Starting phenix.real_space_refine
on Wed Apr 30 23:58:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ibw_35347/04_2025/8ibw_35347.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ibw_35347/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ibw_35347/04_2025/8ibw_35347.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ibw_35347/04_2025/8ibw_35347.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ibw_35347/04_2025/8ibw_35347.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ibw_35347/04_2025/8ibw_35347.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1}
          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: 7.55, per 1000 atoms: 0.77
  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: 2.74
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  
  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: 5.34
  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: 5.64

  Time building geometry restraints manager: 3.28 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:             86.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     36.090
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  126.530
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (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
 TRP   0.021   0.002   TRP C 351 
 HIS   0.010   0.001   HIS C 673 
 PHE   0.013   0.001   PHE C 496 
 TYR   0.027   0.002   TYR C 626 
 ARG   0.015   0.001   ARG C 327 

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

*********************** 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  : 0.984 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 69
  average time/residue: 0.2429
  time to fit residues: 24.2619
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  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4064 r_free = 0.4064 target = 0.106260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.077704 restraints weight = 31591.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.079857 restraints weight = 17040.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.081183 restraints weight = 12042.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10310  Z= 0.175
  Angle     :  0.643   8.992  14475  Z= 0.343
  Chirality :  0.039   0.194   1633
  Planarity :  0.004   0.060   1419
  Dihedral  : 23.903 171.811   2569
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.47 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 27.76 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.28), residues: 914
  helix:  0.79 (0.23), residues: 516
  sheet: -0.52 (0.70), residues: 59
  loop : -1.31 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 823 
 HIS   0.006   0.001   HIS C 744 
 PHE   0.010   0.001   PHE C 496 
 TYR   0.011   0.002   TYR C 626 
 ARG   0.010   0.001   ARG C 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04402 (  492)
  hydrogen bonds       : angle       4.30458 ( 1310)
  metal coordination   : bond        0.00465 (    8)
  metal coordination   : angle       1.92482 (    5)
  covalent geometry    : bond        0.00390 (10302)
  covalent geometry    : angle       0.64228 (14470)

*********************** 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
  98 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8843 (tttp)
REVERT: C  948 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8822 (mp)
REVERT: C 1097 MET cc_start: 0.8083 (tmm) cc_final: 0.7506 (tmm)
  outliers start: 26
  outliers final: 11
  residues processed: 93
  average time/residue: 0.2100
  time to fit residues: 28.2816
Evaluate side-chains
  81 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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  503 LEU
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  624 LEU
Chi-restraints excluded: chain C residue  658 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  974 GLU
Chi-restraints excluded: chain C residue  980 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 67 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0060
   chunk 86 optimal weight:    0.9980
   chunk 82 optimal weight:    9.9990
   chunk 65 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.7400

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.107950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.079788 restraints weight = 32077.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.081974 restraints weight = 17027.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.083315 restraints weight = 11901.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10310  Z= 0.127
  Angle     :  0.577   9.439  14475  Z= 0.307
  Chirality :  0.037   0.187   1633
  Planarity :  0.004   0.058   1419
  Dihedral  : 23.692 171.826   2569
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.27 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 26.71 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.29), residues: 914
  helix:  1.13 (0.24), residues: 516
  sheet: -0.29 (0.71), residues: 59
  loop : -1.17 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 351 
 HIS   0.006   0.001   HIS C 751 
 PHE   0.009   0.001   PHE C 496 
 TYR   0.010   0.001   TYR C 626 
 ARG   0.004   0.000   ARG C 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03783 (  492)
  hydrogen bonds       : angle       4.09289 ( 1310)
  metal coordination   : bond        0.00371 (    8)
  metal coordination   : angle       1.57234 (    5)
  covalent geometry    : bond        0.00276 (10302)
  covalent geometry    : angle       0.57679 (14470)

*********************** 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
  99 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.8768 (tttp)
REVERT: C  270 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7253 (pp)
REVERT: C  393 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8151 (p)
REVERT: C  410 ASP cc_start: 0.7067 (p0) cc_final: 0.6416 (p0)
REVERT: C  748 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7989 (mtp180)
REVERT: C  948 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8608 (mp)
REVERT: C 1095 SER cc_start: 0.8814 (t) cc_final: 0.8552 (p)
REVERT: C 1097 MET cc_start: 0.8229 (tmm) cc_final: 0.7876 (tmm)
  outliers start: 27
  outliers final: 14
  residues processed: 94
  average time/residue: 0.2299
  time to fit residues: 30.3616
Evaluate side-chains
  84 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 65
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 GLN
Chi-restraints excluded: chain C residue  194 LYS
Chi-restraints excluded: chain C residue  270 LEU
Chi-restraints excluded: chain C residue  343 SER
Chi-restraints excluded: chain C residue  370 HIS
Chi-restraints excluded: chain C residue  393 VAL
Chi-restraints excluded: chain C residue  424 LEU
Chi-restraints excluded: chain C residue  503 LEU
Chi-restraints excluded: chain C residue  540 GLU
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  746 ILE
Chi-restraints excluded: chain C residue  748 ARG
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 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 58 optimal weight:    0.0870
   chunk 68 optimal weight:    5.9990
   chunk 95 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 78 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 86 optimal weight:    0.9990
   chunk 59 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.1162

-------------------------------------------------------------------------------
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**
** 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 = 0.4136 r_free = 0.4136 target = 0.109220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.082108 restraints weight = 31926.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.084245 restraints weight = 17178.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.085587 restraints weight = 12083.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10310  Z= 0.128
  Angle     :  0.559   9.365  14475  Z= 0.298
  Chirality :  0.036   0.180   1633
  Planarity :  0.004   0.056   1419
  Dihedral  : 23.636 170.665   2569
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.38 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 27.24 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.29), residues: 914
  helix:  1.30 (0.24), residues: 512
  sheet: -0.18 (0.71), residues: 59
  loop : -1.02 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 351 
 HIS   0.008   0.001   HIS C 751 
 PHE   0.008   0.001   PHE C 968 
 TYR   0.009   0.001   TYR C 626 
 ARG   0.004   0.000   ARG C 151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03621 (  492)
  hydrogen bonds       : angle       3.96947 ( 1310)
  metal coordination   : bond        0.00476 (    8)
  metal coordination   : angle       1.57199 (    5)
  covalent geometry    : bond        0.00279 (10302)
  covalent geometry    : angle       0.55820 (14470)

*********************** 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
  96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 69
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8809 (tttt)
REVERT: C  948 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8786 (mp)
REVERT: C 1097 MET cc_start: 0.8322 (tmm) cc_final: 0.7757 (tmm)
  outliers start: 27
  outliers final: 16
  residues processed: 92
  average time/residue: 0.2111
  time to fit residues: 28.1167
Evaluate side-chains
  82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 GLN
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  503 LEU
Chi-restraints excluded: chain C residue  582 VAL
Chi-restraints excluded: chain C residue  624 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  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 6 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 92 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
C 196 GLN
** 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 = 0.4087 r_free = 0.4087 target = 0.106456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.078941 restraints weight = 31808.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.081074 restraints weight = 16812.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.082404 restraints weight = 11744.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10310  Z= 0.182
  Angle     :  0.598  12.897  14475  Z= 0.317
  Chirality :  0.038   0.175   1633
  Planarity :  0.004   0.055   1419
  Dihedral  : 23.686 168.372   2569
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  5.03 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 25.92 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.29), residues: 914
  helix:  1.21 (0.24), residues: 514
  sheet: -0.26 (0.69), residues: 59
  loop : -1.03 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 701 
 HIS   0.008   0.001   HIS C 751 
 PHE   0.007   0.001   PHE C 968 
 TYR   0.016   0.002   TYR C 626 
 ARG   0.004   0.000   ARG C 517 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  492)
  hydrogen bonds       : angle       4.04289 ( 1310)
  metal coordination   : bond        0.00586 (    8)
  metal coordination   : angle       1.70928 (    5)
  covalent geometry    : bond        0.00404 (10302)
  covalent geometry    : angle       0.59758 (14470)

*********************** 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
  96 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 64
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8837 (tttt)
REVERT: C  196 GLN cc_start: 0.8563 (tm130) cc_final: 0.8263 (tm-30)
REVERT: C  267 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7607 (mm)
REVERT: C  410 ASP cc_start: 0.7471 (p0) cc_final: 0.6834 (p0)
REVERT: C  948 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8756 (mp)
REVERT: C 1097 MET cc_start: 0.8235 (tmm) cc_final: 0.7577 (tmm)
  outliers start: 32
  outliers final: 22
  residues processed: 93
  average time/residue: 0.1927
  time to fit residues: 27.0745
Evaluate side-chains
  88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 63
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  115 GLN
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  189 THR
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  438 ILE
Chi-restraints excluded: chain C residue  503 LEU
Chi-restraints excluded: chain C residue  540 GLU
Chi-restraints excluded: chain C residue  582 VAL
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  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 53 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 95 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
C 598 ASN
** 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 = 0.4101 r_free = 0.4101 target = 0.107279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.079842 restraints weight = 31832.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.082052 restraints weight = 16720.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.083409 restraints weight = 11629.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10310  Z= 0.145
  Angle     :  0.569  13.708  14475  Z= 0.303
  Chirality :  0.036   0.176   1633
  Planarity :  0.004   0.053   1419
  Dihedral  : 23.667 169.469   2569
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.49 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 27.63 %
    Favored  : 68.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 914
  helix:  1.31 (0.24), residues: 514
  sheet: -0.29 (0.69), residues: 59
  loop : -1.04 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 701 
 HIS   0.010   0.001   HIS C 751 
 PHE   0.011   0.001   PHE C 968 
 TYR   0.017   0.001   TYR C 626 
 ARG   0.004   0.000   ARG C 961 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03629 (  492)
  hydrogen bonds       : angle       3.95500 ( 1310)
  metal coordination   : bond        0.00435 (    8)
  metal coordination   : angle       1.56397 (    5)
  covalent geometry    : bond        0.00319 (10302)
  covalent geometry    : angle       0.56805 (14470)

*********************** 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
  93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
REVERT: C  167 LEU cc_start: 0.9051 (tp) cc_final: 0.8791 (tp)
REVERT: C  194 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8835 (tttt)
REVERT: C  196 GLN cc_start: 0.8534 (tm130) cc_final: 0.8150 (tm-30)
REVERT: C  640 MET cc_start: 0.8671 (tpp) cc_final: 0.8418 (tpp)
REVERT: C  948 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8822 (mp)
REVERT: C 1097 MET cc_start: 0.8200 (tmm) cc_final: 0.7573 (tmm)
  outliers start: 27
  outliers final: 20
  residues processed: 90
  average time/residue: 0.2143
  time to fit residues: 29.0090
Evaluate side-chains
  85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  178 ASP
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  424 LEU
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  503 LEU
Chi-restraints excluded: chain C residue  540 GLU
Chi-restraints excluded: chain C residue  582 VAL
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 59 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 598 ASN ** 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 = 0.4108 r_free = 0.4108 target = 0.107754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.080677 restraints weight = 32160.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.082765 restraints weight = 17540.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.084076 restraints weight = 12380.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10310  Z= 0.126
  Angle     :  0.557   8.461  14475  Z= 0.297
  Chirality :  0.036   0.177   1633
  Planarity :  0.004   0.054   1419
  Dihedral  : 23.657 170.168   2569
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.16 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 26.97 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.29), residues: 914
  helix:  1.36 (0.24), residues: 512
  sheet: -0.24 (0.69), residues: 59
  loop : -1.01 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 351 
 HIS   0.010   0.001   HIS C 751 
 PHE   0.012   0.001   PHE C 597 
 TYR   0.015   0.001   TYR C 626 
 ARG   0.006   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03532 (  492)
  hydrogen bonds       : angle       3.92065 ( 1310)
  metal coordination   : bond        0.00442 (    8)
  metal coordination   : angle       1.36400 (    5)
  covalent geometry    : bond        0.00278 (10302)
  covalent geometry    : angle       0.55604 (14470)

*********************** 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
  93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 64
  time to evaluate  : 2.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  167 LEU cc_start: 0.9002 (tp) cc_final: 0.8730 (tp)
REVERT: C  194 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8681 (tttp)
REVERT: C  410 ASP cc_start: 0.7367 (p0) cc_final: 0.6773 (p0)
REVERT: C  948 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8800 (mp)
REVERT: C 1097 MET cc_start: 0.8187 (tmm) cc_final: 0.7595 (tmm)
  outliers start: 29
  outliers final: 23
  residues processed: 90
  average time/residue: 0.2516
  time to fit residues: 35.8766
Evaluate side-chains
  87 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 62
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  178 ASP
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  393 VAL
Chi-restraints excluded: chain C residue  438 ILE
Chi-restraints excluded: chain C residue  502 THR
Chi-restraints excluded: chain C residue  503 LEU
Chi-restraints excluded: chain C residue  540 GLU
Chi-restraints excluded: chain C residue  582 VAL
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  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
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 97 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 24 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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
** 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 = 0.4102 r_free = 0.4102 target = 0.107439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.080347 restraints weight = 32056.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.082432 restraints weight = 17524.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.083705 restraints weight = 12416.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10310  Z= 0.131
  Angle     :  0.568  14.223  14475  Z= 0.301
  Chirality :  0.036   0.174   1633
  Planarity :  0.004   0.055   1419
  Dihedral  : 23.663 170.158   2569
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.49 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 26.97 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.29), residues: 914
  helix:  1.37 (0.24), residues: 512
  sheet: -0.29 (0.69), residues: 59
  loop : -1.02 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 701 
 HIS   0.010   0.001   HIS C 751 
 PHE   0.011   0.001   PHE C 968 
 TYR   0.015   0.001   TYR C 626 
 ARG   0.005   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03541 (  492)
  hydrogen bonds       : angle       3.94221 ( 1310)
  metal coordination   : bond        0.00452 (    8)
  metal coordination   : angle       1.41850 (    5)
  covalent geometry    : bond        0.00290 (10302)
  covalent geometry    : angle       0.56782 (14470)

*********************** 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
  90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 63
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  167 LEU cc_start: 0.9049 (tp) cc_final: 0.8813 (tp)
REVERT: C  194 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8815 (tttt)
REVERT: C  196 GLN cc_start: 0.8369 (tm130) cc_final: 0.7723 (tm-30)
REVERT: C  410 ASP cc_start: 0.7418 (p0) cc_final: 0.6850 (p0)
REVERT: C  626 TYR cc_start: 0.5569 (t80) cc_final: 0.5339 (t80)
REVERT: C  640 MET cc_start: 0.8666 (tpp) cc_final: 0.8452 (tpp)
REVERT: C  948 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8744 (mp)
REVERT: C 1097 MET cc_start: 0.8277 (tmm) cc_final: 0.7659 (tmm)
  outliers start: 27
  outliers final: 22
  residues processed: 88
  average time/residue: 0.1922
  time to fit residues: 25.6401
Evaluate side-chains
  84 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  178 ASP
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  503 LEU
Chi-restraints excluded: chain C residue  540 GLU
Chi-restraints excluded: chain C residue  582 VAL
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  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
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 51 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 57 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0040
   chunk 10 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.3796

-------------------------------------------------------------------------------
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**
** 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 = 0.4102 r_free = 0.4102 target = 0.107435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.080402 restraints weight = 31988.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.082475 restraints weight = 17495.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.083763 restraints weight = 12417.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10310  Z= 0.131
  Angle     :  0.566  11.942  14475  Z= 0.300
  Chirality :  0.036   0.174   1633
  Planarity :  0.004   0.055   1419
  Dihedral  : 23.652 170.787   2569
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.16 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 27.63 %
    Favored  : 69.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 914
  helix:  1.31 (0.24), residues: 512
  sheet: -0.31 (0.69), residues: 59
  loop : -1.02 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 701 
 HIS   0.010   0.001   HIS C 751 
 PHE   0.010   0.001   PHE C 968 
 TYR   0.013   0.001   TYR C 626 
 ARG   0.005   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03577 (  492)
  hydrogen bonds       : angle       3.93589 ( 1310)
  metal coordination   : bond        0.00433 (    8)
  metal coordination   : angle       1.40467 (    5)
  covalent geometry    : bond        0.00289 (10302)
  covalent geometry    : angle       0.56516 (14470)

*********************** 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
  86 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 63
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8680 (tttp)
REVERT: C  196 GLN cc_start: 0.8462 (tm130) cc_final: 0.7982 (tm-30)
REVERT: C  410 ASP cc_start: 0.7391 (p0) cc_final: 0.6856 (p0)
REVERT: C  433 MET cc_start: 0.7091 (tpt) cc_final: 0.6879 (tpt)
REVERT: C  640 MET cc_start: 0.8661 (tpp) cc_final: 0.8426 (tpp)
REVERT: C  948 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8810 (mp)
REVERT: C 1097 MET cc_start: 0.8216 (tmm) cc_final: 0.7614 (tmm)
  outliers start: 23
  outliers final: 20
  residues processed: 84
  average time/residue: 0.1718
  time to fit residues: 22.5094
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  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  178 ASP
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  503 LEU
Chi-restraints excluded: chain C residue  540 GLU
Chi-restraints excluded: chain C residue  582 VAL
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 1000 SER
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 64 optimal weight:    0.3980
   chunk 7 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 77 optimal weight:    8.9990
   overall best weight:    1.8386

-------------------------------------------------------------------------------
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**
** 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 = 0.4092 r_free = 0.4092 target = 0.106879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.079800 restraints weight = 31826.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.081871 restraints weight = 17531.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.083160 restraints weight = 12462.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10310  Z= 0.149
  Angle     :  0.583  12.808  14475  Z= 0.309
  Chirality :  0.037   0.185   1633
  Planarity :  0.004   0.054   1419
  Dihedral  : 23.665 171.328   2569
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.70 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 28.03 %
    Favored  : 69.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.29), residues: 914
  helix:  1.25 (0.24), residues: 515
  sheet: -0.31 (0.69), residues: 59
  loop : -1.02 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 701 
 HIS   0.009   0.001   HIS C 751 
 PHE   0.019   0.001   PHE C 180 
 TYR   0.030   0.002   TYR C 626 
 ARG   0.004   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (  492)
  hydrogen bonds       : angle       4.02770 ( 1310)
  metal coordination   : bond        0.00468 (    8)
  metal coordination   : angle       1.43329 (    5)
  covalent geometry    : bond        0.00329 (10302)
  covalent geometry    : angle       0.58295 (14470)

********************** 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
  84 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.976 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  194 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8680 (tttp)
REVERT: C  196 GLN cc_start: 0.8360 (tm130) cc_final: 0.7919 (tm-30)
REVERT: C  410 ASP cc_start: 0.7455 (p0) cc_final: 0.6928 (p0)
REVERT: C  948 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8736 (mp)
REVERT: C 1095 SER cc_start: 0.8746 (t) cc_final: 0.8546 (p)
REVERT: C 1097 MET cc_start: 0.8173 (tmm) cc_final: 0.7550 (tmm)
  outliers start: 22
  outliers final: 18
  residues processed: 82
  average time/residue: 0.1707
  time to fit residues: 22.1574
Evaluate side-chains
  81 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 61
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  178 ASP
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  503 LEU
Chi-restraints excluded: chain C residue  540 GLU
Chi-restraints excluded: chain C residue  582 VAL
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 1000 SER
Chi-restraints excluded: chain C residue 1006 VAL
Chi-restraints excluded: chain C residue 1051 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0370
   chunk 99 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 102 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    2.0064

-------------------------------------------------------------------------------
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 963 ASN
** 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 = 0.4088 r_free = 0.4088 target = 0.106552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.079298 restraints weight = 32024.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.081475 restraints weight = 16899.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.082800 restraints weight = 11773.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10310  Z= 0.154
  Angle     :  0.590  14.396  14475  Z= 0.311
  Chirality :  0.037   0.171   1633
  Planarity :  0.004   0.053   1419
  Dihedral  : 23.695 172.586   2569
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.33 %
    Allowed  :  4.60 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 28.03 %
    Favored  : 69.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.29), residues: 914
  helix:  1.20 (0.24), residues: 515
  sheet: -0.36 (0.69), residues: 59
  loop : -1.01 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 701 
 HIS   0.010   0.001   HIS C 751 
 PHE   0.011   0.001   PHE C 597 
 TYR   0.027   0.002   TYR C 626 
 ARG   0.005   0.000   ARG C 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  492)
  hydrogen bonds       : angle       4.03763 ( 1310)
  metal coordination   : bond        0.00476 (    8)
  metal coordination   : angle       1.53367 (    5)
  covalent geometry    : bond        0.00342 (10302)
  covalent geometry    : angle       0.58906 (14470)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3757.75 seconds
wall clock time: 67 minutes 37.39 seconds (4057.39 seconds total)