Starting phenix.real_space_refine
on Sat Aug 23 05:36:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ibw_35347/08_2025/8ibw_35347.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ibw_35347/08_2025/8ibw_35347.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2025/8ibw_35347.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2025/8ibw_35347.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2025/8ibw_35347.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ibw_35347/08_2025/8ibw_35347.map"
  }
  resolution = 3.6
  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=   0.002 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     125      5.49       5
     S      38      5.16       5
     C    5750      2.51       5
     N    1874      2.21       5
     O    2059      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9848
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 891
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
    Chain: "B"
      Number of atoms: 872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 872
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
    Chain: "C"
      Number of atoms: 7250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 922, 7250
          Classifications: {'peptide': 922}
          Link IDs: {'PTRANS': 44, 'TRANS': 877}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 5, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "D"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 833
          Classifications: {'RNA': 39}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 15}
          Link IDs: {'rna2p': 6, 'rna3p': 32}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1794  SG  CYS C 114      13.182  85.010  80.553  1.00 94.26           S
  ATOM   1820  SG  CYS C 117      12.830  83.352  84.085  1.00 94.75           S
  ATOM   7643  SG  CYS C 934      46.425  52.273 131.118  1.00104.45           S
  ATOM   7669  SG  CYS C 938      49.604  51.093 132.882  1.00108.40           S
  ATOM   7774  SG  CYS C 951      49.287  50.685 129.072  1.00 96.27           S

  Time building chain proxies: 2.69, per 1000 atoms: 0.27
  Number of scatterers: 9848
  At special positions: 0
  Unit cell: (99.9089, 118.573, 152.608, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      38     16.00
     P     125     15.00
     O    2059      8.00
     N    1874      7.00
     C    5750      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 279.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C1201 "
        pdb="ZN    ZN C1201 " - pdb=" NE2 HIS C 130 "
        pdb="ZN    ZN C1201 " - pdb=" NE2 HIS C 135 "
        pdb="ZN    ZN C1201 " - pdb=" SG  CYS C 114 "
        pdb="ZN    ZN C1201 " - pdb=" SG  CYS C 117 "
      pdb="  ZN C1202 "
        pdb="ZN    ZN C1202 " - pdb=" NE2 HIS C 946 "
        pdb="ZN    ZN C1202 " - pdb=" SG  CYS C 938 "
        pdb="ZN    ZN C1202 " - pdb=" SG  CYS C 934 "
        pdb="ZN    ZN C1202 " - pdb=" SG  CYS C 951 "
      Number of angles added : 5


  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1698

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 10 sheets defined
      60.2% alpha, 5.4% beta
      46 base pairs and 77 stacking pairs defined.
    Time for finding SS restraints: 1.48
  Creating SS restraints...
    Processing helix  chain 'C' and resid 123 through 135
    Processing helix  chain 'C' and resid 135 through 143
      removed outlier: 3.616A  pdb=" N   THR C 139 " --> pdb=" O   HIS C 135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 172
    Processing helix  chain 'C' and resid 175 through 183
      removed outlier: 4.023A  pdb=" N   GLY C 181 " --> pdb=" O   GLY C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 184 through 187
      removed outlier: 4.470A  pdb=" N   GLY C 187 " --> pdb=" O   PRO C 184 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 184 through 187'
    Processing helix  chain 'C' and resid 189 through 198
      removed outlier: 3.656A  pdb=" N   LYS C 194 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 199 through 214
    Processing helix  chain 'C' and resid 261 through 283
    Processing helix  chain 'C' and resid 306 through 322
    Processing helix  chain 'C' and resid 324 through 334
      removed outlier: 3.612A  pdb=" N   ALA C 328 " --> pdb=" O   CYS C 324 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 343 through 357
      removed outlier: 6.173A  pdb=" N   THR C 349 " --> pdb=" O   GLU C 345 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   TYR C 350 " --> pdb=" O   GLU C 346 " (cutoff:3.500A)
      Proline residue:  C 353  - end of helix
    Processing helix  chain 'C' and resid 365 through 373
    Processing helix  chain 'C' and resid 392 through 399
    Processing helix  chain 'C' and resid 413 through 420
      removed outlier: 3.520A  pdb=" N   VAL C 420 " --> pdb=" O   GLN C 416 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 436
    Processing helix  chain 'C' and resid 439 through 444
      removed outlier: 3.609A  pdb=" N   GLN C 444 " --> pdb=" O   ILE C 441 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 460
      No H-bonds generated for 'chain 'C' and resid 458 through 460'
    Processing helix  chain 'C' and resid 469 through 487
      removed outlier: 3.595A  pdb=" N   ILE C 478 " --> pdb=" O   HIS C 474 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU C 479 " --> pdb=" O   PHE C 475 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 501 through 520
    Processing helix  chain 'C' and resid 532 through 536
      removed outlier: 3.513A  pdb=" N   ASP C 535 " --> pdb=" O   LYS C 532 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR C 536 " --> pdb=" O   ALA C 533 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 532 through 536'
    Processing helix  chain 'C' and resid 538 through 549
      removed outlier: 4.345A  pdb=" N   GLU C 544 " --> pdb=" O   GLU C 540 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU C 545 " --> pdb=" O   ALA C 541 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 552 through 565
    Processing helix  chain 'C' and resid 592 through 608
      removed outlier: 3.603A  pdb=" N   ASN C 598 " --> pdb=" O   PRO C 594 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL C 599 " --> pdb=" O   ILE C 595 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   VAL C 600 " --> pdb=" O   LEU C 596 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU C 608 " --> pdb=" O   ILE C 604 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 636 through 655
    Processing helix  chain 'C' and resid 719 through 730
    Processing helix  chain 'C' and resid 733 through 744
    Processing helix  chain 'C' and resid 744 through 756
      removed outlier: 4.234A  pdb=" N   GLY C 752 " --> pdb=" O   ARG C 748 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 759 through 779
    Processing helix  chain 'C' and resid 785 through 791
      removed outlier: 4.210A  pdb=" N   TYR C 789 " --> pdb=" O   PRO C 785 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   HIS C 790 " --> pdb=" O   LYS C 786 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 802 through 817
      Proline residue:  C 808  - end of helix
      removed outlier: 4.478A  pdb=" N   GLY C 817 " --> pdb=" O   ARG C 813 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 818 through 821
    Processing helix  chain 'C' and resid 823 through 831
      removed outlier: 3.714A  pdb=" N   LYS C 831 " --> pdb=" O   ARG C 827 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 832 through 849
    Processing helix  chain 'C' and resid 861 through 870
    Processing helix  chain 'C' and resid 872 through 877
      removed outlier: 4.599A  pdb=" N   GLU C 877 " --> pdb=" O   VAL C 873 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 885 through 889
      removed outlier: 3.908A  pdb=" N   THR C 888 " --> pdb=" O   PRO C 885 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 899 through 911
    Processing helix  chain 'C' and resid 916 through 921
    Processing helix  chain 'C' and resid 943 through 950
    Processing helix  chain 'C' and resid 953 through 974
      removed outlier: 4.421A  pdb=" N   GLY C 957 " --> pdb=" O   ARG C 953 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA C 972 " --> pdb=" O   PHE C 968 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   MET C 973 " --> pdb=" O   VAL C 969 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1018 through 1032
      removed outlier: 3.614A  pdb=" N   LYS C1029 " --> pdb=" O   GLU C1025 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   TYR C1030 " --> pdb=" O   LYS C1026 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1034 through 1045
    Processing helix  chain 'C' and resid 1048 through 1052
      removed outlier: 3.651A  pdb=" N   VAL C1052 " --> pdb=" O   ALA C1049 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1066 through 1076
    Processing helix  chain 'C' and resid 1080 through 1105
      removed outlier: 3.797A  pdb=" N   LEU C1084 " --> pdb=" O   ARG C1080 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL C1087 " --> pdb=" O   THR C1083 " (cutoff:3.500A)
      Proline residue:  C1088  - end of helix
    Processing sheet with id=AA1, first strand: chain 'C' and resid 112 through 113
      removed outlier: 3.763A  pdb=" N   TRP C 112 " --> pdb=" O   PHE C 121 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 448 through 451
    Processing sheet with id=AA3, first strand: chain 'C' and resid 629 through 634
    Processing sheet with id=AA4, first strand: chain 'C' and resid 567 through 568
    Processing sheet with id=AA5, first strand: chain 'C' and resid 571 through 572
    Processing sheet with id=AA6, first strand: chain 'C' and resid 614 through 616
    Processing sheet with id=AA7, first strand: chain 'C' and resid 701 through 702
    Processing sheet with id=AA8, first strand: chain 'C' and resid 851 through 852
    Processing sheet with id=AA9, first strand: chain 'C' and resid 981 through 982
    Processing sheet with id=AB1, first strand: chain 'C' and resid 1007 through 1013
      removed outlier: 5.932A  pdb=" N   ILE C1007 " --> pdb=" O   THR C1055 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   CYS C1057 " --> pdb=" O   ILE C1007 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ASP C1009 " --> pdb=" O   CYS C1057 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   ILE C1059 " --> pdb=" O   ASP C1009 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   GLN C1011 " --> pdb=" O   ILE C1059 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    371 hydrogen bonds defined for protein.
    1068 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      121 hydrogen bonds
      242 hydrogen bond angles
      0 basepair planarities
      46 basepair parallelities
      77 stacking parallelities
  Total time for adding SS restraints: 2.04

  Time building geometry restraints manager: 1.14 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: 2673
        1.33 -     1.45: 2366
        1.45 -     1.57: 4964
        1.57 -     1.70: 245
        1.70 -     1.82: 54
  Bond restraints: 10302
  Sorted by residual:
  bond pdb=" CA  LEU C 344 "
       pdb=" C   LEU C 344 "
    ideal  model  delta    sigma   weight residual
    1.524  1.484  0.040 1.27e-02 6.20e+03 9.77e+00
  bond pdb=" N   GLY C 111 "
       pdb=" CA  GLY C 111 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.16e+00
  bond pdb=" CA  VAL C 340 "
       pdb=" C   VAL C 340 "
    ideal  model  delta    sigma   weight residual
    1.523  1.497  0.026 1.27e-02 6.20e+03 4.10e+00
  bond pdb=" CA  GLY C 341 "
       pdb=" C   GLY C 341 "
    ideal  model  delta    sigma   weight residual
    1.514  1.486  0.028 1.41e-02 5.03e+03 4.01e+00
  bond pdb=" C4'   G D 244 "
       pdb=" O4'   G D 244 "
    ideal  model  delta    sigma   weight residual
    1.454  1.429  0.025 1.50e-02 4.44e+03 2.73e+00
  ... (remaining 10297 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 14121
        2.04 -     4.08: 302
        4.08 -     6.12: 36
        6.12 -     8.16: 8
        8.16 -    10.19: 3
  Bond angle restraints: 14470
  Sorted by residual:
  angle pdb=" N   LEU C 344 "
        pdb=" CA  LEU C 344 "
        pdb=" C   LEU C 344 "
      ideal   model   delta    sigma   weight residual
     111.07  100.88   10.19 1.07e+00 8.73e-01 9.08e+01
  angle pdb=" CA  GLU C 200 "
        pdb=" CB  GLU C 200 "
        pdb=" CG  GLU C 200 "
      ideal   model   delta    sigma   weight residual
     114.10  121.60   -7.50 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" O4'   G D 244 "
        pdb=" C4'   G D 244 "
        pdb=" C3'   G D 244 "
      ideal   model   delta    sigma   weight residual
     106.10  102.40    3.70 1.00e+00 1.00e+00 1.37e+01
  angle pdb=" C4'   G D 244 "
        pdb=" O4'   G D 244 "
        pdb=" C1'   G D 244 "
      ideal   model   delta    sigma   weight residual
     109.70  106.00    3.70 1.00e+00 1.00e+00 1.37e+01
  angle pdb=" CB  MET C1097 "
        pdb=" CG  MET C1097 "
        pdb=" SD  MET C1097 "
      ideal   model   delta    sigma   weight residual
     112.70  122.73  -10.03 3.00e+00 1.11e-01 1.12e+01
  ... (remaining 14465 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.59: 5324
       32.59 -    65.18: 666
       65.18 -    97.77: 42
       97.77 -   130.36: 1
      130.36 -   162.95: 3
  Dihedral angle restraints: 6036
    sinusoidal: 3404
      harmonic: 2632
  Sorted by residual:
  dihedral pdb=" O4'   G D 244 "
           pdb=" C4'   G D 244 "
           pdb=" C3'   G D 244 "
           pdb=" C2'   G D 244 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -40.21   64.21     1      8.00e+00 1.56e-02 8.47e+01
  dihedral pdb=" C5'   G D 244 "
           pdb=" C4'   G D 244 "
           pdb=" C3'   G D 244 "
           pdb=" O3'   G D 244 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   85.24   61.76     1      8.00e+00 1.56e-02 7.90e+01
  dihedral pdb=" C4'   G D 244 "
           pdb=" C3'   G D 244 "
           pdb=" C2'   G D 244 "
           pdb=" C1'   G D 244 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   20.94  -55.94     1      8.00e+00 1.56e-02 6.60e+01
  ... (remaining 6033 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1403
       0.058 -    0.115: 211
       0.115 -    0.173: 18
       0.173 -    0.231: 0
       0.231 -    0.289: 1
  Chirality restraints: 1633
  Sorted by residual:
  chirality pdb=" CA  GLU C 200 "
            pdb=" N   GLU C 200 "
            pdb=" C   GLU C 200 "
            pdb=" CB  GLU C 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CB  ILE C 746 "
            pdb=" CA  ILE C 746 "
            pdb=" CG1 ILE C 746 "
            pdb=" CG2 ILE C 746 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.48e-01
  chirality pdb=" CA  SER C 343 "
            pdb=" N   SER C 343 "
            pdb=" C   SER C 343 "
            pdb=" CB  SER C 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.46e-01
  ... (remaining 1630 not shown)

  Planarity restraints: 1419
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 503 "   -0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   LEU C 503 "    0.059 2.00e-02 2.50e+03
        pdb=" O   LEU C 503 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLU C 504 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 904 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.18e+00
        pdb=" C   VAL C 904 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   VAL C 904 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLN C 905 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D 123 "   -0.025 2.00e-02 2.50e+03   1.55e-02 6.59e+00
        pdb=" N9    A D 123 "    0.042 2.00e-02 2.50e+03
        pdb=" C8    A D 123 "    0.000 2.00e-02 2.50e+03
        pdb=" N7    A D 123 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5    A D 123 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D 123 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6    A D 123 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    A D 123 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    A D 123 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    A D 123 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    A D 123 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1416 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 119
        2.59 -     3.17: 8555
        3.17 -     3.75: 17113
        3.75 -     4.32: 21764
        4.32 -     4.90: 33206
  Nonbonded interactions: 80757
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 989 "
            pdb=" OE1 GLU C1035 "
     model   vdw
     2.018 3.040
  nonbonded pdb=" OD1 ASP C 515 "
            pdb=" NZ  LYS C 519 "
     model   vdw
     2.049 3.120
  nonbonded pdb=" OP1  DT B  49 "
            pdb=" NH1 ARG C 188 "
     model   vdw
     2.151 3.120
  nonbonded pdb=" NH2 ARG C 443 "
            pdb=" OG1 THR C 565 "
     model   vdw
     2.169 3.120
  nonbonded pdb=" O   ARG C 661 "
            pdb=" NH2 ARG C 693 "
     model   vdw
     2.172 3.120
  ... (remaining 80752 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.190
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10310  Z= 0.220
  Angle     :  0.729  10.194  14475  Z= 0.414
  Chirality :  0.040   0.289   1633
  Planarity :  0.006   0.055   1419
  Dihedral  : 23.494 162.948   4338
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  6.13 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 29.08 %
    Favored  : 70.53 %
  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: -0.62 (0.28), residues: 914
  helix:  0.33 (0.24), residues: 503
  sheet: -0.60 (0.66), residues: 65
  loop : -1.39 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 327 
 TYR   0.027   0.002   TYR C 626 
 PHE   0.013   0.001   PHE C 496 
 TRP   0.021   0.002   TRP C 351 
 HIS   0.010   0.001   HIS C 673 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (10302)
  covalent geometry    : angle       0.72949 (14470)
  hydrogen bonds       : bond        0.12320 (  492)
  hydrogen bonds       : angle       5.44297 ( 1310)
  metal coordination   : bond        0.00678 (    8)
  metal coordination   : angle       0.54844 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0973
  time to fit residues: 9.6468
Evaluate side-chains
  60 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.2588

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

Flipped N/Q/H residues before XYZ refinement:
** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 751 HIS
** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.107736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.079389 restraints weight = 31893.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.081581 restraints weight = 17003.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.082904 restraints weight = 11933.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.083553 restraints weight = 9806.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.084141 restraints weight = 8900.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10310  Z= 0.145
  Angle     :  0.620   9.089  14475  Z= 0.331
  Chirality :  0.038   0.198   1633
  Planarity :  0.004   0.061   1419
  Dihedral  : 23.871 172.823   2569
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.03 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 27.76 %
    Favored  : 69.47 %
  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:  0.01 (0.28), residues: 914
  helix:  0.87 (0.23), residues: 517
  sheet: -0.43 (0.71), residues: 59
  loop : -1.20 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 151 
 TYR   0.007   0.001   TYR C 626 
 PHE   0.010   0.001   PHE C 496 
 TRP   0.015   0.001   TRP C 823 
 HIS   0.006   0.001   HIS C 744 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10302)
  covalent geometry    : angle       0.61937 (14470)
  hydrogen bonds       : bond        0.04186 (  492)
  hydrogen bonds       : angle       4.24074 ( 1310)
  metal coordination   : bond        0.00470 (    8)
  metal coordination   : angle       1.77948 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9334 (OUTLIER) cc_final: 0.8790 (tttp)
REVERT: C  483 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8767 (tt)
REVERT: C  948 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8772 (mp)
REVERT: C 1097 MET cc_start: 0.8039 (tmm) cc_final: 0.7528 (tmm)
  outliers start: 21
  outliers final: 7
  residues processed: 90
  average time/residue: 0.0897
  time to fit residues: 11.6014
Evaluate side-chains
  77 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  624 LEU
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  974 GLU
Chi-restraints excluded: chain C residue  980 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 71 optimal weight:    0.3980
   chunk 93 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 87 optimal weight:    0.0270
   chunk 78 optimal weight:    0.2980
   chunk 86 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.5442

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

Flipped N/Q/H residues before XYZ refinement:
** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.109224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.081304 restraints weight = 31900.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.083527 restraints weight = 16855.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.084934 restraints weight = 11713.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.085734 restraints weight = 9585.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.086109 restraints weight = 8600.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10310  Z= 0.122
  Angle     :  0.561   8.177  14475  Z= 0.300
  Chirality :  0.036   0.187   1633
  Planarity :  0.004   0.058   1419
  Dihedral  : 23.646 172.390   2569
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.49 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 25.92 %
    Favored  : 70.53 %
  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:  0.46 (0.29), residues: 914
  helix:  1.33 (0.24), residues: 503
  sheet: -0.22 (0.72), residues: 59
  loop : -1.09 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C1101 
 TYR   0.011   0.001   TYR C 626 
 PHE   0.008   0.001   PHE C 597 
 TRP   0.012   0.001   TRP C 351 
 HIS   0.006   0.001   HIS C 751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10302)
  covalent geometry    : angle       0.56056 (14470)
  hydrogen bonds       : bond        0.03635 (  492)
  hydrogen bonds       : angle       4.01332 ( 1310)
  metal coordination   : bond        0.00472 (    8)
  metal coordination   : angle       1.48142 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 74
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8850 (ptmm)
REVERT: C  410 ASP cc_start: 0.6901 (p0) cc_final: 0.6368 (p0)
REVERT: C  483 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8755 (tt)
REVERT: C  948 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8577 (mp)
REVERT: C 1095 SER cc_start: 0.8695 (t) cc_final: 0.8408 (p)
REVERT: C 1097 MET cc_start: 0.8259 (tmm) cc_final: 0.7933 (tmm)
  outliers start: 27
  outliers final: 10
  residues processed: 93
  average time/residue: 0.0926
  time to fit residues: 12.2791
Evaluate side-chains
  77 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  746 ILE
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  904 VAL
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  974 GLU
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 84 optimal weight:    0.3980
   chunk 31 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 14 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.3982

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

Flipped N/Q/H residues before XYZ refinement:
** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.108925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.081817 restraints weight = 32232.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.083942 restraints weight = 17450.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.085279 restraints weight = 12219.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.086051 restraints weight = 10042.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.086378 restraints weight = 9037.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10310  Z= 0.135
  Angle     :  0.565   9.098  14475  Z= 0.300
  Chirality :  0.036   0.180   1633
  Planarity :  0.004   0.056   1419
  Dihedral  : 23.629 170.264   2569
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.38 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 26.18 %
    Favored  : 70.66 %
  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:  0.48 (0.29), residues: 914
  helix:  1.32 (0.24), residues: 510
  sheet: -0.25 (0.71), residues: 59
  loop : -1.08 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 151 
 TYR   0.012   0.001   TYR C 626 
 PHE   0.011   0.001   PHE C 213 
 TRP   0.012   0.001   TRP C 701 
 HIS   0.007   0.001   HIS C 751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10302)
  covalent geometry    : angle       0.56412 (14470)
  hydrogen bonds       : bond        0.03606 (  492)
  hydrogen bonds       : angle       3.89711 ( 1310)
  metal coordination   : bond        0.00521 (    8)
  metal coordination   : angle       1.63387 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8797 (ptmm)
REVERT: C  196 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8095 (tm-30)
REVERT: C  410 ASP cc_start: 0.6943 (p0) cc_final: 0.6593 (p0)
REVERT: C  483 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8749 (tt)
REVERT: C  948 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8753 (mp)
REVERT: C 1097 MET cc_start: 0.8301 (tmm) cc_final: 0.7744 (tmm)
  outliers start: 24
  outliers final: 14
  residues processed: 86
  average time/residue: 0.0750
  time to fit residues: 9.8131
Evaluate side-chains
  79 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  370 HIS
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  624 LEU
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  899 THR
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  954 THR
Chi-restraints excluded: chain C residue  974 GLU
Chi-restraints excluded: chain C residue  980 VAL
Chi-restraints excluded: chain C residue 1000 SER
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 101 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 87 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0470
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.7880

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

Flipped N/Q/H residues before XYZ refinement:
C 153 HIS
C 196 GLN
C 598 ASN
** C1104 GLN ** 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 = 0.4150 r_free = 0.4150 target = 0.110153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.083346 restraints weight = 32105.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.085513 restraints weight = 17183.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.086858 restraints weight = 11978.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.087620 restraints weight = 9839.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.087844 restraints weight = 8841.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10310  Z= 0.117
  Angle     :  0.542   9.813  14475  Z= 0.287
  Chirality :  0.035   0.182   1633
  Planarity :  0.004   0.056   1419
  Dihedral  : 23.592 170.518   2569
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.83 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 26.58 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.29), residues: 914
  helix:  1.40 (0.24), residues: 511
  sheet: -0.03 (0.71), residues: 59
  loop : -0.95 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 151 
 TYR   0.008   0.001   TYR C 626 
 PHE   0.012   0.001   PHE C 597 
 TRP   0.010   0.001   TRP C 701 
 HIS   0.007   0.001   HIS C 751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10302)
  covalent geometry    : angle       0.54190 (14470)
  hydrogen bonds       : bond        0.03365 (  492)
  hydrogen bonds       : angle       3.81925 ( 1310)
  metal coordination   : bond        0.00574 (    8)
  metal coordination   : angle       1.46047 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  167 LEU cc_start: 0.9010 (tp) cc_final: 0.8782 (tp)
REVERT: C  194 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8742 (ptmm)
REVERT: C  196 GLN cc_start: 0.8470 (tm130) cc_final: 0.8116 (tm-30)
REVERT: C  267 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7512 (mm)
REVERT: C  483 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8710 (tt)
REVERT: C  948 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8669 (mp)
REVERT: C 1097 MET cc_start: 0.8358 (tmm) cc_final: 0.7784 (tmm)
  outliers start: 26
  outliers final: 12
  residues processed: 88
  average time/residue: 0.0753
  time to fit residues: 10.0662
Evaluate side-chains
  80 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  267 LEU
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  370 HIS
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  899 THR
Chi-restraints excluded: chain C residue  911 ILE
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  980 VAL
Chi-restraints excluded: chain C residue 1000 SER
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 87 optimal weight:    9.9990
   chunk 30 optimal weight:    0.0070
   chunk 46 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0980
   chunk 12 optimal weight:    6.9990
   chunk 60 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
C 196 GLN
C 598 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.110906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.084210 restraints weight = 32226.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.086380 restraints weight = 16792.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.087752 restraints weight = 11599.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.088567 restraints weight = 9466.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.088869 restraints weight = 8470.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10310  Z= 0.112
  Angle     :  0.540   9.489  14475  Z= 0.285
  Chirality :  0.035   0.179   1633
  Planarity :  0.004   0.056   1419
  Dihedral  : 23.592 170.905   2569
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  3.94 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 26.97 %
    Favored  : 69.87 %
  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:  0.78 (0.29), residues: 914
  helix:  1.51 (0.24), residues: 505
  sheet:  0.05 (0.70), residues: 59
  loop : -0.86 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 151 
 TYR   0.016   0.001   TYR C 626 
 PHE   0.016   0.001   PHE C 597 
 TRP   0.009   0.001   TRP C 351 
 HIS   0.010   0.001   HIS C 751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (10302)
  covalent geometry    : angle       0.53894 (14470)
  hydrogen bonds       : bond        0.03245 (  492)
  hydrogen bonds       : angle       3.73292 ( 1310)
  metal coordination   : bond        0.00602 (    8)
  metal coordination   : angle       1.43044 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8762 (ptmm)
REVERT: C  410 ASP cc_start: 0.6992 (p0) cc_final: 0.6483 (p0)
REVERT: C  483 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8697 (tt)
REVERT: C  640 MET cc_start: 0.8544 (tpp) cc_final: 0.8312 (tpp)
REVERT: C  948 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8634 (mp)
REVERT: C 1097 MET cc_start: 0.8321 (tmm) cc_final: 0.7857 (tmm)
  outliers start: 24
  outliers final: 14
  residues processed: 87
  average time/residue: 0.0737
  time to fit residues: 9.8571
Evaluate side-chains
  79 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  370 HIS
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  899 THR
Chi-restraints excluded: chain C residue  911 ILE
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  954 THR
Chi-restraints excluded: chain C residue  980 VAL
Chi-restraints excluded: chain C residue 1000 SER
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 85 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0770
   chunk 29 optimal weight:    8.9990
   chunk 88 optimal weight:   10.0000
   chunk 82 optimal weight:    8.9990
   chunk 48 optimal weight:    0.4980
   chunk 5 optimal weight:    8.9990
   chunk 11 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.2940

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

Flipped N/Q/H residues before XYZ refinement:
C 196 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.109781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.082852 restraints weight = 31916.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.084999 restraints weight = 17142.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.086323 restraints weight = 12028.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.087087 restraints weight = 9886.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.087429 restraints weight = 8894.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10310  Z= 0.128
  Angle     :  0.553  10.095  14475  Z= 0.292
  Chirality :  0.036   0.174   1633
  Planarity :  0.004   0.055   1419
  Dihedral  : 23.602 170.220   2569
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.27 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 26.71 %
    Favored  : 70.26 %
  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:  0.76 (0.29), residues: 914
  helix:  1.49 (0.24), residues: 512
  sheet: -0.03 (0.69), residues: 59
  loop : -0.90 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 151 
 TYR   0.023   0.001   TYR C 626 
 PHE   0.010   0.001   PHE C 597 
 TRP   0.011   0.001   TRP C 701 
 HIS   0.010   0.001   HIS C 751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (10302)
  covalent geometry    : angle       0.55221 (14470)
  hydrogen bonds       : bond        0.03393 (  492)
  hydrogen bonds       : angle       3.79527 ( 1310)
  metal coordination   : bond        0.00514 (    8)
  metal coordination   : angle       1.44982 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  167 LEU cc_start: 0.9103 (tp) cc_final: 0.8884 (tp)
REVERT: C  194 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8796 (ptmm)
REVERT: C  196 GLN cc_start: 0.8527 (tm130) cc_final: 0.8147 (tm-30)
REVERT: C  410 ASP cc_start: 0.7296 (p0) cc_final: 0.6814 (p0)
REVERT: C  483 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8755 (tt)
REVERT: C  948 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8582 (mp)
REVERT: C 1097 MET cc_start: 0.8328 (tmm) cc_final: 0.7733 (tmm)
  outliers start: 23
  outliers final: 18
  residues processed: 85
  average time/residue: 0.0751
  time to fit residues: 9.7369
Evaluate side-chains
  85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  370 HIS
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  592 LEU
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  686 ASN
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  868 HIS
Chi-restraints excluded: chain C residue  899 THR
Chi-restraints excluded: chain C residue  911 ILE
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  954 THR
Chi-restraints excluded: chain C residue 1000 SER
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Chi-restraints excluded: chain C residue 1059 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
C 962 HIS
C 963 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.109181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.082243 restraints weight = 31826.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.084366 restraints weight = 17194.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.085690 restraints weight = 12097.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.086470 restraints weight = 9946.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.086873 restraints weight = 8953.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10310  Z= 0.129
  Angle     :  0.549  10.201  14475  Z= 0.292
  Chirality :  0.036   0.175   1633
  Planarity :  0.004   0.055   1419
  Dihedral  : 23.588 170.884   2569
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.27 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.97 %
    Favored  : 70.26 %
  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:  0.72 (0.29), residues: 914
  helix:  1.50 (0.24), residues: 513
  sheet: -0.36 (0.66), residues: 59
  loop : -0.92 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 961 
 TYR   0.022   0.001   TYR C 626 
 PHE   0.010   0.001   PHE C 597 
 TRP   0.010   0.001   TRP C 701 
 HIS   0.011   0.001   HIS C 751 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10302)
  covalent geometry    : angle       0.54824 (14470)
  hydrogen bonds       : bond        0.03405 (  492)
  hydrogen bonds       : angle       3.75854 ( 1310)
  metal coordination   : bond        0.00480 (    8)
  metal coordination   : angle       1.42054 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  167 LEU cc_start: 0.9079 (tp) cc_final: 0.8858 (tp)
REVERT: C  194 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8820 (tttt)
REVERT: C  196 GLN cc_start: 0.8441 (tm130) cc_final: 0.7881 (tm-30)
REVERT: C  410 ASP cc_start: 0.7225 (p0) cc_final: 0.6779 (p0)
REVERT: C  483 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8784 (tt)
REVERT: C  640 MET cc_start: 0.8655 (tpp) cc_final: 0.8443 (tpp)
REVERT: C  948 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8707 (mp)
REVERT: C 1097 MET cc_start: 0.8347 (tmm) cc_final: 0.7789 (tmm)
  outliers start: 21
  outliers final: 17
  residues processed: 82
  average time/residue: 0.0686
  time to fit residues: 8.7083
Evaluate side-chains
  83 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  592 LEU
Chi-restraints excluded: chain C residue  621 VAL
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  686 ASN
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  868 HIS
Chi-restraints excluded: chain C residue  899 THR
Chi-restraints excluded: chain C residue  911 ILE
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  954 THR
Chi-restraints excluded: chain C residue 1000 SER
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Chi-restraints excluded: chain C residue 1059 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 82 optimal weight:    0.0270
   chunk 13 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
C 751 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.110161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.083345 restraints weight = 31889.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.085524 restraints weight = 16887.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.086869 restraints weight = 11744.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.087673 restraints weight = 9607.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.088097 restraints weight = 8623.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10310  Z= 0.115
  Angle     :  0.558  10.899  14475  Z= 0.294
  Chirality :  0.036   0.176   1633
  Planarity :  0.004   0.055   1419
  Dihedral  : 23.565 172.500   2569
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.27 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 27.11 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.29), residues: 914
  helix:  1.48 (0.24), residues: 507
  sheet: -0.22 (0.66), residues: 59
  loop : -0.87 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 492 
 TYR   0.017   0.001   TYR C 626 
 PHE   0.025   0.001   PHE C 180 
 TRP   0.008   0.001   TRP C 351 
 HIS   0.004   0.001   HIS C1096 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10302)
  covalent geometry    : angle       0.55735 (14470)
  hydrogen bonds       : bond        0.03347 (  492)
  hydrogen bonds       : angle       3.85705 ( 1310)
  metal coordination   : bond        0.00502 (    8)
  metal coordination   : angle       1.29690 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8735 (ptmm)
REVERT: C  196 GLN cc_start: 0.8303 (tm130) cc_final: 0.7789 (tm-30)
REVERT: C  410 ASP cc_start: 0.6972 (p0) cc_final: 0.6441 (p0)
REVERT: C  483 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8738 (tt)
REVERT: C  640 MET cc_start: 0.8563 (tpp) cc_final: 0.8320 (tpp)
REVERT: C  948 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8620 (mp)
REVERT: C 1097 MET cc_start: 0.8254 (tmm) cc_final: 0.7635 (tmm)
  outliers start: 22
  outliers final: 17
  residues processed: 80
  average time/residue: 0.0711
  time to fit residues: 8.8280
Evaluate side-chains
  83 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  452 LYS
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  515 ASP
Chi-restraints excluded: chain C residue  592 LEU
Chi-restraints excluded: chain C residue  593 SER
Chi-restraints excluded: chain C residue  621 VAL
Chi-restraints excluded: chain C residue  686 ASN
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  899 THR
Chi-restraints excluded: chain C residue  911 ILE
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  954 THR
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Chi-restraints excluded: chain C residue 1059 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 88 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
C 751 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.108468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.081471 restraints weight = 31505.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.083546 restraints weight = 17196.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.084822 restraints weight = 12202.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.085587 restraints weight = 10085.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.085930 restraints weight = 9092.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10310  Z= 0.146
  Angle     :  0.585  10.853  14475  Z= 0.307
  Chirality :  0.036   0.172   1633
  Planarity :  0.004   0.056   1419
  Dihedral  : 23.595 172.500   2569
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.81 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 27.11 %
    Favored  : 70.13 %
  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:  0.67 (0.29), residues: 914
  helix:  1.45 (0.24), residues: 512
  sheet: -0.36 (0.66), residues: 59
  loop : -0.93 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 492 
 TYR   0.020   0.001   TYR C 626 
 PHE   0.012   0.001   PHE C 597 
 TRP   0.014   0.001   TRP C 701 
 HIS   0.006   0.001   HIS C 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10302)
  covalent geometry    : angle       0.58414 (14470)
  hydrogen bonds       : bond        0.03670 (  492)
  hydrogen bonds       : angle       3.96263 ( 1310)
  metal coordination   : bond        0.00490 (    8)
  metal coordination   : angle       1.50184 (    5)

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

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

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1828 Ramachandran restraints generated.
    914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8667 (ptmm)
REVERT: C  196 GLN cc_start: 0.8341 (tm130) cc_final: 0.7907 (tm-30)
REVERT: C  438 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6690 (mp)
REVERT: C  640 MET cc_start: 0.8597 (tpp) cc_final: 0.8342 (tpp)
REVERT: C  948 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8734 (mp)
REVERT: C  982 LEU cc_start: 0.8813 (tt) cc_final: 0.8588 (pt)
REVERT: C 1097 MET cc_start: 0.8189 (tmm) cc_final: 0.7588 (tmm)
  outliers start: 21
  outliers final: 16
  residues processed: 83
  average time/residue: 0.0710
  time to fit residues: 8.8433
Evaluate side-chains
  85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  189 THR
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  452 LYS
Chi-restraints excluded: chain C residue  592 LEU
Chi-restraints excluded: chain C residue  593 SER
Chi-restraints excluded: chain C residue  621 VAL
Chi-restraints excluded: chain C residue  686 ASN
Chi-restraints excluded: chain C residue  698 VAL
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  868 HIS
Chi-restraints excluded: chain C residue  899 THR
Chi-restraints excluded: chain C residue  911 ILE
Chi-restraints excluded: chain C residue  948 LEU
Chi-restraints excluded: chain C residue  954 THR
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Chi-restraints excluded: chain C residue 1059 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 93 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 60 optimal weight:    9.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
C 751 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.107250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.080201 restraints weight = 31962.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.082250 restraints weight = 17551.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.083525 restraints weight = 12479.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.084253 restraints weight = 10316.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.084683 restraints weight = 9319.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10310  Z= 0.154
  Angle     :  0.605  10.662  14475  Z= 0.315
  Chirality :  0.037   0.172   1633
  Planarity :  0.004   0.056   1419
  Dihedral  : 23.637 174.740   2569
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.49 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 27.63 %
    Favored  : 69.87 %
  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:  0.52 (0.29), residues: 914
  helix:  1.34 (0.24), residues: 513
  sheet: -0.51 (0.66), residues: 59
  loop : -0.99 (0.33), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 150 
 TYR   0.024   0.002   TYR C 626 
 PHE   0.013   0.001   PHE C 180 
 TRP   0.014   0.001   TRP C 701 
 HIS   0.004   0.001   HIS C 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10302)
  covalent geometry    : angle       0.60413 (14470)
  hydrogen bonds       : bond        0.03706 (  492)
  hydrogen bonds       : angle       3.98567 ( 1310)
  metal coordination   : bond        0.00545 (    8)
  metal coordination   : angle       1.62590 (    5)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1592.25 seconds
wall clock time: 28 minutes 11.53 seconds (1691.53 seconds total)