Starting phenix.real_space_refine
on Tue Mar  3 13:05:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7z4z_14511/03_2026/7z4z_14511.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z4z_14511/03_2026/7z4z_14511.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z4z_14511/03_2026/7z4z_14511.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z4z_14511/03_2026/7z4z_14511.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z4z_14511/03_2026/7z4z_14511.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z4z_14511/03_2026/7z4z_14511.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      11      5.16       5
     C    3082      2.51       5
     N     838      2.21       5
     O     886      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4817
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1096
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1096
          Classifications: {'peptide': 149}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 7, 'TRANS': 141}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 147
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 4, 'ARG:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 72
    Chain: "B"
      Number of atoms: 1317
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 188, 1317
          Classifications: {'peptide': 188}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 13, 'TRANS': 174}
          Unresolved non-hydrogen bonds: 193
          Unresolved non-hydrogen angles: 237
          Unresolved non-hydrogen dihedrals: 162
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 3, 'ARG:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 114
    Chain: "C"
      Number of atoms: 1111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1111
          Classifications: {'peptide': 152}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 7, 'TRANS': 144}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 129
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 2, 'GLN:plan1': 4, 'ASN:plan1': 4, 'ASP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 89
    Chain: "D"
      Number of atoms: 1293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1293
          Classifications: {'peptide': 184}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 13, 'TRANS': 170}
          Unresolved non-hydrogen bonds: 187
          Unresolved non-hydrogen angles: 229
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'TYR:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 101
  Time building chain proxies: 1.40, per 1000 atoms: 0.29
  Number of scatterers: 4817
  At special positions: 0
  Unit cell: (67.828, 74.392, 110.494, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      11     16.00
     O     886      8.00
     N     838      7.00
     C    3082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.41
  Conformation dependent library (CDL) restraints added in 421.2 milliseconds
  

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1282

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 3 sheets defined
      29.1% alpha, 9.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 74
      removed outlier: 4.007A  pdb=" N   ASN A  67 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   GLU A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ARG A  72 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LYS A  73 " --> pdb=" O   GLU A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 124
      removed outlier: 3.664A  pdb=" N   GLU A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 645
      removed outlier: 3.799A  pdb=" N   TYR B 643 " --> pdb=" O   GLU B 639 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 650 through 654
    Processing helix  chain 'B' and resid 703 through 710
      removed outlier: 3.698A  pdb=" N   ASN B 709 " --> pdb=" O   GLU B 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 755 through 767
      removed outlier: 3.517A  pdb=" N   GLN B 767 " --> pdb=" O   ILE B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 789 through 807
    Processing helix  chain 'C' and resid 62 through 74
      removed outlier: 3.853A  pdb=" N   GLN C  68 " --> pdb=" O   ARG C  64 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   GLU C  69 " --> pdb=" O   ALA C  65 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   LYS C  71 " --> pdb=" O   ASN C  67 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ARG C  72 " --> pdb=" O   GLN C  68 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LYS C  73 " --> pdb=" O   GLU C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 107
      removed outlier: 3.716A  pdb=" N   GLN C 107 " --> pdb=" O   ILE C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 126
      removed outlier: 4.070A  pdb=" N   VAL C 120 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LYS C 121 " --> pdb=" O   SER C 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 625 through 641
      removed outlier: 3.915A  pdb=" N   GLU D 641 " --> pdb=" O   GLY D 637 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 703 through 709
      removed outlier: 4.299A  pdb=" N   ASN D 709 " --> pdb=" O   GLU D 705 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 734 through 736
      No H-bonds generated for 'chain 'D' and resid 734 through 736'
    Processing helix  chain 'D' and resid 754 through 770
      removed outlier: 3.641A  pdb=" N   SER D 758 " --> pdb=" O   ASP D 754 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL D 759 " --> pdb=" O   ASN D 755 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LEU D 760 " --> pdb=" O   ARG D 756 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LYS D 768 " --> pdb=" O   GLN D 764 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 788 through 805
      removed outlier: 3.617A  pdb=" N   TYR D 805 " --> pdb=" O   GLU D 801 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 182
      removed outlier: 3.800A  pdb=" N   SER A 171 " --> pdb=" O   LYS A 182 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE C  97 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   TYR A 174 " --> pdb=" O   LEU C  95 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   LEU C  95 " --> pdb=" O   TYR A 174 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY C 170 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 725 through 732
      removed outlier: 6.856A  pdb=" N   VAL B 695 " --> pdb=" O   PHE B 677 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   PHE B 677 " --> pdb=" O   VAL B 695 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   GLU B 697 " --> pdb=" O   VAL B 675 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL B 673 " --> pdb=" O   LEU B 699 " (cutoff:3.500A)
      removed outlier: 5.741A  pdb=" N   ARG B 701 " --> pdb=" O   TRP B 671 " (cutoff:3.500A)
      removed outlier: 8.393A  pdb=" N   TRP B 671 " --> pdb=" O   ARG B 701 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLY B 672 " --> pdb=" O   VAL B 660 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   LYS B 661 " --> pdb=" O   SER B 737 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 727 through 732
      removed outlier: 3.701A  pdb=" N   VAL D 673 " --> pdb=" O   LEU D 699 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ASP D 668 " --> pdb=" O   ASN D 664 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ASN D 664 " --> pdb=" O   ASP D 668 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   GLY D 670 " --> pdb=" O   VAL D 662 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   VAL D 662 " --> pdb=" O   GLY D 670 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ARG D 658 " --> pdb=" O   VAL D 674 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   VAL D 742 " --> pdb=" O   LEU D 659 " (cutoff:3.500A)
      removed outlier: 7.911A  pdb=" N   LYS D 661 " --> pdb=" O   SER D 740 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   SER D 740 " --> pdb=" O   LYS D 661 " (cutoff:3.500A)

    146 hydrogen bonds defined for protein.
    420 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.66

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 827
        1.29 -     1.42: 1136
        1.42 -     1.55: 2927
        1.55 -     1.68: 0
        1.68 -     1.81: 16
  Bond restraints: 4906
  Sorted by residual:
  bond pdb=" C   PHE C 207 "
       pdb=" O   PHE C 207 "
    ideal  model  delta    sigma   weight residual
    1.230  1.164  0.066 1.74e-02 3.30e+03 1.44e+01
  bond pdb=" CG  ASP B 754 "
       pdb=" OD1 ASP B 754 "
    ideal  model  delta    sigma   weight residual
    1.249  1.185  0.064 1.90e-02 2.77e+03 1.15e+01
  bond pdb=" N   ARG B 751 "
       pdb=" CA  ARG B 751 "
    ideal  model  delta    sigma   weight residual
    1.457  1.504 -0.047 1.41e-02 5.03e+03 1.11e+01
  bond pdb=" CA  PHE C 207 "
       pdb=" C   PHE C 207 "
    ideal  model  delta    sigma   weight residual
    1.532  1.490  0.042 1.41e-02 5.03e+03 9.05e+00
  bond pdb=" N   VAL B 753 "
       pdb=" CA  VAL B 753 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.90e+00
  ... (remaining 4901 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 6586
        2.59 -     5.19: 93
        5.19 -     7.78: 14
        7.78 -    10.38: 2
       10.38 -    12.97: 1
  Bond angle restraints: 6696
  Sorted by residual:
  angle pdb=" N   ASN B 755 "
        pdb=" CA  ASN B 755 "
        pdb=" C   ASN B 755 "
      ideal   model   delta    sigma   weight residual
     112.23   99.26   12.97 1.26e+00 6.30e-01 1.06e+02
  angle pdb=" CA  ASP B 754 "
        pdb=" CB  ASP B 754 "
        pdb=" CG  ASP B 754 "
      ideal   model   delta    sigma   weight residual
     112.60  105.68    6.92 1.00e+00 1.00e+00 4.78e+01
  angle pdb=" N   ASP B 754 "
        pdb=" CA  ASP B 754 "
        pdb=" C   ASP B 754 "
      ideal   model   delta    sigma   weight residual
     114.75  107.82    6.93 1.26e+00 6.30e-01 3.03e+01
  angle pdb=" C   VAL C 206 "
        pdb=" N   PHE C 207 "
        pdb=" CA  PHE C 207 "
      ideal   model   delta    sigma   weight residual
     123.04  115.84    7.20 1.59e+00 3.96e-01 2.05e+01
  angle pdb=" CA  ASP B 754 "
        pdb=" C   ASP B 754 "
        pdb=" N   ASN B 755 "
      ideal   model   delta    sigma   weight residual
     119.80  114.03    5.77 1.34e+00 5.57e-01 1.85e+01
  ... (remaining 6691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 2712
       17.69 -    35.37: 220
       35.37 -    53.06: 42
       53.06 -    70.74: 8
       70.74 -    88.43: 4
  Dihedral angle restraints: 2986
    sinusoidal: 1024
      harmonic: 1962
  Sorted by residual:
  dihedral pdb=" C   ARG B 751 "
           pdb=" N   ARG B 751 "
           pdb=" CA  ARG B 751 "
           pdb=" CB  ARG B 751 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.03   14.43     0      2.50e+00 1.60e-01 3.33e+01
  dihedral pdb=" N   ARG B 751 "
           pdb=" C   ARG B 751 "
           pdb=" CA  ARG B 751 "
           pdb=" CB  ARG B 751 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  136.97  -14.17     0      2.50e+00 1.60e-01 3.21e+01
  dihedral pdb=" CA  ALA A 165 "
           pdb=" C   ALA A 165 "
           pdb=" N   PHE A 166 "
           pdb=" CA  PHE A 166 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.43  -27.57     0      5.00e+00 4.00e-02 3.04e+01
  ... (remaining 2983 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 756
       0.100 -    0.200: 41
       0.200 -    0.299: 1
       0.299 -    0.399: 0
       0.399 -    0.499: 1
  Chirality restraints: 799
  Sorted by residual:
  chirality pdb=" CA  ARG B 751 "
            pdb=" N   ARG B 751 "
            pdb=" C   ARG B 751 "
            pdb=" CB  ARG B 751 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.22e+00
  chirality pdb=" CA  HIS C 209 "
            pdb=" N   HIS C 209 "
            pdb=" C   HIS C 209 "
            pdb=" CB  HIS C 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  ASN B 755 "
            pdb=" N   ASN B 755 "
            pdb=" C   ASN B 755 "
            pdb=" CB  ASN B 755 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.47e-01
  ... (remaining 796 not shown)

  Planarity restraints: 881
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 754 "    0.019 2.00e-02 2.50e+03   3.93e-02 1.54e+01
        pdb=" C   ASP B 754 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   ASP B 754 "    0.027 2.00e-02 2.50e+03
        pdb=" N   ASN B 755 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 207 "   -0.013 2.00e-02 2.50e+03   2.68e-02 7.19e+00
        pdb=" C   PHE C 207 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PHE C 207 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   SER C 208 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS D 719 "    0.043 5.00e-02 4.00e+02   6.50e-02 6.77e+00
        pdb=" N   PRO D 720 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO D 720 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO D 720 "    0.036 5.00e-02 4.00e+02
  ... (remaining 878 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.82: 1476
        2.82 -     3.34: 4438
        3.34 -     3.86: 7059
        3.86 -     4.38: 7728
        4.38 -     4.90: 13370
  Nonbonded interactions: 34071
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  77 "
            pdb=" OG1 THR A  78 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" OD1 ASN A 189 "
            pdb=" N   GLU A 190 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" O   GLU B 641 "
            pdb=" ND1 HIS B 645 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" OD2 ASP A 181 "
            pdb=" NH1 ARG B 743 "
     model   vdw
     2.391 3.120
  nonbonded pdb=" N   ASN B 755 "
            pdb=" N   ARG B 756 "
     model   vdw
     2.402 2.560
  ... (remaining 34066 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 61 through 78 or (resid 79 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 80 through 89 or (resid 90 through 91 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 92 through 100 or (re \ 
sid 101 through 103 and (name N or name CA or name C or name O or name CB )) or  \ 
resid 104 through 120 or (resid 121 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 122 through 123 or (resid 124 through 125 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 126 through 131 or (resid 132  \ 
through 136 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 
7 through 148 or (resid 149 through 165 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 166 through 195 or (resid 196 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 197 through 198 or (resid 199 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 200 through 208 or (re \ 
sid 209 and (name N or name CA or name C or name O or name CB )) or resid 210 th \ 
rough 218))
  selection = (chain 'C' and ((resid 61 through 66 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 67 through 68 or (resid 69 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 70 through 84 or (resid 85 through 91 and (n \ 
ame N or name CA or name C or name O or name CB )) or resid 92 through 130 or (r \ 
esid 131 through 136 and (name N or name CA or name C or name O or name CB )) or \ 
 resid 137 through 147 or (resid 148 through 165 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 166 through 168 or (resid 169 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 170 through 211 or (resid 212 \ 
 through 214 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 
15 through 218))
}
ncs_group {
  reference = (chain 'B' and (resid 624 through 637 or (resid 638 through 639 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 640 through 703 or (resid 704  \ 
and (name N or name CA or name C or name O or name CB )) or resid 705 through 72 \ 
4 or (resid 725 through 726 and (name N or name CA or name C or name O or name C \ 
B )) or resid 727 through 744 or (resid 745 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 746 through 773 or (resid 774 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 775 through 792 or (resid 793 thro \ 
ugh 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or \ 
 (resid 796 through 807 and (name N or name CA or name C or name O or name CB )) \ 
))
  selection = (chain 'D' and (resid 624 through 641 or (resid 642 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 643 through 663 or (resid 664 through 665  \ 
and (name N or name CA or name C or name O or name CB )) or resid 666 or (resid  \ 
667 and (name N or name CA or name C or name O or name CB )) or resid 668 throug \ 
h 677 or (resid 678 through 684 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 685 through 718 or (resid 719 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 720 or (resid 721 through 723 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 724 through 730 or (resid 731  \ 
and (name N or name CA or name C or name O or name CB )) or resid 732 through 76 \ 
3 or (resid 764 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 765 through 779 or (resid 780 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 781 through 801 or (resid 802 through 807 and (name N or name  \ 
CA or name C or name O or name CB ))))
}

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=0.00 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.880
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   4906  Z= 0.194
  Angle     :  0.751  12.974   6696  Z= 0.431
  Chirality :  0.050   0.499    799
  Planarity :  0.006   0.065    881
  Dihedral  : 14.175  88.428   1704
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  :  2.12 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.82 (0.25), residues: 661
  helix: -2.09 (0.32), residues: 184
  sheet: -1.39 (1.44), residues: 16
  loop : -4.10 (0.22), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 701 
 TYR   0.008   0.001   TYR D 649 
 PHE   0.039   0.001   PHE C 207 
 TRP   0.004   0.001   TRP A 198 
 HIS   0.002   0.000   HIS B 645 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4906)
  covalent geometry    : angle       0.75105 ( 6696)
  hydrogen bonds       : bond        0.20526 (  146)
  hydrogen bonds       : angle       7.16464 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  658 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8160 (mmm160)
REVERT: B  708 LYS cc_start: 0.9000 (tppt) cc_final: 0.8467 (mtmm)
REVERT: B  761 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7627 (mptt)
REVERT: C  173 LEU cc_start: 0.9141 (tp) cc_final: 0.8752 (tp)
REVERT: C  191 ASN cc_start: 0.9025 (t0) cc_final: 0.8719 (t0)
REVERT: D  642 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6767 (mp0)
REVERT: D  655 GLN cc_start: 0.8110 (mt0) cc_final: 0.7851 (mt0)
REVERT: D  768 LYS cc_start: 0.8696 (pttm) cc_final: 0.7556 (tppt)
REVERT: D  788 GLN cc_start: 0.7973 (mp10) cc_final: 0.7748 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 223
  average time/residue: 0.0750
  time to fit residues: 20.7819
Evaluate side-chains
  181 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0470
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0770
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    0.0470
   chunk 64 optimal weight:    6.9990
   overall best weight:    0.2134

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

Flipped N/Q/H residues before XYZ refinement:
B 757 GLN
C  67 ASN
C 118 ASN
** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 764 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.160068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.126889 restraints weight = 7907.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.130676 restraints weight = 4652.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.133392 restraints weight = 3234.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.135029 restraints weight = 2526.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.136409 restraints weight = 2158.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   4906  Z= 0.127
  Angle     :  0.696   9.980   6696  Z= 0.344
  Chirality :  0.047   0.188    799
  Planarity :  0.005   0.062    881
  Dihedral  :  4.593  20.479    697
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.83 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 18.06 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.46 (0.29), residues: 661
  helix: -0.34 (0.36), residues: 194
  sheet: -2.58 (1.20), residues: 15
  loop : -3.48 (0.25), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 751 
 TYR   0.011   0.001   TYR D 649 
 PHE   0.007   0.001   PHE B 669 
 TRP   0.004   0.001   TRP C 198 
 HIS   0.002   0.000   HIS B 645 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4906)
  covalent geometry    : angle       0.69586 ( 6696)
  hydrogen bonds       : bond        0.03078 (  146)
  hydrogen bonds       : angle       4.61469 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 211
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A  111 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7746 (mt-10)
REVERT: B  658 ARG cc_start: 0.9068 (mmm160) cc_final: 0.7838 (mmm160)
REVERT: B  708 LYS cc_start: 0.9099 (tppt) cc_final: 0.8381 (mtmm)
REVERT: B  725 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7011 (tm-30)
REVERT: B  754 ASP cc_start: 0.8436 (p0) cc_final: 0.8209 (p0)
REVERT: B  761 LYS cc_start: 0.8356 (mtpp) cc_final: 0.7494 (mmtm)
REVERT: B  769 ARG cc_start: 0.9426 (mmm160) cc_final: 0.9183 (mmm-85)
REVERT: C  108 TYR cc_start: 0.8446 (m-80) cc_final: 0.8218 (m-80)
REVERT: C  114 GLU cc_start: 0.8151 (tp30) cc_final: 0.7680 (tp30)
REVERT: C  173 LEU cc_start: 0.8824 (tp) cc_final: 0.8436 (tp)
REVERT: C  189 ASN cc_start: 0.8646 (m110) cc_final: 0.8208 (p0)
REVERT: C  190 GLU cc_start: 0.8841 (pt0) cc_final: 0.8618 (pm20)
REVERT: C  191 ASN cc_start: 0.9300 (t0) cc_final: 0.8730 (t0)
REVERT: D  641 GLU cc_start: 0.8647 (mp0) cc_final: 0.8099 (pm20)
REVERT: D  642 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7011 (mp0)
REVERT: D  675 VAL cc_start: 0.9189 (t) cc_final: 0.8897 (p)
REVERT: D  768 LYS cc_start: 0.9085 (pttm) cc_final: 0.8105 (tppt)
  outliers start: 14
  outliers final: 7
  residues processed: 214
  average time/residue: 0.0707
  time to fit residues: 19.0679
Evaluate side-chains
  198 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 191
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  195 SER
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  776 LEU
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 767 GLN
C  67 ASN
** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 764 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.150753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.117750 restraints weight = 8185.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.121045 restraints weight = 4944.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.123424 restraints weight = 3549.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.124655 restraints weight = 2833.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.125930 restraints weight = 2486.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   4906  Z= 0.150
  Angle     :  0.670   9.239   6696  Z= 0.336
  Chirality :  0.046   0.170    799
  Planarity :  0.005   0.067    881
  Dihedral  :  4.717  21.632    697
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.56 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 21.59 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.87 (0.30), residues: 661
  helix:  0.35 (0.38), residues: 193
  sheet:  0.13 (1.73), residues: 11
  loop : -3.26 (0.25), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 751 
 TYR   0.006   0.001   TYR D 649 
 PHE   0.014   0.001   PHE A 166 
 TRP   0.005   0.001   TRP D 671 
 HIS   0.004   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4906)
  covalent geometry    : angle       0.67001 ( 6696)
  hydrogen bonds       : bond        0.03522 (  146)
  hydrogen bonds       : angle       4.30664 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 200
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: B  661 LYS cc_start: 0.6293 (tttt) cc_final: 0.5537 (tttp)
REVERT: B  708 LYS cc_start: 0.9141 (tppt) cc_final: 0.8438 (mttp)
REVERT: B  725 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7114 (tm-30)
REVERT: B  761 LYS cc_start: 0.8431 (mtpp) cc_final: 0.7582 (mmtm)
REVERT: C  111 GLU cc_start: 0.8859 (mp0) cc_final: 0.8626 (pm20)
REVERT: C  173 LEU cc_start: 0.8949 (tp) cc_final: 0.8552 (tp)
REVERT: C  191 ASN cc_start: 0.9335 (t0) cc_final: 0.8825 (t0)
REVERT: D  641 GLU cc_start: 0.8641 (mp0) cc_final: 0.8085 (mp0)
REVERT: D  642 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7023 (mp0)
REVERT: D  675 VAL cc_start: 0.9199 (t) cc_final: 0.8879 (p)
REVERT: D  768 LYS cc_start: 0.9028 (pttm) cc_final: 0.8039 (tppp)
  outliers start: 29
  outliers final: 21
  residues processed: 209
  average time/residue: 0.0602
  time to fit residues: 16.1941
Evaluate side-chains
  214 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  643 TYR
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  767 GLN
Chi-restraints excluded: chain B residue  785 ILE
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue  646 LYS
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  709 ASN
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  733 VAL
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   chunk 64 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
B 709 ASN
C  67 ASN
C 118 ASN
** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.143397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.112071 restraints weight = 8267.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.115276 restraints weight = 4911.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.117480 restraints weight = 3479.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.118783 restraints weight = 2760.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.119505 restraints weight = 2395.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7424
moved from start:          0.4070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4906  Z= 0.201
  Angle     :  0.720  10.354   6696  Z= 0.365
  Chirality :  0.047   0.179    799
  Planarity :  0.005   0.066    881
  Dihedral  :  5.105  24.196    697
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  : 15.13 %
    Favored  : 84.72 %
  Rotamer:
    Outliers :  7.93 %
    Allowed  : 24.67 %
    Favored  : 67.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.61 (0.31), residues: 661
  helix:  0.79 (0.38), residues: 192
  sheet:  0.24 (1.63), residues: 11
  loop : -3.20 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 751 
 TYR   0.009   0.001   TYR A 203 
 PHE   0.010   0.002   PHE C 123 
 TRP   0.006   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 4906)
  covalent geometry    : angle       0.72039 ( 6696)
  hydrogen bonds       : bond        0.03919 (  146)
  hydrogen bonds       : angle       4.33988 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 198
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7695 (mt-10)
REVERT: B  725 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7281 (tm-30)
REVERT: B  761 LYS cc_start: 0.8516 (mtpp) cc_final: 0.7661 (mmtm)
REVERT: C  108 TYR cc_start: 0.8531 (m-80) cc_final: 0.8249 (m-80)
REVERT: C  111 GLU cc_start: 0.8873 (mp0) cc_final: 0.8623 (pm20)
REVERT: C  173 LEU cc_start: 0.8971 (tp) cc_final: 0.8656 (tp)
REVERT: C  191 ASN cc_start: 0.9370 (t0) cc_final: 0.8973 (t0)
REVERT: C  203 TYR cc_start: 0.8206 (p90) cc_final: 0.7910 (p90)
REVERT: D  641 GLU cc_start: 0.8642 (mp0) cc_final: 0.8092 (mp0)
REVERT: D  642 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7038 (mp0)
REVERT: D  743 ARG cc_start: 0.8833 (ttt-90) cc_final: 0.8629 (ttt-90)
REVERT: D  768 LYS cc_start: 0.9085 (pttm) cc_final: 0.8173 (tppt)
REVERT: D  782 ASP cc_start: 0.8689 (m-30) cc_final: 0.8230 (m-30)
REVERT: D  788 GLN cc_start: 0.8316 (mp10) cc_final: 0.8088 (mp10)
  outliers start: 36
  outliers final: 25
  residues processed: 212
  average time/residue: 0.0625
  time to fit residues: 16.8140
Evaluate side-chains
  217 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 192
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain B residue  643 TYR
Chi-restraints excluded: chain B residue  644 ILE
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  660 VAL
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  726 MET
Chi-restraints excluded: chain B residue  785 ILE
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue  646 LYS
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  709 ASN
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  733 VAL
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  781 ASP
Chi-restraints excluded: chain D residue  790 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    0.0570
   chunk 29 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    7.9990
   overall best weight:    1.4104

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
B 655 GLN
C 118 ASN
** D 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.114975 restraints weight = 8441.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.118509 restraints weight = 4810.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.120750 restraints weight = 3269.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.122506 restraints weight = 2532.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.123412 restraints weight = 2100.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.4376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4906  Z= 0.149
  Angle     :  0.691  11.164   6696  Z= 0.341
  Chirality :  0.046   0.176    799
  Planarity :  0.005   0.065    881
  Dihedral  :  4.945  23.967    697
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 13.16 %
    Favored  : 86.54 %
  Rotamer:
    Outliers :  7.05 %
    Allowed  : 25.99 %
    Favored  : 66.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.30 (0.32), residues: 661
  helix:  1.25 (0.39), residues: 192
  sheet:  0.65 (1.49), residues: 11
  loop : -3.11 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 751 
 TYR   0.006   0.001   TYR A 203 
 PHE   0.009   0.001   PHE A 178 
 TRP   0.003   0.001   TRP B 671 
 HIS   0.003   0.001   HIS A 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 4906)
  covalent geometry    : angle       0.69147 ( 6696)
  hydrogen bonds       : bond        0.03211 (  146)
  hydrogen bonds       : angle       4.08407 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 197
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8004 (mt-10)
REVERT: B  725 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7180 (tm-30)
REVERT: B  727 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8565 (mm-40)
REVERT: B  761 LYS cc_start: 0.8473 (mtpp) cc_final: 0.7638 (mmtm)
REVERT: C  108 TYR cc_start: 0.8469 (m-80) cc_final: 0.8240 (m-80)
REVERT: C  111 GLU cc_start: 0.8876 (mp0) cc_final: 0.8633 (pm20)
REVERT: C  191 ASN cc_start: 0.9392 (t0) cc_final: 0.9089 (t0)
REVERT: D  641 GLU cc_start: 0.8673 (mp0) cc_final: 0.8036 (mp0)
REVERT: D  642 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6844 (mp0)
REVERT: D  655 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8527 (mm-40)
REVERT: D  768 LYS cc_start: 0.8931 (pttm) cc_final: 0.8004 (tppp)
REVERT: D  782 ASP cc_start: 0.8796 (m-30) cc_final: 0.8416 (m-30)
  outliers start: 32
  outliers final: 22
  residues processed: 207
  average time/residue: 0.0678
  time to fit residues: 17.6509
Evaluate side-chains
  210 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain B residue  643 TYR
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  733 VAL
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:   50.0000
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.139931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.110982 restraints weight = 8582.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.114263 restraints weight = 4992.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.116604 restraints weight = 3458.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.117806 restraints weight = 2684.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.119031 restraints weight = 2314.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.4790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4906  Z= 0.196
  Angle     :  0.741  11.446   6696  Z= 0.367
  Chirality :  0.048   0.181    799
  Planarity :  0.005   0.064    881
  Dihedral  :  5.138  24.159    697
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 15.13 %
    Favored  : 84.57 %
  Rotamer:
    Outliers :  8.15 %
    Allowed  : 26.87 %
    Favored  : 64.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.32), residues: 661
  helix:  1.22 (0.39), residues: 189
  sheet:  0.72 (1.44), residues: 11
  loop : -3.02 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 751 
 TYR   0.007   0.001   TYR A 203 
 PHE   0.010   0.002   PHE A 178 
 TRP   0.003   0.001   TRP D 671 
 HIS   0.004   0.001   HIS B 645 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 4906)
  covalent geometry    : angle       0.74143 ( 6696)
  hydrogen bonds       : bond        0.03765 (  146)
  hydrogen bonds       : angle       4.22626 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 193
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7926 (mt-10)
REVERT: B  658 ARG cc_start: 0.9224 (mmm160) cc_final: 0.8989 (mmm160)
REVERT: B  725 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7109 (tm-30)
REVERT: B  761 LYS cc_start: 0.8507 (mtpp) cc_final: 0.7693 (mmtm)
REVERT: C  108 TYR cc_start: 0.8585 (m-80) cc_final: 0.8278 (m-80)
REVERT: C  111 GLU cc_start: 0.8912 (mp0) cc_final: 0.8589 (pm20)
REVERT: C  113 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7797 (mt-10)
REVERT: C  173 LEU cc_start: 0.8804 (tp) cc_final: 0.8584 (tp)
REVERT: C  191 ASN cc_start: 0.9271 (t0) cc_final: 0.8995 (t0)
REVERT: D  641 GLU cc_start: 0.8748 (mp0) cc_final: 0.8139 (mp0)
REVERT: D  642 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6835 (mp0)
REVERT: D  768 LYS cc_start: 0.8952 (pttm) cc_final: 0.8031 (tppp)
  outliers start: 37
  outliers final: 31
  residues processed: 205
  average time/residue: 0.0707
  time to fit residues: 18.1466
Evaluate side-chains
  218 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 187
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  210 ILE
Chi-restraints excluded: chain B residue  643 TYR
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  726 MET
Chi-restraints excluded: chain B residue  776 LEU
Chi-restraints excluded: chain B residue  785 ILE
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  659 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  712 THR
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  733 VAL
Chi-restraints excluded: chain D residue  735 LEU
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 51 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 56 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0050
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
** B 655 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 = 0.3691 r_free = 0.3691 target = 0.145661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.115196 restraints weight = 8408.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.118661 restraints weight = 4914.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.121058 restraints weight = 3417.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.122111 restraints weight = 2682.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.123512 restraints weight = 2348.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4906  Z= 0.120
  Angle     :  0.703  12.000   6696  Z= 0.339
  Chirality :  0.047   0.170    799
  Planarity :  0.005   0.063    881
  Dihedral  :  4.701  22.521    697
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.10 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 29.74 %
    Favored  : 64.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.09 (0.33), residues: 661
  helix:  1.31 (0.39), residues: 198
  sheet:  1.13 (1.49), residues: 11
  loop : -2.99 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 751 
 TYR   0.008   0.001   TYR D 649 
 PHE   0.011   0.001   PHE C 115 
 TRP   0.004   0.001   TRP A 198 
 HIS   0.002   0.001   HIS B 645 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4906)
  covalent geometry    : angle       0.70324 ( 6696)
  hydrogen bonds       : bond        0.02716 (  146)
  hydrogen bonds       : angle       3.85365 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 206
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7885 (mt-10)
REVERT: B  658 ARG cc_start: 0.9157 (mmm160) cc_final: 0.8923 (mmm160)
REVERT: B  725 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7043 (tm-30)
REVERT: B  727 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8522 (mm-40)
REVERT: B  761 LYS cc_start: 0.8457 (mtpp) cc_final: 0.7621 (mmtm)
REVERT: C  108 TYR cc_start: 0.8549 (m-80) cc_final: 0.8265 (m-80)
REVERT: C  191 ASN cc_start: 0.9235 (t0) cc_final: 0.8907 (t0)
REVERT: D  641 GLU cc_start: 0.8852 (mp0) cc_final: 0.8274 (mp0)
REVERT: D  642 GLU cc_start: 0.7411 (mm-30) cc_final: 0.6819 (mp0)
REVERT: D  651 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8950 (mm)
REVERT: D  768 LYS cc_start: 0.8804 (pttm) cc_final: 0.7961 (tppp)
  outliers start: 24
  outliers final: 19
  residues processed: 216
  average time/residue: 0.0657
  time to fit residues: 18.1259
Evaluate side-chains
  208 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 188
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  731 VAL
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 44 optimal weight:    0.0010
   chunk 63 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 61 optimal weight:    0.1980
   chunk 5 optimal weight:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
** B 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.147046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.117702 restraints weight = 8362.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.121233 restraints weight = 4876.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.123678 restraints weight = 3372.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.125123 restraints weight = 2619.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.126360 restraints weight = 2235.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4906  Z= 0.124
  Angle     :  0.715  12.349   6696  Z= 0.343
  Chirality :  0.047   0.170    799
  Planarity :  0.005   0.061    881
  Dihedral  :  4.532  24.519    697
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 13.01 %
    Favored  : 86.69 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 29.74 %
    Favored  : 64.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.33), residues: 661
  helix:  1.48 (0.39), residues: 198
  sheet:  1.23 (1.53), residues: 11
  loop : -2.93 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 751 
 TYR   0.011   0.001   TYR D 649 
 PHE   0.007   0.001   PHE C 115 
 TRP   0.002   0.000   TRP A 198 
 HIS   0.002   0.001   HIS B 645 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 4906)
  covalent geometry    : angle       0.71454 ( 6696)
  hydrogen bonds       : bond        0.02659 (  146)
  hydrogen bonds       : angle       3.78606 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 193
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7897 (mt-10)
REVERT: B  658 ARG cc_start: 0.9173 (mmm160) cc_final: 0.8941 (mmm160)
REVERT: B  725 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7009 (tm-30)
REVERT: B  761 LYS cc_start: 0.8451 (mtpp) cc_final: 0.7606 (mmtm)
REVERT: B  790 LEU cc_start: 0.9052 (mm) cc_final: 0.8838 (mm)
REVERT: C  108 TYR cc_start: 0.8412 (m-80) cc_final: 0.8171 (m-80)
REVERT: C  190 GLU cc_start: 0.8760 (pm20) cc_final: 0.8423 (pm20)
REVERT: C  191 ASN cc_start: 0.9195 (t0) cc_final: 0.8896 (t0)
REVERT: D  651 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8911 (mm)
REVERT: D  768 LYS cc_start: 0.8805 (pttm) cc_final: 0.7887 (tppp)
  outliers start: 25
  outliers final: 19
  residues processed: 203
  average time/residue: 0.0672
  time to fit residues: 17.3443
Evaluate side-chains
  209 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 189
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ASN
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  643 TYR
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  145 ILE
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  753 VAL
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 7 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0370
   chunk 56 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
** B 655 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 = 0.3714 r_free = 0.3714 target = 0.147735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.118405 restraints weight = 8220.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.121863 restraints weight = 4829.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.124295 restraints weight = 3359.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.125546 restraints weight = 2616.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.126874 restraints weight = 2257.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.4993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4906  Z= 0.126
  Angle     :  0.732  12.480   6696  Z= 0.353
  Chirality :  0.047   0.178    799
  Planarity :  0.005   0.060    881
  Dihedral  :  4.513  24.571    697
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.56 %
    Favored  : 87.14 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 31.06 %
    Favored  : 64.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.33), residues: 661
  helix:  1.62 (0.39), residues: 198
  sheet:  1.35 (1.57), residues: 11
  loop : -2.93 (0.27), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 751 
 TYR   0.015   0.001   TYR D 649 
 PHE   0.006   0.001   PHE A 123 
 TRP   0.002   0.000   TRP A 198 
 HIS   0.002   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 4906)
  covalent geometry    : angle       0.73160 ( 6696)
  hydrogen bonds       : bond        0.02606 (  146)
  hydrogen bonds       : angle       3.78429 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 190
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7840 (mt-10)
REVERT: B  658 ARG cc_start: 0.9153 (mmm160) cc_final: 0.8887 (mmm160)
REVERT: B  725 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7036 (tm-30)
REVERT: B  761 LYS cc_start: 0.8406 (mtpp) cc_final: 0.7597 (mmtm)
REVERT: B  790 LEU cc_start: 0.9048 (mm) cc_final: 0.8830 (mm)
REVERT: C  190 GLU cc_start: 0.8787 (pm20) cc_final: 0.8419 (pm20)
REVERT: C  191 ASN cc_start: 0.9179 (t0) cc_final: 0.8898 (t0)
REVERT: D  641 GLU cc_start: 0.8373 (mp0) cc_final: 0.7979 (pm20)
REVERT: D  642 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6853 (mp0)
REVERT: D  648 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7716 (tmmt)
REVERT: D  651 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8877 (mm)
REVERT: D  768 LYS cc_start: 0.8765 (pttm) cc_final: 0.7926 (tppp)
  outliers start: 19
  outliers final: 18
  residues processed: 200
  average time/residue: 0.0680
  time to fit residues: 17.1361
Evaluate side-chains
  208 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 189
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  646 LYS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  726 MET
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  741 SER
Chi-restraints excluded: chain D residue  753 VAL
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 10 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0570
   chunk 24 optimal weight:    0.9980
   chunk 44 optimal weight:    0.2980
   chunk 32 optimal weight:    0.0010
   chunk 40 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0370
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 185 GLN
** B 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.152952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.121736 restraints weight = 8166.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.125274 restraints weight = 4756.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.127807 restraints weight = 3316.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.129554 restraints weight = 2588.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.130397 restraints weight = 2192.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.5062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4906  Z= 0.125
  Angle     :  0.738  12.826   6696  Z= 0.352
  Chirality :  0.047   0.162    799
  Planarity :  0.005   0.061    881
  Dihedral  :  4.221  22.695    697
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 11.04 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 31.50 %
    Favored  : 64.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.33), residues: 661
  helix:  1.86 (0.39), residues: 196
  sheet:  1.63 (1.64), residues: 11
  loop : -2.83 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 751 
 TYR   0.014   0.001   TYR D 649 
 PHE   0.006   0.001   PHE B 669 
 TRP   0.002   0.000   TRP A 198 
 HIS   0.002   0.000   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4906)
  covalent geometry    : angle       0.73817 ( 6696)
  hydrogen bonds       : bond        0.02267 (  146)
  hydrogen bonds       : angle       3.65403 (  420)

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

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

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1322 Ramachandran restraints generated.
    661 Oldfield, 0 Emsley, 661 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7861 (mt-10)
REVERT: B  661 LYS cc_start: 0.6240 (tttt) cc_final: 0.5336 (tttp)
REVERT: B  725 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7118 (tm-30)
REVERT: B  761 LYS cc_start: 0.8393 (mtpp) cc_final: 0.7607 (mmtm)
REVERT: B  790 LEU cc_start: 0.9050 (mm) cc_final: 0.8832 (mm)
REVERT: C  107 GLN cc_start: 0.8379 (pt0) cc_final: 0.8015 (pp30)
REVERT: C  190 GLU cc_start: 0.8831 (pm20) cc_final: 0.8579 (pm20)
REVERT: C  191 ASN cc_start: 0.9097 (t0) cc_final: 0.8787 (t0)
REVERT: D  641 GLU cc_start: 0.8336 (mp0) cc_final: 0.7983 (pm20)
REVERT: D  642 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6775 (mp0)
REVERT: D  648 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7793 (tmmt)
REVERT: D  651 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8911 (mm)
REVERT: D  768 LYS cc_start: 0.8737 (pttm) cc_final: 0.7805 (tppp)
  outliers start: 18
  outliers final: 16
  residues processed: 201
  average time/residue: 0.0705
  time to fit residues: 17.7014
Evaluate side-chains
  200 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 183
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  171 SER
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain B residue  645 HIS
Chi-restraints excluded: chain B residue  669 PHE
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  118 ASN
Chi-restraints excluded: chain C residue  210 ILE
Chi-restraints excluded: chain D residue  650 CYS
Chi-restraints excluded: chain D residue  651 LEU
Chi-restraints excluded: chain D residue  663 LYS
Chi-restraints excluded: chain D residue  696 VAL
Chi-restraints excluded: chain D residue  710 SER
Chi-restraints excluded: chain D residue  753 VAL
Chi-restraints excluded: chain D residue  781 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 64 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0070
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** B 655 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 118 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.150934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.119128 restraints weight = 8244.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.122540 restraints weight = 4881.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.124966 restraints weight = 3456.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.126633 restraints weight = 2729.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.127526 restraints weight = 2330.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.5142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4906  Z= 0.127
  Angle     :  0.740  12.554   6696  Z= 0.357
  Chirality :  0.046   0.153    799
  Planarity :  0.005   0.056    881
  Dihedral  :  4.249  22.816    697
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 11.95 %
    Favored  : 87.75 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 33.70 %
    Favored  : 62.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.33), residues: 661
  helix:  1.89 (0.39), residues: 197
  sheet:  1.72 (1.65), residues: 11
  loop : -2.79 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 751 
 TYR   0.014   0.001   TYR D 649 
 PHE   0.006   0.001   PHE C 115 
 TRP   0.002   0.001   TRP A 198 
 HIS   0.002   0.000   HIS B 645 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4906)
  covalent geometry    : angle       0.73951 ( 6696)
  hydrogen bonds       : bond        0.02480 (  146)
  hydrogen bonds       : angle       3.70743 (  420)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 963.12 seconds
wall clock time: 17 minutes 12.49 seconds (1032.49 seconds total)