chain 'B' and resid 167 through 196
      removed outlier: 3.694A  pdb=" N   ALA B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
      removed outlier: 3.554A  pdb=" N   ASN B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      Proline residue:  B 182  - end of helix
    Processing helix  chain 'B' and resid 203 through 216
    Processing helix  chain 'B' and resid 217 through 233
      removed outlier: 3.539A  pdb=" N   PHE B 221 " --> pdb=" O   ASN B 217 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL B 223 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 250
      removed outlier: 4.221A  pdb=" N   ASN B 243 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   PHE B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 264
      removed outlier: 3.651A  pdb=" N   LEU B 257 " --> pdb=" O   SER B 253 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   PHE B 258 " --> pdb=" O   GLY B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 288
    Processing helix  chain 'B' and resid 288 through 302
      removed outlier: 3.730A  pdb=" N   LEU B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 322
      removed outlier: 3.568A  pdb=" N   GLY B 321 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL B 322 " --> pdb=" O   PHE B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 337
    Processing helix  chain 'B' and resid 339 through 366
      removed outlier: 3.519A  pdb=" N   PHE B 352 " --> pdb=" O   VAL B 348 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ALA B 355 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      Proline residue:  B 356  - end of helix
      removed outlier: 3.581A  pdb=" N   THR B 366 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 370
      removed outlier: 3.763A  pdb=" N   MET B 370 " --> pdb=" O   PHE B 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 367 through 370'
    Processing helix  chain 'B' and resid 371 through 404
    Processing helix  chain 'B' and resid 409 through 434
      removed outlier: 3.511A  pdb=" N   CYS B 426 " --> pdb=" O   GLN B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 473
      removed outlier: 4.233A  pdb=" N   ILE B 444 " --> pdb=" O   PHE B 440 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   LEU B 445 " --> pdb=" O   VAL B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 502
      Proline residue:  B 492  - end of helix
    Processing helix  chain 'B' and resid 511 through 515
      removed outlier: 3.780A  pdb=" N   PHE B 514 " --> pdb=" O   ASP B 511 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   PHE B 515 " --> pdb=" O   SER B 512 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 511 through 515'
    Processing helix  chain 'B' and resid 517 through 541
      removed outlier: 3.529A  pdb=" N   THR B 527 " --> pdb=" O   THR B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 638
      removed outlier: 4.056A  pdb=" N   CYS B 638 " --> pdb=" O   SER B 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 639 through 651
      removed outlier: 3.824A  pdb=" N   LEU B 648 " --> pdb=" O   GLU B 644 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   GLN B 649 " --> pdb=" O   GLU B 645 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 682
      removed outlier: 3.828A  pdb=" N   GLY B 668 " --> pdb=" O   LEU B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 701
      removed outlier: 3.949A  pdb=" N   PHE B 701 " --> pdb=" O   ALA B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 702 through 711
      removed outlier: 3.679A  pdb=" N   ILE B 706 " --> pdb=" O   GLY B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 745 through 758
    Processing helix  chain 'B' and resid 758 through 764
      removed outlier: 3.945A  pdb=" N   ARG B 764 " --> pdb=" O   ASP B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 783 through 794
    Processing helix  chain 'B' and resid 798 through 812
    Processing sheet with id=AA1, first strand: chain 'A' and resid 781 through 782
    Processing sheet with id=AA2, first strand: chain 'B' and resid 781 through 782

    762 hydrogen bonds defined for protein.
    2253 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: 3.51

  Time building geometry restraints manager: 3.87 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1832
        1.33 -     1.45: 3016
        1.45 -     1.57: 6992
        1.57 -     1.69: 24
        1.69 -     1.81: 110
  Bond restraints: 11974
  Sorted by residual:
  bond pdb=" CA  SER B 383 "
       pdb=" CB  SER B 383 "
    ideal  model  delta    sigma   weight residual
    1.529  1.490  0.039 1.55e-02 4.16e+03 6.46e+00
  bond pdb=" N   PHE B 384 "
       pdb=" CA  PHE B 384 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.34e+00
  bond pdb=" N   ILE B 386 "
       pdb=" CA  ILE B 386 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.41e-02 5.03e+03 5.28e+00
  bond pdb=" N   SER B 387 "
       pdb=" CA  SER B 387 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.24e-02 6.50e+03 5.08e+00
  bond pdb=" N   LEU B 648 "
       pdb=" CA  LEU B 648 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.025 1.17e-02 7.31e+03 4.72e+00
  ... (remaining 11969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 15790
        2.02 -     4.05: 268
        4.05 -     6.07: 67
        6.07 -     8.10: 6
        8.10 -    10.12: 5
  Bond angle restraints: 16136
  Sorted by residual:
  angle pdb=" N   ILE B 386 "
        pdb=" CA  ILE B 386 "
        pdb=" C   ILE B 386 "
      ideal   model   delta    sigma   weight residual
     112.04  107.50    4.54 1.40e+00 5.10e-01 1.05e+01
  angle pdb=" CA  GLN B 649 "
        pdb=" CB  GLN B 649 "
        pdb=" CG  GLN B 649 "
      ideal   model   delta    sigma   weight residual
     114.10  120.35   -6.25 2.00e+00 2.50e-01 9.76e+00
  angle pdb=" CA  SER B 387 "
        pdb=" C   SER B 387 "
        pdb=" O   SER B 387 "
      ideal   model   delta    sigma   weight residual
     120.55  117.35    3.20 1.07e+00 8.73e-01 8.95e+00
  angle pdb=" N   SER B 383 "
        pdb=" CA  SER B 383 "
        pdb=" C   SER B 383 "
      ideal   model   delta    sigma   weight residual
     111.07  107.91    3.16 1.07e+00 8.73e-01 8.71e+00
  angle pdb=" CA  LEU A 533 "
        pdb=" CB  LEU A 533 "
        pdb=" CG  LEU A 533 "
      ideal   model   delta    sigma   weight residual
     116.30  126.42  -10.12 3.50e+00 8.16e-02 8.36e+00
  ... (remaining 16131 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.44: 7176
       35.44 -    70.87: 354
       70.87 -   106.30: 30
      106.30 -   141.74: 10
      141.74 -   177.17: 12
  Dihedral angle restraints: 7582
    sinusoidal: 3568
      harmonic: 4014
  Sorted by residual:
  dihedral pdb=" C17 P5S A 906 "
           pdb=" C20 P5S A 906 "
           pdb=" C21 P5S A 906 "
           pdb=" C22 P5S A 906 "
      ideal   model   delta sinusoidal    sigma   weight residual
      71.45 -111.38 -177.17     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CB  P5S A 909 "
           pdb=" OG  P5S A 909 "
           pdb=" P12 P5S A 909 "
           pdb=" O13 P5S A 909 "
      ideal   model   delta sinusoidal    sigma   weight residual
      47.21 -124.09  171.30     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" CB  P5S A 909 "
           pdb=" OG  P5S A 909 "
           pdb=" P12 P5S A 909 "
           pdb=" O16 P5S A 909 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.68  126.70  168.98     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 7579 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1605
       0.061 -    0.123: 220
       0.123 -    0.184: 14
       0.184 -    0.245: 1
       0.245 -    0.307: 4
  Chirality restraints: 1844
  Sorted by residual:
  chirality pdb=" C2  P5S B 908 "
            pdb=" C1  P5S B 908 "
            pdb=" C3  P5S B 908 "
            pdb=" O37 P5S B 908 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.29    0.31 2.00e-01 2.50e+01 2.35e+00
  chirality pdb=" C2  P5S A 906 "
            pdb=" C1  P5S A 906 "
            pdb=" C3  P5S A 906 "
            pdb=" O37 P5S A 906 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.29    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" C2  P5S A 909 "
            pdb=" C1  P5S A 909 "
            pdb=" C3  P5S A 909 "
            pdb=" O37 P5S A 909 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.31    0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 1841 not shown)

  Planarity restraints: 1888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 371 "   -0.036 5.00e-02 4.00e+02   5.53e-02 4.89e+00
        pdb=" N   PRO A 372 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 372 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 372 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 371 "   -0.034 5.00e-02 4.00e+02   5.19e-02 4.30e+00
        pdb=" N   PRO B 372 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO B 372 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 372 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B  55 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.86e+00
        pdb=" C   CYS B  55 "    0.034 2.00e-02 2.50e+03
        pdb=" O   CYS B  55 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   GLY B  56 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1885 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 951
        2.74 -     3.28: 12356
        3.28 -     3.82: 19917
        3.82 -     4.36: 23421
        4.36 -     4.90: 40147
  Nonbonded interactions: 96792
  Sorted by model distance:
  nonbonded pdb=" O   SER B 452 "
            pdb=" OG  SER B 456 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   HIS B 412 "
            pdb=" OG1 THR B 416 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   SER A 452 "
            pdb=" OG  SER A 456 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG  SER B 797 "
            pdb=" OD1 ASP B 798 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   LEU B 454 "
            pdb=" OG1 THR B 457 "
     model   vdw
     2.260 3.040
  ... (remaining 96787 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: 0.05
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 34 through 835)
  selection = (chain 'B' and resid 34 through 835)
}

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:             3.620
  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:          0.510
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     30.650
  Find NCS groups from input model:        0.570
  Set up NCS constraints:                  0.050
  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:3.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
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      :  0.004   0.076  11974  Z= 0.173
  Angle     :  0.682  10.120  16136  Z= 0.338
  Chirality :  0.044   0.307   1844
  Planarity :  0.004   0.055   1888
  Dihedral  : 21.146 177.175   4994
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 25.42 %
    Favored  : 74.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.23), residues: 1370
  helix:  0.98 (0.17), residues: 1028
  sheet:  None (None), residues: 0
  loop : -0.99 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 460 
 HIS   0.003   0.001   HIS A 758 
 PHE   0.032   0.001   PHE A 384 
 TYR   0.028   0.002   TYR B 320 
 ARG   0.003   0.000   ARG B 832 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12518 (  762)
  hydrogen bonds       : angle       5.91823 ( 2253)
  covalent geometry    : bond        0.00371 (11974)
  covalent geometry    : angle       0.68154 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 236
  time to evaluate  : 1.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  181 ASN cc_start: 0.7817 (t0) cc_final: 0.7608 (t0)
REVERT: A  189 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7659 (mm-30)
REVERT: A  444 ILE cc_start: 0.8836 (mm) cc_final: 0.8627 (mm)
REVERT: A  458 TYR cc_start: 0.7485 (m-10) cc_final: 0.6411 (m-10)
REVERT: A  749 MET cc_start: 0.8548 (ttm) cc_final: 0.8237 (ttp)
REVERT: B  189 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7637 (mm-30)
REVERT: B  193 TRP cc_start: 0.6806 (t60) cc_final: 0.6085 (t60)
REVERT: B  203 LYS cc_start: 0.6033 (mtpt) cc_final: 0.5566 (pttp)
REVERT: B  400 ILE cc_start: 0.7700 (mm) cc_final: 0.7482 (mm)
REVERT: B  451 TYR cc_start: 0.6793 (m-80) cc_final: 0.6377 (m-80)
REVERT: B  534 ILE cc_start: 0.8306 (mt) cc_final: 0.8068 (mm)
REVERT: B  657 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7452 (mtp85)
REVERT: B  752 GLN cc_start: 0.9250 (tp40) cc_final: 0.8895 (mm-40)
REVERT: B  825 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7411 (ptp-170)
  outliers start: 4
  outliers final: 0
  residues processed: 236
  average time/residue: 0.2109
  time to fit residues: 74.8794
Evaluate side-chains
  185 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    0.0770
   chunk 104 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 125 optimal weight:    0.5980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A  97 ASN
A 181 ASN
A 422 GLN
A 520 GLN
A 683 GLN
A 693 GLN
A 753 GLN
B  89 ASN
B 216 GLN
B 422 GLN
B 506 ASN
B 520 GLN
B 672 ASN
B 683 GLN
B 693 GLN
B 716 HIS
B 758 HIS
B 811 GLN

Total number of N/Q/H flips: 19

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.182968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.138832 restraints weight = 16080.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 2.00
r_work: 0.3585 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11974  Z= 0.139
  Angle     :  0.585  10.182  16136  Z= 0.293
  Chirality :  0.041   0.147   1844
  Planarity :  0.004   0.044   1888
  Dihedral  : 19.471 177.472   2506
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 20.93 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.23), residues: 1370
  helix:  1.36 (0.16), residues: 1048
  sheet:  None (None), residues: 0
  loop : -0.86 (0.33), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 460 
 HIS   0.004   0.001   HIS A 758 
 PHE   0.023   0.001   PHE A 221 
 TYR   0.018   0.001   TYR A 451 
 ARG   0.005   0.000   ARG B 759 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04771 (  762)
  hydrogen bonds       : angle       4.47298 ( 2253)
  covalent geometry    : bond        0.00309 (11974)
  covalent geometry    : angle       0.58493 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 199
  time to evaluate  : 1.513 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.7127 (t) cc_final: 0.6901 (m)
REVERT: A  181 ASN cc_start: 0.7552 (t160) cc_final: 0.6784 (t0)
REVERT: A  185 PHE cc_start: 0.8617 (m-10) cc_final: 0.8385 (m-80)
REVERT: A  189 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7492 (mm-30)
REVERT: A  458 TYR cc_start: 0.7622 (m-10) cc_final: 0.6494 (m-10)
REVERT: A  501 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8275 (mm)
REVERT: B  193 TRP cc_start: 0.6917 (t60) cc_final: 0.6247 (t60)
REVERT: B  203 LYS cc_start: 0.6061 (mtpt) cc_final: 0.5439 (pttp)
REVERT: B  367 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6315 (t80)
REVERT: B  451 TYR cc_start: 0.6825 (m-80) cc_final: 0.6395 (m-80)
REVERT: B  534 ILE cc_start: 0.8397 (mt) cc_final: 0.8161 (mm)
REVERT: B  657 ARG cc_start: 0.7758 (mtt90) cc_final: 0.7505 (mtp85)
REVERT: B  823 GLU cc_start: 0.6452 (tt0) cc_final: 0.6002 (tt0)
REVERT: B  825 ARG cc_start: 0.7898 (mtt90) cc_final: 0.7408 (mtt90)
  outliers start: 43
  outliers final: 19
  residues processed: 232
  average time/residue: 0.2312
  time to fit residues: 81.6971
Evaluate side-chains
  192 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 171
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLU
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain B residue  204 ILE
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  367 PHE
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  674 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0170
   chunk 136 optimal weight:    4.9990
   chunk 135 optimal weight:    0.8980
   chunk 85 optimal weight:    7.9990
   chunk 108 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
A 753 GLN
A 756 HIS
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 672 ASN
B 693 GLN
B 753 GLN
B 756 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.182004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.137984 restraints weight = 16199.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 1.98
r_work: 0.3571 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11974  Z= 0.142
  Angle     :  0.576   9.117  16136  Z= 0.291
  Chirality :  0.041   0.155   1844
  Planarity :  0.004   0.042   1888
  Dihedral  : 18.638 178.803   2506
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.18 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.23), residues: 1370
  helix:  1.42 (0.16), residues: 1054
  sheet:  None (None), residues: 0
  loop : -0.88 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 432 
 HIS   0.004   0.001   HIS A 758 
 PHE   0.025   0.001   PHE A 221 
 TYR   0.018   0.001   TYR A 451 
 ARG   0.007   0.000   ARG B 759 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04581 (  762)
  hydrogen bonds       : angle       4.30611 ( 2253)
  covalent geometry    : bond        0.00320 (11974)
  covalent geometry    : angle       0.57579 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 189
  time to evaluate  : 1.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.7276 (t) cc_final: 0.7068 (m)
REVERT: A  189 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7469 (mm-30)
REVERT: A  451 TYR cc_start: 0.6756 (m-80) cc_final: 0.6418 (m-80)
REVERT: A  458 TYR cc_start: 0.7813 (m-10) cc_final: 0.6554 (m-10)
REVERT: A  501 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8355 (mm)
REVERT: A  689 TYR cc_start: 0.7534 (t80) cc_final: 0.7220 (t80)
REVERT: B  189 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7878 (mm-30)
REVERT: B  193 TRP cc_start: 0.7017 (t60) cc_final: 0.6294 (t60)
REVERT: B  203 LYS cc_start: 0.6022 (mtpt) cc_final: 0.5382 (pttp)
REVERT: B  367 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6288 (t80)
REVERT: B  431 ILE cc_start: 0.8708 (mp) cc_final: 0.8418 (mp)
REVERT: B  451 TYR cc_start: 0.7021 (m-80) cc_final: 0.6592 (m-80)
REVERT: B  534 ILE cc_start: 0.8414 (mt) cc_final: 0.8193 (mm)
REVERT: B  657 ARG cc_start: 0.7819 (mtt90) cc_final: 0.7551 (mtp85)
REVERT: B  823 GLU cc_start: 0.6605 (tt0) cc_final: 0.6253 (tt0)
  outliers start: 42
  outliers final: 20
  residues processed: 222
  average time/residue: 0.2414
  time to fit residues: 83.5532
Evaluate side-chains
  196 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 1.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  299 GLU
Chi-restraints excluded: chain B residue  367 PHE
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  672 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9980
   chunk 119 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0870
   chunk 64 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.9762

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 693 GLN
A 753 GLN
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 672 ASN
B 753 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.180535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136493 restraints weight = 15996.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 1.96
r_work: 0.3561 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.3412 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11974  Z= 0.159
  Angle     :  0.573   8.655  16136  Z= 0.290
  Chirality :  0.041   0.157   1844
  Planarity :  0.004   0.039   1888
  Dihedral  : 18.123 177.882   2506
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 20.93 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.23), residues: 1370
  helix:  1.42 (0.16), residues: 1054
  sheet:  None (None), residues: 0
  loop : -0.88 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 432 
 HIS   0.010   0.001   HIS A 505 
 PHE   0.026   0.002   PHE A 221 
 TYR   0.017   0.001   TYR A 451 
 ARG   0.005   0.000   ARG B 759 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04541 (  762)
  hydrogen bonds       : angle       4.28927 ( 2253)
  covalent geometry    : bond        0.00373 (11974)
  covalent geometry    : angle       0.57281 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 187
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.7372 (t) cc_final: 0.7155 (m)
REVERT: A  189 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7566 (mm-30)
REVERT: A  444 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8534 (mm)
REVERT: A  451 TYR cc_start: 0.6784 (m-80) cc_final: 0.6375 (m-80)
REVERT: A  458 TYR cc_start: 0.7903 (m-10) cc_final: 0.6593 (m-10)
REVERT: A  501 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8395 (mm)
REVERT: A  516 TYR cc_start: 0.6722 (m-10) cc_final: 0.6461 (m-10)
REVERT: B  193 TRP cc_start: 0.7046 (t60) cc_final: 0.6282 (t60)
REVERT: B  203 LYS cc_start: 0.6026 (mtpt) cc_final: 0.5644 (tttm)
REVERT: B  367 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6041 (t80)
REVERT: B  431 ILE cc_start: 0.8703 (mp) cc_final: 0.8424 (mp)
REVERT: B  451 TYR cc_start: 0.7069 (m-80) cc_final: 0.6609 (m-80)
REVERT: B  640 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6519 (tt)
REVERT: B  644 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6991 (pp20)
REVERT: B  657 ARG cc_start: 0.7769 (mtt90) cc_final: 0.7406 (mtp85)
REVERT: B  752 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8777 (tp40)
REVERT: B  823 GLU cc_start: 0.6674 (tt0) cc_final: 0.6373 (tt0)
REVERT: B  830 PHE cc_start: 0.6904 (m-10) cc_final: 0.5909 (m-10)
  outliers start: 47
  outliers final: 29
  residues processed: 220
  average time/residue: 0.2146
  time to fit residues: 73.2865
Evaluate side-chains
  206 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  444 ILE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  299 GLU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  367 PHE
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  698 VAL
Chi-restraints excluded: chain B residue  757 TYR
Chi-restraints excluded: chain B residue  793 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0270
   chunk 95 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 127 optimal weight:    0.7980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 693 GLN
A 753 GLN
A 756 HIS
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 693 GLN
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 753 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.182523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.138580 restraints weight = 15978.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 1.99
r_work: 0.3575 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3426 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11974  Z= 0.129
  Angle     :  0.551   9.312  16136  Z= 0.277
  Chirality :  0.041   0.163   1844
  Planarity :  0.004   0.036   1888
  Dihedral  : 17.409 179.415   2506
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.93 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.23), residues: 1370
  helix:  1.58 (0.16), residues: 1052
  sheet:  None (None), residues: 0
  loop : -0.91 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 432 
 HIS   0.007   0.001   HIS A 505 
 PHE   0.024   0.001   PHE A 221 
 TYR   0.018   0.001   TYR A 451 
 ARG   0.005   0.000   ARG B 759 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04284 (  762)
  hydrogen bonds       : angle       4.18196 ( 2253)
  covalent geometry    : bond        0.00284 (11974)
  covalent geometry    : angle       0.55098 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 182
  time to evaluate  : 1.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.7339 (t) cc_final: 0.7126 (m)
REVERT: A  189 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7530 (mm-30)
REVERT: A  458 TYR cc_start: 0.7811 (m-10) cc_final: 0.6706 (m-10)
REVERT: A  501 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8406 (mm)
REVERT: B  193 TRP cc_start: 0.6983 (t60) cc_final: 0.6270 (t60)
REVERT: B  203 LYS cc_start: 0.6027 (mtpt) cc_final: 0.5641 (tttm)
REVERT: B  367 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.5888 (t80)
REVERT: B  431 ILE cc_start: 0.8714 (mp) cc_final: 0.8419 (mp)
REVERT: B  451 TYR cc_start: 0.6999 (m-80) cc_final: 0.6600 (m-80)
REVERT: B  640 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6631 (tt)
REVERT: B  657 ARG cc_start: 0.7724 (mtt90) cc_final: 0.7460 (mtp85)
REVERT: B  752 GLN cc_start: 0.9171 (mm-40) cc_final: 0.8591 (tp40)
REVERT: B  823 GLU cc_start: 0.6674 (tt0) cc_final: 0.6386 (tt0)
REVERT: B  830 PHE cc_start: 0.7000 (m-10) cc_final: 0.6147 (m-10)
  outliers start: 38
  outliers final: 25
  residues processed: 211
  average time/residue: 0.1946
  time to fit residues: 63.3397
Evaluate side-chains
  191 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  299 GLU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  367 PHE
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  640 LEU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  757 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 120 optimal weight:   20.0000
   chunk 82 optimal weight:    1.9990
   chunk 128 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 105 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 HIS
A 693 GLN
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 756 HIS
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 693 GLN
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 753 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.181307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.137019 restraints weight = 16189.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.00
r_work: 0.3573 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11974  Z= 0.142
  Angle     :  0.569   9.368  16136  Z= 0.286
  Chirality :  0.042   0.324   1844
  Planarity :  0.004   0.032   1888
  Dihedral  : 16.956 176.573   2506
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.68 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.23), residues: 1370
  helix:  1.56 (0.16), residues: 1046
  sheet:  None (None), residues: 0
  loop : -0.89 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 789 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.025   0.001   PHE A 221 
 TYR   0.017   0.001   TYR A 451 
 ARG   0.008   0.000   ARG A 764 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04328 (  762)
  hydrogen bonds       : angle       4.21867 ( 2253)
  covalent geometry    : bond        0.00327 (11974)
  covalent geometry    : angle       0.56949 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 168
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.7331 (t) cc_final: 0.7091 (m)
REVERT: A  451 TYR cc_start: 0.6741 (m-80) cc_final: 0.6397 (m-80)
REVERT: A  458 TYR cc_start: 0.7626 (m-10) cc_final: 0.6549 (m-10)
REVERT: B  189 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7790 (mm-30)
REVERT: B  193 TRP cc_start: 0.6862 (t60) cc_final: 0.6213 (t60)
REVERT: B  203 LYS cc_start: 0.6118 (mtpt) cc_final: 0.5746 (tttm)
REVERT: B  367 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.5898 (t80)
REVERT: B  431 ILE cc_start: 0.8712 (mp) cc_final: 0.8435 (mp)
REVERT: B  451 TYR cc_start: 0.6840 (m-80) cc_final: 0.6499 (m-80)
REVERT: B  644 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6961 (pp20)
REVERT: B  657 ARG cc_start: 0.7618 (mtt90) cc_final: 0.7402 (mtp85)
REVERT: B  752 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8556 (tp40)
REVERT: B  823 GLU cc_start: 0.6776 (tt0) cc_final: 0.6486 (tt0)
  outliers start: 41
  outliers final: 29
  residues processed: 201
  average time/residue: 0.1899
  time to fit residues: 59.1808
Evaluate side-chains
  194 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 163
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  299 GLU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  367 PHE
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  663 LEU
Chi-restraints excluded: chain B residue  757 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 56 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9980
   chunk 85 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 118 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 132 optimal weight:    0.0970
   chunk 64 optimal weight:    0.8980
   chunk 51 optimal weight:   20.0000
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 693 GLN
A 753 GLN
A 756 HIS
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 753 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.182201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.137977 restraints weight = 16075.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3717 rms_B_bonded: 2.01
r_work: 0.3570 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11974  Z= 0.131
  Angle     :  0.557   8.349  16136  Z= 0.281
  Chirality :  0.041   0.183   1844
  Planarity :  0.004   0.032   1888
  Dihedral  : 16.343 179.191   2506
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.01 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.23), residues: 1370
  helix:  1.58 (0.16), residues: 1054
  sheet:  None (None), residues: 0
  loop : -0.92 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 789 
 HIS   0.003   0.001   HIS A 758 
 PHE   0.024   0.001   PHE A 221 
 TYR   0.018   0.001   TYR A 451 
 ARG   0.009   0.000   ARG A 764 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04222 (  762)
  hydrogen bonds       : angle       4.16806 ( 2253)
  covalent geometry    : bond        0.00298 (11974)
  covalent geometry    : angle       0.55660 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 174
  time to evaluate  : 1.925 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.7288 (t) cc_final: 0.7068 (m)
REVERT: A  189 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7490 (mm-30)
REVERT: A  458 TYR cc_start: 0.7541 (m-10) cc_final: 0.6494 (m-10)
REVERT: B  189 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7767 (mm-30)
REVERT: B  193 TRP cc_start: 0.6860 (t60) cc_final: 0.6211 (t60)
REVERT: B  203 LYS cc_start: 0.6126 (mtpt) cc_final: 0.5780 (tttm)
REVERT: B  211 LEU cc_start: 0.7883 (mm) cc_final: 0.7511 (mp)
REVERT: B  367 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.5862 (t80)
REVERT: B  417 ASN cc_start: 0.8189 (m-40) cc_final: 0.7818 (t0)
REVERT: B  431 ILE cc_start: 0.8674 (mp) cc_final: 0.8395 (mp)
REVERT: B  451 TYR cc_start: 0.6766 (m-80) cc_final: 0.6427 (m-80)
REVERT: B  644 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7033 (pp20)
REVERT: B  657 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7384 (mtp85)
REVERT: B  752 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8571 (tp40)
REVERT: B  823 GLU cc_start: 0.6785 (tt0) cc_final: 0.6469 (tt0)
REVERT: B  825 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7383 (mtt90)
  outliers start: 36
  outliers final: 27
  residues processed: 203
  average time/residue: 0.2335
  time to fit residues: 72.2069
Evaluate side-chains
  197 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 168
  time to evaluate  : 1.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  400 ILE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain A residue  793 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  299 GLU
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  367 PHE
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  757 TYR
Chi-restraints excluded: chain B residue  790 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 8 optimal weight:    0.2980
   chunk 80 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0980
   chunk 113 optimal weight:    0.0040
   chunk 81 optimal weight:    0.7980
   chunk 90 optimal weight:    2.9990
   chunk 114 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.3192

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
A 693 GLN
A 753 GLN
A 756 HIS
B 693 GLN
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 753 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.184684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.141105 restraints weight = 16113.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.01
r_work: 0.3520 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11974  Z= 0.116
  Angle     :  0.553   9.154  16136  Z= 0.277
  Chirality :  0.040   0.181   1844
  Planarity :  0.004   0.033   1888
  Dihedral  : 15.467 170.638   2506
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.68 %
    Favored  : 75.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.23), residues: 1370
  helix:  1.68 (0.16), residues: 1056
  sheet:  None (None), residues: 0
  loop : -0.86 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 432 
 HIS   0.005   0.001   HIS A 756 
 PHE   0.022   0.001   PHE A 221 
 TYR   0.019   0.001   TYR A 451 
 ARG   0.008   0.000   ARG A 764 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  762)
  hydrogen bonds       : angle       4.09489 ( 2253)
  covalent geometry    : bond        0.00251 (11974)
  covalent geometry    : angle       0.55294 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 182
  time to evaluate  : 1.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.7204 (t) cc_final: 0.6994 (m)
REVERT: A  189 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7366 (mm-30)
REVERT: A  211 LEU cc_start: 0.7332 (mp) cc_final: 0.7127 (mp)
REVERT: A  458 TYR cc_start: 0.7417 (m-10) cc_final: 0.6650 (m-10)
REVERT: B  189 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7766 (mm-30)
REVERT: B  193 TRP cc_start: 0.6806 (t60) cc_final: 0.6162 (t60)
REVERT: B  203 LYS cc_start: 0.6115 (mtpt) cc_final: 0.5748 (tttm)
REVERT: B  367 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.5769 (t80)
REVERT: B  417 ASN cc_start: 0.8321 (m-40) cc_final: 0.8068 (t0)
REVERT: B  431 ILE cc_start: 0.8641 (mp) cc_final: 0.8365 (mp)
REVERT: B  451 TYR cc_start: 0.6713 (m-80) cc_final: 0.6484 (m-80)
REVERT: B  499 LEU cc_start: 0.8568 (tp) cc_final: 0.8232 (mt)
REVERT: B  644 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7145 (pp20)
REVERT: B  657 ARG cc_start: 0.7656 (mtt90) cc_final: 0.7369 (mtp85)
REVERT: B  823 GLU cc_start: 0.6528 (tt0) cc_final: 0.6294 (tt0)
  outliers start: 36
  outliers final: 23
  residues processed: 211
  average time/residue: 0.2109
  time to fit residues: 67.2581
Evaluate side-chains
  191 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  299 GLU
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  367 PHE
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  757 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 118 optimal weight:    0.9990
   chunk 99 optimal weight:    0.0470
   chunk 9 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 52 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9980
   chunk 65 optimal weight:    9.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.7482

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 693 GLN
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 753 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.182029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.137916 restraints weight = 16159.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.02
r_work: 0.3589 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11974  Z= 0.142
  Angle     :  0.587   9.995  16136  Z= 0.296
  Chirality :  0.042   0.258   1844
  Planarity :  0.004   0.033   1888
  Dihedral  : 15.232 166.793   2506
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.09 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.23), residues: 1370
  helix:  1.60 (0.16), residues: 1052
  sheet:  None (None), residues: 0
  loop : -1.00 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 396 
 HIS   0.004   0.001   HIS A 758 
 PHE   0.023   0.001   PHE A 221 
 TYR   0.017   0.001   TYR A 451 
 ARG   0.014   0.001   ARG A 764 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  762)
  hydrogen bonds       : angle       4.21119 ( 2253)
  covalent geometry    : bond        0.00332 (11974)
  covalent geometry    : angle       0.58735 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 173
  time to evaluate  : 1.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.7300 (t) cc_final: 0.7072 (m)
REVERT: A  501 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8551 (mm)
REVERT: B  189 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7755 (mm-30)
REVERT: B  193 TRP cc_start: 0.6872 (t60) cc_final: 0.6193 (t60)
REVERT: B  203 LYS cc_start: 0.6109 (mtpt) cc_final: 0.5816 (tttm)
REVERT: B  211 LEU cc_start: 0.7946 (mm) cc_final: 0.7560 (mp)
REVERT: B  367 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.5857 (t80)
REVERT: B  417 ASN cc_start: 0.8418 (m-40) cc_final: 0.8098 (t0)
REVERT: B  431 ILE cc_start: 0.8673 (mp) cc_final: 0.8400 (mp)
REVERT: B  499 LEU cc_start: 0.8521 (tp) cc_final: 0.8257 (mt)
REVERT: B  644 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7282 (pp20)
REVERT: B  657 ARG cc_start: 0.7659 (mtt90) cc_final: 0.7352 (mtp85)
REVERT: B  823 GLU cc_start: 0.6751 (tt0) cc_final: 0.6462 (tt0)
REVERT: B  825 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7385 (mtt90)
REVERT: B  830 PHE cc_start: 0.6955 (m-10) cc_final: 0.6614 (m-10)
  outliers start: 33
  outliers final: 26
  residues processed: 199
  average time/residue: 0.2013
  time to fit residues: 61.9743
Evaluate side-chains
  195 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 166
  time to evaluate  : 1.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  501 ILE
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain A residue  674 SER
Chi-restraints excluded: chain A residue  690 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  367 PHE
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  757 TYR
Chi-restraints excluded: chain B residue  790 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 51 optimal weight:    0.0770
   chunk 77 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 110 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 126 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   chunk 115 optimal weight:    0.0270
   chunk 52 optimal weight:    3.9990
   chunk 72 optimal weight:    0.4980
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.184350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.140699 restraints weight = 15973.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.02
r_work: 0.3622 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11974  Z= 0.121
  Angle     :  0.572  10.640  16136  Z= 0.287
  Chirality :  0.042   0.265   1844
  Planarity :  0.004   0.050   1888
  Dihedral  : 14.896 169.861   2506
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.34 %
    Favored  : 75.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.23), residues: 1370
  helix:  1.69 (0.16), residues: 1052
  sheet:  None (None), residues: 0
  loop : -0.95 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 789 
 HIS   0.013   0.001   HIS A 756 
 PHE   0.021   0.001   PHE A 221 
 TYR   0.018   0.001   TYR B 451 
 ARG   0.012   0.000   ARG A 764 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  762)
  hydrogen bonds       : angle       4.14890 ( 2253)
  covalent geometry    : bond        0.00267 (11974)
  covalent geometry    : angle       0.57244 (16136)

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

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

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2740 Ramachandran restraints generated.
    1370 Oldfield, 0 Emsley, 1370 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 173
  time to evaluate  : 1.886 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.7205 (t) cc_final: 0.6987 (m)
REVERT: A  189 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7425 (mm-30)
REVERT: B  193 TRP cc_start: 0.6754 (t60) cc_final: 0.6142 (t60)
REVERT: B  203 LYS cc_start: 0.6213 (mtpt) cc_final: 0.5819 (tttm)
REVERT: B  211 LEU cc_start: 0.7901 (mm) cc_final: 0.7490 (mp)
REVERT: B  367 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.5723 (t80)
REVERT: B  417 ASN cc_start: 0.8358 (m-40) cc_final: 0.8065 (t0)
REVERT: B  431 ILE cc_start: 0.8640 (mp) cc_final: 0.8369 (mp)
REVERT: B  644 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7260 (pp20)
REVERT: B  657 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7344 (mtp85)
REVERT: B  752 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8514 (tp40)
REVERT: B  756 HIS cc_start: 0.7866 (m-70) cc_final: 0.7542 (m-70)
REVERT: B  823 GLU cc_start: 0.6621 (tt0) cc_final: 0.6352 (tt0)
REVERT: B  825 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7376 (mtt90)
  outliers start: 30
  outliers final: 25
  residues processed: 197
  average time/residue: 0.2310
  time to fit residues: 70.0727
Evaluate side-chains
  190 residues out of total 1204 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 1.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  334 THR
Chi-restraints excluded: chain A residue  340 VAL
Chi-restraints excluded: chain A residue  367 PHE
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  496 VAL
Chi-restraints excluded: chain A residue  669 LEU
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  149 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  195 ASP
Chi-restraints excluded: chain B residue  239 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  367 PHE
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  644 GLU
Chi-restraints excluded: chain B residue  654 GLN
Chi-restraints excluded: chain B residue  757 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 80 optimal weight:    0.1980
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 106 optimal weight:    0.4980
   chunk 81 optimal weight:    0.6980
   chunk 8 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 86 optimal weight:    0.2980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 181 ASN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 756 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 693 GLN
** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.183988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.140536 restraints weight = 16039.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.00
r_work: 0.3622 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11974  Z= 0.125
  Angle     :  0.602  13.746  16136  Z= 0.298
  Chirality :  0.043   0.240   1844
  Planarity :  0.004   0.049   1888
  Dihedral  : 14.708 171.659   2506
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 22.59 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.23), residues: 1370
  helix:  1.76 (0.16), residues: 1034
  sheet:  None (None), residues: 0
  loop : -0.75 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 432 
 HIS   0.014   0.001   HIS A 756 
 PHE   0.023   0.001   PHE A 221 
 TYR   0.017   0.001   TYR A 451 
 ARG   0.013   0.000   ARG A 764 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04082 (  762)
  hydrogen bonds       : angle       4.15443 ( 2253)
  covalent geometry    : bond        0.00282 (11974)
  covalent geometry    : angle       0.60191 (16136)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6808.80 seconds
wall clock time: 123 minutes 51.48 seconds (7431.48 seconds total)