Starting phenix.real_space_refine
on Wed Sep 17 19:31:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x1h_32941/09_2025/7x1h_32941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x1h_32941/09_2025/7x1h_32941.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.96
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x1h_32941/09_2025/7x1h_32941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x1h_32941/09_2025/7x1h_32941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x1h_32941/09_2025/7x1h_32941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x1h_32941/09_2025/7x1h_32941.cif"
  }
  resolution = 2.96
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    7084      2.51       5
     N    1770      2.21       5
     O    1846      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10760
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 676, 5380
          Classifications: {'peptide': 676}
          Link IDs: {'PTRANS': 28, 'TRANS': 647}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 5380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 676, 5380
          Classifications: {'peptide': 676}
          Link IDs: {'PTRANS': 28, 'TRANS': 647}
          Chain breaks: 6
  Time building chain proxies: 2.59, per 1000 atoms: 0.24
  Number of scatterers: 10760
  At special positions: 0
  Unit cell: (100.983, 105.909, 102.625, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    1846      8.00
     N    1770      7.00
     C    7084      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 328.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2556

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 5 sheets defined
      66.9% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 132 through 137
    Processing helix  chain 'A' and resid 147 through 160
      removed outlier: 3.700A  pdb=" N   PHE A 159 " --> pdb=" O   MET A 155 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ALA A 160 " --> pdb=" O   LEU A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 180
    Processing helix  chain 'A' and resid 265 through 277
    Processing helix  chain 'A' and resid 278 through 288
      removed outlier: 3.603A  pdb=" N   GLN A 283 " --> pdb=" O   ILE A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 306
    Processing helix  chain 'A' and resid 343 through 354
    Processing helix  chain 'A' and resid 356 through 363
      removed outlier: 3.579A  pdb=" N   PHE A 361 " --> pdb=" O   TYR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 401
      Proline residue:  A 389  - end of helix
    Processing helix  chain 'A' and resid 406 through 424
    Processing helix  chain 'A' and resid 435 through 453
    Processing helix  chain 'A' and resid 455 through 477
    Processing helix  chain 'A' and resid 478 through 486
      removed outlier: 3.614A  pdb=" N   LEU A 481 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 518
      removed outlier: 3.501A  pdb=" N   GLU A 491 " --> pdb=" O   LYS A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 594
    Processing helix  chain 'A' and resid 595 through 597
      No H-bonds generated for 'chain 'A' and resid 595 through 597'
    Processing helix  chain 'A' and resid 601 through 611
      removed outlier: 3.710A  pdb=" N   SER A 609 " --> pdb=" O   ARG A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 626
      removed outlier: 3.531A  pdb=" N   ILE A 615 " --> pdb=" O   CYS A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 684
    Processing helix  chain 'A' and resid 685 through 689
    Processing helix  chain 'A' and resid 696 through 713
      removed outlier: 3.624A  pdb=" N   PHE A 713 " --> pdb=" O   GLY A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 732
      removed outlier: 3.820A  pdb=" N   LEU A 727 " --> pdb=" O   PRO A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 768
    Processing helix  chain 'A' and resid 769 through 772
    Processing helix  chain 'A' and resid 780 through 795
    Processing helix  chain 'A' and resid 799 through 807
    Processing helix  chain 'A' and resid 811 through 815
    Processing helix  chain 'A' and resid 819 through 824
    Processing helix  chain 'A' and resid 825 through 848
    Processing helix  chain 'A' and resid 851 through 856
    Processing helix  chain 'A' and resid 857 through 877
      removed outlier: 3.581A  pdb=" N   ILE A 861 " --> pdb=" O   ILE A 857 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ILE A 866 " --> pdb=" O   MET A 862 " (cutoff:3.500A)
      Proline residue:  A 867  - end of helix
      removed outlier: 4.297A  pdb=" N   LEU A 873 " --> pdb=" O   ARG A 869 " (cutoff:3.500A)
      Proline residue:  A 874  - end of helix
    Processing helix  chain 'A' and resid 878 through 887
    Processing helix  chain 'B' and resid 132 through 137
    Processing helix  chain 'B' and resid 147 through 160
      removed outlier: 3.652A  pdb=" N   PHE B 159 " --> pdb=" O   MET B 155 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ALA B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'B' and resid 265 through 277
    Processing helix  chain 'B' and resid 278 through 288
      removed outlier: 3.604A  pdb=" N   GLN B 283 " --> pdb=" O   ILE B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 306
    Processing helix  chain 'B' and resid 343 through 354
    Processing helix  chain 'B' and resid 356 through 363
      removed outlier: 3.574A  pdb=" N   PHE B 361 " --> pdb=" O   TYR B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 401
      Proline residue:  B 389  - end of helix
    Processing helix  chain 'B' and resid 406 through 424
    Processing helix  chain 'B' and resid 435 through 453
    Processing helix  chain 'B' and resid 455 through 477
    Processing helix  chain 'B' and resid 478 through 486
      removed outlier: 3.611A  pdb=" N   LEU B 481 " --> pdb=" O   ASN B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 518
    Processing helix  chain 'B' and resid 570 through 594
    Processing helix  chain 'B' and resid 595 through 597
      No H-bonds generated for 'chain 'B' and resid 595 through 597'
    Processing helix  chain 'B' and resid 601 through 611
    Processing helix  chain 'B' and resid 612 through 626
    Processing helix  chain 'B' and resid 654 through 684
    Processing helix  chain 'B' and resid 685 through 689
    Processing helix  chain 'B' and resid 696 through 713
      removed outlier: 3.624A  pdb=" N   PHE B 713 " --> pdb=" O   GLY B 709 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 723 through 732
      removed outlier: 3.826A  pdb=" N   LEU B 727 " --> pdb=" O   PRO B 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 755 through 768
    Processing helix  chain 'B' and resid 769 through 772
    Processing helix  chain 'B' and resid 780 through 795
    Processing helix  chain 'B' and resid 799 through 807
    Processing helix  chain 'B' and resid 811 through 815
    Processing helix  chain 'B' and resid 819 through 824
    Processing helix  chain 'B' and resid 825 through 848
    Processing helix  chain 'B' and resid 851 through 856
    Processing helix  chain 'B' and resid 857 through 877
      removed outlier: 3.572A  pdb=" N   ILE B 861 " --> pdb=" O   ILE B 857 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ILE B 866 " --> pdb=" O   MET B 862 " (cutoff:3.500A)
      Proline residue:  B 867  - end of helix
      removed outlier: 4.309A  pdb=" N   LEU B 873 " --> pdb=" O   ARG B 869 " (cutoff:3.500A)
      Proline residue:  B 874  - end of helix
    Processing helix  chain 'B' and resid 878 through 887
    Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 143
      removed outlier: 5.469A  pdb=" N   VAL A 235 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
      removed outlier: 6.495A  pdb=" N   ARG A 248 " --> pdb=" O   LEU A 234 " (cutoff:3.500A)
      removed outlier: 13.208A  pdb=" N   VAL A 247 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 11.909A  pdb=" N   GLN A 211 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.657A  pdb=" N   PHE A 249 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   SER A 213 " --> pdb=" O   PHE A 249 " (cutoff:3.500A)
      removed outlier: 8.564A  pdb=" N   ILE A 251 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LEU A 215 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   VAL A 253 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   ILE A 217 " --> pdb=" O   VAL A 253 " (cutoff:3.500A)
      removed outlier: 8.086A  pdb=" N   ALA A 255 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   CYS A 219 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   GLY A 200 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      removed outlier: 9.074A  pdb=" N   SER A 213 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 11.851A  pdb=" N   ILE A 198 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
      removed outlier: 9.752A  pdb=" N   LEU A 215 " --> pdb=" O   ASP A 196 " (cutoff:3.500A)
      removed outlier: 10.947A  pdb=" N   ASP A 196 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU B 107 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU A 107 " --> pdb=" O   LEU B 115 " (cutoff:3.500A)
      removed outlier: 10.837A  pdb=" N   ASP B 196 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 9.641A  pdb=" N   LEU B 215 " --> pdb=" O   ASP B 196 " (cutoff:3.500A)
      removed outlier: 11.863A  pdb=" N   ILE B 198 " --> pdb=" O   SER B 213 " (cutoff:3.500A)
      removed outlier: 9.152A  pdb=" N   SER B 213 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLY B 200 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      removed outlier: 13.199A  pdb=" N   VAL B 247 " --> pdb=" O   ARG B 209 " (cutoff:3.500A)
      removed outlier: 12.011A  pdb=" N   GLN B 211 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 8.713A  pdb=" N   PHE B 249 " --> pdb=" O   GLN B 211 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   SER B 213 " --> pdb=" O   PHE B 249 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   ILE B 251 " --> pdb=" O   SER B 213 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   LEU B 215 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   VAL B 253 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ILE B 217 " --> pdb=" O   VAL B 253 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ALA B 255 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   CYS B 219 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 234 " (cutoff:3.500A)
      removed outlier: 5.492A  pdb=" N   VAL B 235 " --> pdb=" O   ASN B 142 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 432 through 433
    Processing sheet with id=AA3, first strand: chain 'A' and resid 733 through 740
      removed outlier: 6.742A  pdb=" N   LEU A 734 " --> pdb=" O   VAL A 749 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 432 through 433
    Processing sheet with id=AA5, first strand: chain 'B' and resid 733 through 740
      removed outlier: 6.745A  pdb=" N   LEU B 734 " --> pdb=" O   VAL B 749 " (cutoff:3.500A)

    688 hydrogen bonds defined for protein.
    1962 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.92

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2309
        1.33 -     1.45: 2352
        1.45 -     1.57: 6245
        1.57 -     1.69: 0
        1.69 -     1.81: 98
  Bond restraints: 11004
  Sorted by residual:
  bond pdb=" CA  GLN A 238 "
       pdb=" C   GLN A 238 "
    ideal  model  delta    sigma   weight residual
    1.522  1.473  0.050 1.20e-02 6.94e+03 1.72e+01
  bond pdb=" C   ILE B 251 "
       pdb=" O   ILE B 251 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.026 1.08e-02 8.57e+03 5.74e+00
  bond pdb=" C   ASP B 360 "
       pdb=" O   ASP B 360 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.17e-02 7.31e+03 4.54e+00
  bond pdb=" C   ASP A 360 "
       pdb=" O   ASP A 360 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.17e-02 7.31e+03 4.42e+00
  bond pdb=" C   PRO A 816 "
       pdb=" O   PRO A 816 "
    ideal  model  delta    sigma   weight residual
    1.240  1.217  0.023 1.12e-02 7.97e+03 4.25e+00
  ... (remaining 10999 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 14646
        1.70 -     3.40: 225
        3.40 -     5.10: 48
        5.10 -     6.80: 13
        6.80 -     8.50: 2
  Bond angle restraints: 14934
  Sorted by residual:
  angle pdb=" N   CYS B 245 "
        pdb=" CA  CYS B 245 "
        pdb=" C   CYS B 245 "
      ideal   model   delta    sigma   weight residual
     112.54  119.16   -6.62 1.22e+00 6.72e-01 2.94e+01
  angle pdb=" N   THR A 362 "
        pdb=" CA  THR A 362 "
        pdb=" C   THR A 362 "
      ideal   model   delta    sigma   weight residual
     112.59  118.28   -5.69 1.22e+00 6.72e-01 2.18e+01
  angle pdb=" N   THR B 362 "
        pdb=" CA  THR B 362 "
        pdb=" C   THR B 362 "
      ideal   model   delta    sigma   weight residual
     112.26  118.22   -5.96 1.32e+00 5.74e-01 2.04e+01
  angle pdb=" N   VAL B 247 "
        pdb=" CA  VAL B 247 "
        pdb=" C   VAL B 247 "
      ideal   model   delta    sigma   weight residual
     109.34  117.45   -8.11 2.08e+00 2.31e-01 1.52e+01
  angle pdb=" N   ASP B 360 "
        pdb=" CA  ASP B 360 "
        pdb=" C   ASP B 360 "
      ideal   model   delta    sigma   weight residual
     111.28  107.19    4.09 1.09e+00 8.42e-01 1.41e+01
  ... (remaining 14929 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.27: 5805
       16.27 -    32.53: 587
       32.53 -    48.80: 110
       48.80 -    65.07: 16
       65.07 -    81.33: 8
  Dihedral angle restraints: 6526
    sinusoidal: 2574
      harmonic: 3952
  Sorted by residual:
  dihedral pdb=" C   PHE A 361 "
           pdb=" N   PHE A 361 "
           pdb=" CA  PHE A 361 "
           pdb=" CB  PHE A 361 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.92    8.32     0      2.50e+00 1.60e-01 1.11e+01
  dihedral pdb=" C   PHE B 361 "
           pdb=" N   PHE B 361 "
           pdb=" CA  PHE B 361 "
           pdb=" CB  PHE B 361 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.79    8.19     0      2.50e+00 1.60e-01 1.07e+01
  dihedral pdb=" CB  LYS B 512 "
           pdb=" CG  LYS B 512 "
           pdb=" CD  LYS B 512 "
           pdb=" CE  LYS B 512 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.60   59.60     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 6523 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1564
       0.065 -    0.129: 179
       0.129 -    0.194: 15
       0.194 -    0.259: 2
       0.259 -    0.323: 4
  Chirality restraints: 1764
  Sorted by residual:
  chirality pdb=" CA  PHE A 361 "
            pdb=" N   PHE A 361 "
            pdb=" C   PHE A 361 "
            pdb=" CB  PHE A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CA  PHE B 361 "
            pdb=" N   PHE B 361 "
            pdb=" C   PHE B 361 "
            pdb=" CB  PHE B 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  PHE A 354 "
            pdb=" N   PHE A 354 "
            pdb=" C   PHE A 354 "
            pdb=" CB  PHE A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1761 not shown)

  Planarity restraints: 1828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 213 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.23e+00
        pdb=" C   SER B 213 "    0.047 2.00e-02 2.50e+03
        pdb=" O   SER B 213 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   TRP B 214 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 774 "    0.038 5.00e-02 4.00e+02   5.78e-02 5.34e+00
        pdb=" N   PRO B 775 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO B 775 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 775 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 774 "   -0.038 5.00e-02 4.00e+02   5.71e-02 5.21e+00
        pdb=" N   PRO A 775 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO A 775 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 775 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1825 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1409
        2.75 -     3.29: 10665
        3.29 -     3.83: 18273
        3.83 -     4.36: 21592
        4.36 -     4.90: 38037
  Nonbonded interactions: 89976
  Sorted by model distance:
  nonbonded pdb=" O   CYS B 386 "
            pdb=" OG1 THR B 390 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   CYS A 386 "
            pdb=" OG1 THR A 390 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   LEU A 600 "
            pdb=" NH1 ARG A 605 "
     model   vdw
     2.261 3.120
  nonbonded pdb=" NE2 GLN B 414 "
            pdb=" O   LEU B 432 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" NE2 GLN A 414 "
            pdb=" O   LEU A 432 "
     model   vdw
     2.271 3.120
  ... (remaining 89971 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.550
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  11004  Z= 0.177
  Angle     :  0.564   8.498  14934  Z= 0.328
  Chirality :  0.042   0.323   1764
  Planarity :  0.004   0.058   1828
  Dihedral  : 13.096  81.334   3970
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.26 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.24), residues: 1324
  helix:  2.33 (0.18), residues: 848
  sheet:  0.18 (0.42), residues: 108
  loop :  0.20 (0.35), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 822 
 TYR   0.014   0.001   TYR B 357 
 PHE   0.019   0.001   PHE A 846 
 TRP   0.006   0.001   TRP A 515 
 HIS   0.003   0.001   HIS B 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11004)
  covalent geometry    : angle       0.56449 (14934)
  hydrogen bonds       : bond        0.12385 (  688)
  hydrogen bonds       : angle       4.62633 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 268
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A  175 LEU cc_start: 0.7450 (mp) cc_final: 0.7189 (tt)
REVERT: A  267 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6479 (pt0)
REVERT: A  354 PHE cc_start: 0.8632 (t80) cc_final: 0.8406 (t80)
REVERT: A  477 PHE cc_start: 0.8225 (m-80) cc_final: 0.7900 (m-10)
REVERT: B  175 LEU cc_start: 0.7469 (mp) cc_final: 0.7175 (tt)
REVERT: B  354 PHE cc_start: 0.8657 (t80) cc_final: 0.8415 (t80)
REVERT: B  477 PHE cc_start: 0.8222 (m-80) cc_final: 0.7949 (m-10)
  outliers start: 2
  outliers final: 1
  residues processed: 270
  average time/residue: 0.6048
  time to fit residues: 175.6683
Evaluate side-chains
  163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  868 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.5980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 243 ASN
B 649 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.128532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.103267 restraints weight = 12900.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.93
r_work: 0.2986 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  11004  Z= 0.233
  Angle     :  0.653   7.820  14934  Z= 0.328
  Chirality :  0.045   0.168   1764
  Planarity :  0.005   0.043   1828
  Dihedral  :  4.255  18.675   1464
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 12.59 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.23), residues: 1324
  helix:  1.72 (0.18), residues: 844
  sheet:  0.15 (0.42), residues: 112
  loop : -0.25 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 233 
 TYR   0.013   0.002   TYR A 441 
 PHE   0.020   0.002   PHE B 620 
 TRP   0.015   0.002   TRP A 466 
 HIS   0.010   0.002   HIS B 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 (11004)
  covalent geometry    : angle       0.65292 (14934)
  hydrogen bonds       : bond        0.05017 (  688)
  hydrogen bonds       : angle       4.28540 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 175
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 THR cc_start: 0.8220 (m) cc_final: 0.7694 (p)
REVERT: A  175 LEU cc_start: 0.7663 (mp) cc_final: 0.7088 (tt)
REVERT: A  178 MET cc_start: 0.7502 (mtt) cc_final: 0.7176 (mtt)
REVERT: A  221 MET cc_start: 0.5705 (mtp) cc_final: 0.5396 (mmt)
REVERT: A  267 GLU cc_start: 0.7707 (mm-30) cc_final: 0.6621 (pt0)
REVERT: A  289 ARG cc_start: 0.7578 (mmt180) cc_final: 0.7247 (mmt-90)
REVERT: A  354 PHE cc_start: 0.8538 (t80) cc_final: 0.8289 (t80)
REVERT: A  521 HIS cc_start: 0.7769 (m170) cc_final: 0.7543 (m170)
REVERT: A  687 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7562 (pm20)
REVERT: A  878 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6554 (mp0)
REVERT: A  881 TYR cc_start: 0.7542 (m-10) cc_final: 0.7156 (m-80)
REVERT: B  154 THR cc_start: 0.8211 (m) cc_final: 0.7682 (p)
REVERT: B  175 LEU cc_start: 0.7629 (mp) cc_final: 0.7046 (tt)
REVERT: B  267 GLU cc_start: 0.7666 (mm-30) cc_final: 0.6583 (pt0)
REVERT: B  289 ARG cc_start: 0.7553 (mmt180) cc_final: 0.7220 (mmt-90)
REVERT: B  354 PHE cc_start: 0.8539 (t80) cc_final: 0.8282 (t80)
REVERT: B  521 HIS cc_start: 0.7788 (m170) cc_final: 0.7560 (m170)
REVERT: B  662 MET cc_start: 0.8512 (ttm) cc_final: 0.8145 (ttm)
REVERT: B  878 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6492 (mp0)
REVERT: B  881 TYR cc_start: 0.7523 (m-10) cc_final: 0.7085 (m-80)
  outliers start: 34
  outliers final: 6
  residues processed: 201
  average time/residue: 0.5166
  time to fit residues: 113.1653
Evaluate side-chains
  155 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 146
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  878 GLU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  878 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 124 optimal weight:    0.4980
   chunk 128 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 11 optimal weight:    0.1980
   chunk 43 optimal weight:    1.9990
   chunk 115 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 300 HIS
A 593 GLN
B 142 ASN
B 228 HIS
B 300 HIS
B 593 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.125810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.100627 restraints weight = 12969.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.90
r_work: 0.2983 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11004  Z= 0.134
  Angle     :  0.502   5.528  14934  Z= 0.259
  Chirality :  0.039   0.150   1764
  Planarity :  0.004   0.039   1828
  Dihedral  :  3.929  16.677   1462
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 14.90 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.75 (0.23), residues: 1324
  helix:  1.90 (0.18), residues: 836
  sheet:  0.32 (0.42), residues: 112
  loop : -0.18 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 233 
 TYR   0.010   0.001   TYR A 441 
 PHE   0.019   0.001   PHE B 620 
 TRP   0.006   0.001   TRP A 462 
 HIS   0.005   0.001   HIS B 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (11004)
  covalent geometry    : angle       0.50240 (14934)
  hydrogen bonds       : bond        0.04225 (  688)
  hydrogen bonds       : angle       4.05472 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 154
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  154 THR cc_start: 0.8183 (m) cc_final: 0.7715 (p)
REVERT: A  221 MET cc_start: 0.5729 (mtp) cc_final: 0.5418 (mtt)
REVERT: A  289 ARG cc_start: 0.7587 (mmt180) cc_final: 0.7248 (mmt-90)
REVERT: A  354 PHE cc_start: 0.8647 (t80) cc_final: 0.8354 (t80)
REVERT: A  521 HIS cc_start: 0.7803 (m170) cc_final: 0.7559 (m170)
REVERT: A  662 MET cc_start: 0.8384 (ttm) cc_final: 0.8010 (ttm)
REVERT: A  687 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7560 (pm20)
REVERT: A  881 TYR cc_start: 0.7521 (m-10) cc_final: 0.7088 (m-80)
REVERT: B  154 THR cc_start: 0.8178 (m) cc_final: 0.7696 (p)
REVERT: B  289 ARG cc_start: 0.7582 (mmt180) cc_final: 0.7242 (mmt-90)
REVERT: B  354 PHE cc_start: 0.8657 (t80) cc_final: 0.8360 (t80)
REVERT: B  521 HIS cc_start: 0.7802 (m170) cc_final: 0.7548 (m170)
REVERT: B  662 MET cc_start: 0.8387 (ttm) cc_final: 0.8027 (ttm)
REVERT: B  878 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7165 (mp0)
REVERT: B  881 TYR cc_start: 0.7475 (m-10) cc_final: 0.7078 (m-80)
  outliers start: 43
  outliers final: 19
  residues processed: 185
  average time/residue: 0.5425
  time to fit residues: 108.8479
Evaluate side-chains
  161 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  370 LYS
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  878 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 114 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 99 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 111 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 228 HIS
B 142 ASN
** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.140393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.117587 restraints weight = 12249.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.63
r_work: 0.3209 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11004  Z= 0.171
  Angle     :  0.531   6.811  14934  Z= 0.270
  Chirality :  0.041   0.160   1764
  Planarity :  0.004   0.039   1828
  Dihedral  :  3.998  17.548   1462
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 14.73 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.23), residues: 1324
  helix:  1.81 (0.18), residues: 836
  sheet:  0.30 (0.41), residues: 112
  loop : -0.20 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 157 
 TYR   0.012   0.001   TYR A 441 
 PHE   0.019   0.002   PHE B 620 
 TRP   0.006   0.001   TRP A 586 
 HIS   0.007   0.001   HIS A 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (11004)
  covalent geometry    : angle       0.53063 (14934)
  hydrogen bonds       : bond        0.04412 (  688)
  hydrogen bonds       : angle       4.13047 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 148
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  154 THR cc_start: 0.8452 (m) cc_final: 0.7961 (p)
REVERT: A  354 PHE cc_start: 0.8760 (t80) cc_final: 0.8484 (t80)
REVERT: A  647 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7881 (ttt)
REVERT: A  662 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8203 (ttm)
REVERT: A  687 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7798 (pm20)
REVERT: A  793 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8724 (mp)
REVERT: A  881 TYR cc_start: 0.7647 (m-10) cc_final: 0.7252 (m-80)
REVERT: B  154 THR cc_start: 0.8452 (m) cc_final: 0.7967 (p)
REVERT: B  354 PHE cc_start: 0.8755 (t80) cc_final: 0.8485 (t80)
REVERT: B  477 PHE cc_start: 0.8325 (m-80) cc_final: 0.8037 (m-10)
REVERT: B  504 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8329 (mp)
REVERT: B  662 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8216 (ttm)
REVERT: B  793 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8754 (mp)
REVERT: B  881 TYR cc_start: 0.7656 (m-10) cc_final: 0.7344 (m-80)
  outliers start: 47
  outliers final: 17
  residues processed: 176
  average time/residue: 0.5284
  time to fit residues: 101.3495
Evaluate side-chains
  155 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 128 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 102 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
B 142 ASN
** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 649 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.137678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.115550 restraints weight = 12322.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.61
r_work: 0.3217 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.3592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11004  Z= 0.140
  Angle     :  0.509   7.493  14934  Z= 0.259
  Chirality :  0.040   0.155   1764
  Planarity :  0.004   0.041   1828
  Dihedral  :  3.916  16.700   1462
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 16.18 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.23), residues: 1324
  helix:  1.84 (0.18), residues: 834
  sheet:  0.36 (0.42), residues: 112
  loop : -0.20 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 157 
 TYR   0.012   0.001   TYR A 441 
 PHE   0.019   0.001   PHE A 620 
 TRP   0.008   0.001   TRP A 515 
 HIS   0.005   0.001   HIS B 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (11004)
  covalent geometry    : angle       0.50857 (14934)
  hydrogen bonds       : bond        0.04177 (  688)
  hydrogen bonds       : angle       4.07093 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 132
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A  154 THR cc_start: 0.8393 (m) cc_final: 0.7935 (p)
REVERT: A  354 PHE cc_start: 0.8750 (t80) cc_final: 0.8491 (t80)
REVERT: A  647 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7830 (ttt)
REVERT: A  662 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8197 (ttm)
REVERT: A  687 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7816 (pm20)
REVERT: A  793 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8745 (mp)
REVERT: A  881 TYR cc_start: 0.7669 (m-10) cc_final: 0.7241 (m-80)
REVERT: B  154 THR cc_start: 0.8399 (m) cc_final: 0.7943 (p)
REVERT: B  354 PHE cc_start: 0.8735 (t80) cc_final: 0.8474 (t80)
REVERT: B  647 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7850 (ttt)
REVERT: B  662 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8225 (ttm)
REVERT: B  793 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8750 (mp)
REVERT: B  881 TYR cc_start: 0.7653 (m-10) cc_final: 0.7383 (m-80)
  outliers start: 50
  outliers final: 22
  residues processed: 160
  average time/residue: 0.5295
  time to fit residues: 92.4442
Evaluate side-chains
  160 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  370 LYS
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  647 MET
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 649 GLN
B 800 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.138298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.115863 restraints weight = 12372.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.63
r_work: 0.3201 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11004  Z= 0.170
  Angle     :  0.530   6.914  14934  Z= 0.269
  Chirality :  0.041   0.162   1764
  Planarity :  0.004   0.041   1828
  Dihedral  :  3.990  17.329   1462
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 16.01 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.23), residues: 1324
  helix:  1.71 (0.18), residues: 842
  sheet:  0.20 (0.42), residues: 114
  loop : -0.31 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 153 
 TYR   0.012   0.001   TYR A 441 
 PHE   0.018   0.001   PHE B 620 
 TRP   0.009   0.001   TRP B 515 
 HIS   0.006   0.001   HIS A 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (11004)
  covalent geometry    : angle       0.53014 (14934)
  hydrogen bonds       : bond        0.04395 (  688)
  hydrogen bonds       : angle       4.14349 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 135
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A  106 VAL cc_start: 0.7980 (m) cc_final: 0.7728 (p)
REVERT: A  154 THR cc_start: 0.8408 (m) cc_final: 0.7887 (p)
REVERT: A  354 PHE cc_start: 0.8746 (t80) cc_final: 0.8488 (t80)
REVERT: A  633 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8383 (ptm)
REVERT: A  647 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.7871 (ttt)
REVERT: A  662 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8217 (ttm)
REVERT: A  687 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7820 (pm20)
REVERT: A  793 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8747 (mp)
REVERT: A  881 TYR cc_start: 0.7648 (m-10) cc_final: 0.7283 (m-80)
REVERT: B  106 VAL cc_start: 0.8006 (m) cc_final: 0.7741 (p)
REVERT: B  154 THR cc_start: 0.8430 (m) cc_final: 0.7941 (p)
REVERT: B  354 PHE cc_start: 0.8736 (t80) cc_final: 0.8477 (t80)
REVERT: B  477 PHE cc_start: 0.8370 (m-80) cc_final: 0.8124 (m-10)
REVERT: B  504 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8293 (mp)
REVERT: B  647 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7875 (ttt)
REVERT: B  662 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8268 (ttm)
REVERT: B  793 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8758 (mp)
REVERT: B  881 TYR cc_start: 0.7655 (m-10) cc_final: 0.7389 (m-80)
  outliers start: 50
  outliers final: 24
  residues processed: 165
  average time/residue: 0.4890
  time to fit residues: 88.6450
Evaluate side-chains
  164 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  687 GLU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  512 LYS
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  647 MET
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 118 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN
** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 649 GLN
B 800 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.135165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.112522 restraints weight = 12300.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 1.63
r_work: 0.3113 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  11004  Z= 0.213
  Angle     :  0.592   9.947  14934  Z= 0.294
  Chirality :  0.042   0.171   1764
  Planarity :  0.005   0.040   1828
  Dihedral  :  4.154  18.628   1462
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 16.70 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.23), residues: 1324
  helix:  1.59 (0.18), residues: 834
  sheet: -0.03 (0.42), residues: 112
  loop : -0.35 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 270 
 TYR   0.012   0.001   TYR B 441 
 PHE   0.020   0.002   PHE B 858 
 TRP   0.009   0.002   TRP A 515 
 HIS   0.007   0.001   HIS B 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (11004)
  covalent geometry    : angle       0.59223 (14934)
  hydrogen bonds       : bond        0.04749 (  688)
  hydrogen bonds       : angle       4.28240 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 136
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A  106 VAL cc_start: 0.7791 (m) cc_final: 0.7500 (p)
REVERT: A  154 THR cc_start: 0.8076 (m) cc_final: 0.7449 (p)
REVERT: A  155 MET cc_start: 0.8797 (mtm) cc_final: 0.8520 (mtm)
REVERT: A  292 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7105 (mp0)
REVERT: A  354 PHE cc_start: 0.8595 (t80) cc_final: 0.8297 (t80)
REVERT: A  441 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8252 (m-80)
REVERT: A  633 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8304 (ptm)
REVERT: A  647 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7855 (ttt)
REVERT: A  662 MET cc_start: 0.8463 (ttm) cc_final: 0.8081 (ttm)
REVERT: A  793 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8455 (mp)
REVERT: A  881 TYR cc_start: 0.7441 (m-10) cc_final: 0.7078 (m-80)
REVERT: B  106 VAL cc_start: 0.7787 (m) cc_final: 0.7504 (p)
REVERT: B  154 THR cc_start: 0.8098 (m) cc_final: 0.7517 (p)
REVERT: B  354 PHE cc_start: 0.8602 (t80) cc_final: 0.8304 (t80)
REVERT: B  441 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8218 (m-80)
REVERT: B  504 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7800 (mp)
REVERT: B  647 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7867 (ttt)
REVERT: B  662 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8075 (ttm)
REVERT: B  793 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8472 (mp)
REVERT: B  881 TYR cc_start: 0.7403 (m-10) cc_final: 0.7165 (m-80)
  outliers start: 47
  outliers final: 22
  residues processed: 165
  average time/residue: 0.4719
  time to fit residues: 85.6760
Evaluate side-chains
  163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 132
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  441 TYR
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  647 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  441 TYR
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  647 MET
Chi-restraints excluded: chain B residue  655 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  865 MET
Chi-restraints excluded: chain B residue  876 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 131 optimal weight:    0.5980
   chunk 120 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 68 optimal weight:    0.2980
   chunk 103 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN
** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 639 ASN
B 649 GLN
B 800 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.138093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115721 restraints weight = 12242.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.62
r_work: 0.3210 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.3976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11004  Z= 0.132
  Angle     :  0.521   9.252  14934  Z= 0.259
  Chirality :  0.039   0.153   1764
  Planarity :  0.004   0.038   1828
  Dihedral  :  3.953  16.516   1462
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 17.29 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.23), residues: 1324
  helix:  1.73 (0.18), residues: 842
  sheet:  0.34 (0.45), residues: 110
  loop : -0.25 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 270 
 TYR   0.011   0.001   TYR B 441 
 PHE   0.018   0.001   PHE A 620 
 TRP   0.010   0.001   TRP A 515 
 HIS   0.004   0.001   HIS A 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (11004)
  covalent geometry    : angle       0.52128 (14934)
  hydrogen bonds       : bond        0.04142 (  688)
  hydrogen bonds       : angle       4.12756 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 134
  time to evaluate  : 0.456 
Fit side-chains
REVERT: A  106 VAL cc_start: 0.7966 (m) cc_final: 0.7732 (p)
REVERT: A  154 THR cc_start: 0.8322 (m) cc_final: 0.7794 (p)
REVERT: A  155 MET cc_start: 0.9009 (mtm) cc_final: 0.8738 (mtm)
REVERT: A  278 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7221 (t70)
REVERT: A  354 PHE cc_start: 0.8694 (t80) cc_final: 0.8453 (t80)
REVERT: A  633 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8385 (ptm)
REVERT: A  662 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8194 (ttm)
REVERT: A  793 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8694 (mp)
REVERT: B  106 VAL cc_start: 0.8016 (m) cc_final: 0.7768 (p)
REVERT: B  154 THR cc_start: 0.8342 (m) cc_final: 0.7845 (p)
REVERT: B  155 MET cc_start: 0.9006 (mtm) cc_final: 0.8737 (mtm)
REVERT: B  354 PHE cc_start: 0.8682 (t80) cc_final: 0.8425 (t80)
REVERT: B  662 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8204 (ttm)
REVERT: B  793 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8716 (mp)
REVERT: B  881 TYR cc_start: 0.7589 (m-10) cc_final: 0.7278 (m-80)
  outliers start: 41
  outliers final: 22
  residues processed: 161
  average time/residue: 0.4542
  time to fit residues: 80.9119
Evaluate side-chains
  159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  278 ASP
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  344 LYS
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  875 ARG
Chi-restraints excluded: chain B residue  876 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 110 optimal weight:    0.6980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 639 ASN
A 741 ASN
B 478 ASN
B 639 ASN
B 649 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.135003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.112519 restraints weight = 12285.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 1.62
r_work: 0.3139 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11004  Z= 0.212
  Angle     :  0.592   9.384  14934  Z= 0.292
  Chirality :  0.042   0.174   1764
  Planarity :  0.005   0.038   1828
  Dihedral  :  4.122  18.397   1462
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 17.47 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.23), residues: 1324
  helix:  1.63 (0.18), residues: 836
  sheet:  0.14 (0.44), residues: 112
  loop : -0.40 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 270 
 TYR   0.011   0.001   TYR B 722 
 PHE   0.020   0.002   PHE B 858 
 TRP   0.014   0.002   TRP B 515 
 HIS   0.007   0.001   HIS B 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (11004)
  covalent geometry    : angle       0.59168 (14934)
  hydrogen bonds       : bond        0.04684 (  688)
  hydrogen bonds       : angle       4.26543 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  106 VAL cc_start: 0.7953 (m) cc_final: 0.7703 (p)
REVERT: A  292 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7368 (mp0)
REVERT: A  354 PHE cc_start: 0.8708 (t80) cc_final: 0.8428 (t80)
REVERT: A  633 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8384 (ptm)
REVERT: A  662 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8298 (ttm)
REVERT: A  793 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8686 (mp)
REVERT: B  106 VAL cc_start: 0.8003 (m) cc_final: 0.7728 (p)
REVERT: B  292 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7363 (mp0)
REVERT: B  354 PHE cc_start: 0.8724 (t80) cc_final: 0.8441 (t80)
REVERT: B  662 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8318 (ttm)
REVERT: B  793 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8709 (mp)
REVERT: B  881 TYR cc_start: 0.7594 (m-10) cc_final: 0.7279 (m-80)
  outliers start: 39
  outliers final: 24
  residues processed: 157
  average time/residue: 0.4730
  time to fit residues: 81.6948
Evaluate side-chains
  160 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  395 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  344 LYS
Chi-restraints excluded: chain B residue  395 SER
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    0.5980
   chunk 59 optimal weight:    0.3980
   chunk 75 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 93 optimal weight:    0.5980
   chunk 115 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 124 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 741 ASN
B 639 ASN
B 649 GLN
B 741 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.137989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115683 restraints weight = 12126.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.60
r_work: 0.3185 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11004  Z= 0.135
  Angle     :  0.531  10.349  14934  Z= 0.263
  Chirality :  0.039   0.153   1764
  Planarity :  0.004   0.038   1828
  Dihedral  :  3.966  16.613   1462
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 17.98 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.23), residues: 1324
  helix:  1.73 (0.18), residues: 842
  sheet:  0.38 (0.46), residues: 110
  loop : -0.32 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 270 
 TYR   0.011   0.001   TYR B 441 
 PHE   0.018   0.001   PHE A 620 
 TRP   0.014   0.001   TRP A 515 
 HIS   0.004   0.001   HIS A 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (11004)
  covalent geometry    : angle       0.53107 (14934)
  hydrogen bonds       : bond        0.04159 (  688)
  hydrogen bonds       : angle       4.14625 ( 1962)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A  106 VAL cc_start: 0.7995 (m) cc_final: 0.7776 (p)
REVERT: A  292 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7320 (mp0)
REVERT: A  354 PHE cc_start: 0.8674 (t80) cc_final: 0.8420 (t80)
REVERT: A  633 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8410 (ptm)
REVERT: A  662 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8202 (ttm)
REVERT: A  793 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8687 (mp)
REVERT: B  106 VAL cc_start: 0.8021 (m) cc_final: 0.7781 (p)
REVERT: B  278 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7149 (t70)
REVERT: B  354 PHE cc_start: 0.8672 (t80) cc_final: 0.8418 (t80)
REVERT: B  662 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8215 (ttm)
REVERT: B  793 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8717 (mp)
REVERT: B  881 TYR cc_start: 0.7589 (m-10) cc_final: 0.7260 (m-80)
  outliers start: 33
  outliers final: 24
  residues processed: 158
  average time/residue: 0.4703
  time to fit residues: 81.9346
Evaluate side-chains
  162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  433 LEU
Chi-restraints excluded: chain A residue  434 THR
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  512 LYS
Chi-restraints excluded: chain A residue  573 THR
Chi-restraints excluded: chain A residue  597 SER
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  633 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  662 MET
Chi-restraints excluded: chain A residue  749 VAL
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  876 ILE
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  278 ASP
Chi-restraints excluded: chain B residue  344 LYS
Chi-restraints excluded: chain B residue  433 LEU
Chi-restraints excluded: chain B residue  434 THR
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  573 THR
Chi-restraints excluded: chain B residue  597 SER
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  662 MET
Chi-restraints excluded: chain B residue  749 VAL
Chi-restraints excluded: chain B residue  793 LEU
Chi-restraints excluded: chain B residue  838 LEU
Chi-restraints excluded: chain B residue  876 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 114 optimal weight:    1.9990
   chunk 132 optimal weight:    0.3980
   chunk 99 optimal weight:    0.8980
   chunk 107 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 51 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 741 ASN
B 639 ASN
B 649 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.136460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.114565 restraints weight = 12244.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.58
r_work: 0.3172 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11004  Z= 0.140
  Angle     :  0.542  10.369  14934  Z= 0.269
  Chirality :  0.040   0.173   1764
  Planarity :  0.004   0.038   1828
  Dihedral  :  3.943  16.574   1462
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 17.98 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.23), residues: 1324
  helix:  1.76 (0.18), residues: 842
  sheet:  0.47 (0.46), residues: 110
  loop : -0.32 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 270 
 TYR   0.011   0.001   TYR B 441 
 PHE   0.018   0.001   PHE A 620 
 TRP   0.014   0.001   TRP B 515 
 HIS   0.005   0.001   HIS B 719 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (11004)
  covalent geometry    : angle       0.54229 (14934)
  hydrogen bonds       : bond        0.04157 (  688)
  hydrogen bonds       : angle       4.11824 ( 1962)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3485.35 seconds
wall clock time: 60 minutes 19.57 seconds (3619.57 seconds total)