Starting phenix.real_space_refine
on Mon May 12 05:05:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ivd_60925/05_2025/9ivd_60925.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ivd_60925/05_2025/9ivd_60925.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ivd_60925/05_2025/9ivd_60925.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ivd_60925/05_2025/9ivd_60925.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ivd_60925/05_2025/9ivd_60925.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ivd_60925/05_2025/9ivd_60925.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.043
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 52 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      43      5.16       5
     C    5544      2.51       5
     N    1496      2.21       5
     O    1544      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 8628
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "E"
      Number of atoms: 89
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 89
          Classifications: {'peptide': 11}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 9}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2824
          Classifications: {'peptide': 364}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 19, 'TRANS': 344}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 43
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 28
    Chain: "A"
      Number of atoms: 5715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 785, 5715
          Classifications: {'peptide': 785}
          Incomplete info: {'truncation_to_alanine': 130}
          Link IDs: {'PTRANS': 26, 'TRANS': 758}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 478
          Unresolved non-hydrogen angles: 587
          Unresolved non-hydrogen dihedrals: 375
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 23, 'ASN:plan1': 4, 'HIS:plan': 3, 'GLU:plan': 48, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 365
  Time building chain proxies: 4.91, per 1000 atoms: 0.57
  Number of scatterers: 8628
  At special positions: 0
  Unit cell: (92.65, 111.35, 107.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      43     16.00
     P       1     15.00
     O    1544      8.00
     N    1496      7.00
     C    5544      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  18 " - pdb=" SG  CYS A 313 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.89
  Conformation dependent library (CDL) restraints added in 983.9 milliseconds
  

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2162

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 27 sheets defined
      5.9% alpha, 32.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 18
      removed outlier: 3.668A  pdb=" N   ARG B  18 " --> pdb=" O   TRP B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 36
    Processing helix  chain 'B' and resid 891 through 895
      removed outlier: 4.161A  pdb=" N   CYS B 895 " --> pdb=" O   ASP B 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1046 through 1058
      removed outlier: 3.668A  pdb=" N   LEU A1050 " --> pdb=" O   SER A1046 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ASP A1053 " --> pdb=" O   ASN A1049 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG A1057 " --> pdb=" O   ASP A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1096
    Processing helix  chain 'A' and resid 1097 through 1099
      No H-bonds generated for 'chain 'A' and resid 1097 through 1099'
    Processing helix  chain 'A' and resid 1104 through 1108
    Processing helix  chain 'A' and resid 1125 through 1130
    Processing helix  chain 'A' and resid 1131 through 1137
    Processing sheet with id=AA1, first strand: chain 'B' and resid 41 through 46
      removed outlier: 3.700A  pdb=" N   VAL B1034 " --> pdb=" O   TYR B1026 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR B1026 " --> pdb=" O   VAL B1034 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 56 through 61
      removed outlier: 4.714A  pdb=" N   LEU B  58 " --> pdb=" O   THR B  71 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B  68 " --> pdb=" O   THR B  80 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   HIS B  72 " --> pdb=" O   ASN B  76 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ASN B  76 " --> pdb=" O   HIS B  72 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ILE B  77 " --> pdb=" O   SER B  90 " (cutoff:3.500A)
      removed outlier: 5.026A  pdb=" N   SER B  90 " --> pdb=" O   ILE B  77 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   ILE B  79 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 120
    Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145
    Processing sheet with id=AA5, first strand: chain 'B' and resid 183 through 185
      removed outlier: 6.587A  pdb=" N   ALA B 198 " --> pdb=" O   ARG B 184 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR B 197 " --> pdb=" O   GLN B 863 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   THR B 859 " --> pdb=" O   ASN B 201 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 903 through 906
      removed outlier: 3.601A  pdb=" N   ALA B 922 " --> pdb=" O   ALA B 906 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 949
      removed outlier: 3.902A  pdb=" N   SER B 946 " --> pdb=" O   GLY B 959 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   VAL B 975 " --> pdb=" O   LEU B 960 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ARG B 980 " --> pdb=" O   ARG B 992 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   ARG B 992 " --> pdb=" O   ARG B 980 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 944 through 949
      removed outlier: 3.902A  pdb=" N   SER B 946 " --> pdb=" O   GLY B 959 " (cutoff:3.500A)
      removed outlier: 5.761A  pdb=" N   VAL B 975 " --> pdb=" O   LEU B 960 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   VAL B 997 " --> pdb=" O   VAL B 975 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 4 through 10
      removed outlier: 6.262A  pdb=" N   ILE A1037 " --> pdb=" O   ALA A   9 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   PHE A1030 " --> pdb=" O   GLY A1038 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU A1029 " --> pdb=" O   PHE A1007 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   PHE A1007 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   GLY A1031 " --> pdb=" O   ASN A1005 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 18 through 21
      removed outlier: 3.785A  pdb=" N   LYS A  53 " --> pdb=" O   ILE A  41 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   VAL A  43 " --> pdb=" O   PRO A  51 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 61 through 67
      removed outlier: 7.033A  pdb=" N   LEU A  80 " --> pdb=" O   ALA A  62 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   MET A  64 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   PHE A  78 " --> pdb=" O   MET A  64 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   LEU A  66 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU A  76 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 85 through 89
      removed outlier: 6.975A  pdb=" N   ALA A  86 " --> pdb=" O   HIS A 105 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   HIS A 105 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ILE A  88 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 92 through 94
      removed outlier: 3.543A  pdb=" N   ASP A  99 " --> pdb=" O   LYS A  92 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 121 through 124
      removed outlier: 3.660A  pdb=" N   ILE A 121 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 139 through 142
      removed outlier: 3.690A  pdb=" N   VAL A 142 " --> pdb=" O   PHE A 155 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   PHE A 155 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 163 through 169
      removed outlier: 4.392A  pdb=" N   HIS A 163 " --> pdb=" O   GLN A 183 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   VAL A 167 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   CYS A 179 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   PHE A 169 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   THR A 177 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLU A 201 " --> pdb=" O   SER A 196 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 163 through 169
      removed outlier: 4.392A  pdb=" N   HIS A 163 " --> pdb=" O   GLN A 183 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   VAL A 167 " --> pdb=" O   CYS A 179 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   CYS A 179 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 4.971A  pdb=" N   PHE A 169 " --> pdb=" O   THR A 177 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   THR A 177 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   VAL A 190 " --> pdb=" O   GLU A 210 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 219 through 221
      removed outlier: 3.607A  pdb=" N   HIS A 240 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU A 246 " --> pdb=" O   TYR A 239 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 258 through 263
      removed outlier: 4.555A  pdb=" N   CYS A 260 " --> pdb=" O   GLY A 274 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY A 274 " --> pdb=" O   CYS A 260 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A 273 " --> pdb=" O   PHE A 281 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   ASP A 275 " --> pdb=" O   ARG A 279 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   ARG A 279 " --> pdb=" O   ASP A 275 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG A 301 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 314 through 318
      removed outlier: 6.910A  pdb=" N   VAL A 321 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   LEU A 333 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 362 through 365
      removed outlier: 3.874A  pdb=" N   LEU A 387 " --> pdb=" O   VAL A 715 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'A' and resid 720 through 726
      removed outlier: 6.678A  pdb=" N   LEU A 736 " --> pdb=" O   ARG A 722 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ILE A 724 " --> pdb=" O   GLY A 734 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   GLY A 734 " --> pdb=" O   ILE A 724 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 811 through 819
      removed outlier: 5.476A  pdb=" N   ALA A 813 " --> pdb=" O   ALA A 834 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   ALA A 834 " --> pdb=" O   ALA A 813 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER A 815 " --> pdb=" O   GLY A 832 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   CYS A 819 " --> pdb=" O   TYR A 828 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'A' and resid 811 through 819
      removed outlier: 5.476A  pdb=" N   ALA A 813 " --> pdb=" O   ALA A 834 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   ALA A 834 " --> pdb=" O   ALA A 813 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER A 815 " --> pdb=" O   GLY A 832 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   CYS A 819 " --> pdb=" O   TYR A 828 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLN A 852 " --> pdb=" O   GLN A 859 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'A' and resid 870 through 873
      removed outlier: 4.702A  pdb=" N   SER A 872 " --> pdb=" O   SER A 883 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   VAL A 888 " --> pdb=" O   ASN A 904 " (cutoff:3.500A)
      removed outlier: 4.463A  pdb=" N   ASN A 904 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   LEU A 890 " --> pdb=" O   GLU A 902 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ARG A 900 " --> pdb=" O   GLU A 892 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'A' and resid 921 through 922
      removed outlier: 3.829A  pdb=" N   LEU A 922 " --> pdb=" O   LEU A 933 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU A 933 " --> pdb=" O   LEU A 922 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   LEU A 932 " --> pdb=" O   ILE A 945 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'A' and resid 954 through 959
      removed outlier: 3.929A  pdb=" N   ALA A 956 " --> pdb=" O   ALA A 968 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE A 965 " --> pdb=" O   CYS A 977 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE A 975 " --> pdb=" O   GLY A 967 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ASN A 973 " --> pdb=" O   GLU A 969 " (cutoff:3.500A)

    209 hydrogen bonds defined for protein.
    564 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: 2.86

  Time building geometry restraints manager: 2.24 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2802
        1.34 -     1.46: 1851
        1.46 -     1.58: 4084
        1.58 -     1.69: 4
        1.69 -     1.81: 65
  Bond restraints: 8806
  Sorted by residual:
  bond pdb=" OG1 TPO E 286 "
       pdb=" P   TPO E 286 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" CG  PRO B  63 "
       pdb=" CD  PRO B  63 "
    ideal  model  delta    sigma   weight residual
    1.503  1.319  0.184 3.40e-02 8.65e+02 2.92e+01
  bond pdb=" N   PRO B  63 "
       pdb=" CD  PRO B  63 "
    ideal  model  delta    sigma   weight residual
    1.473  1.532 -0.059 1.40e-02 5.10e+03 1.77e+01
  bond pdb=" O2P TPO E 286 "
       pdb=" P   TPO E 286 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.66e+01
  bond pdb=" O3P TPO E 286 "
       pdb=" P   TPO E 286 "
    ideal  model  delta    sigma   weight residual
    1.528  1.609 -0.081 2.00e-02 2.50e+03 1.65e+01
  ... (remaining 8801 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.41: 11928
        3.41 -     6.81: 60
        6.81 -    10.22: 6
       10.22 -    13.62: 3
       13.62 -    17.03: 1
  Bond angle restraints: 11998
  Sorted by residual:
  angle pdb=" CA  PRO B  63 "
        pdb=" N   PRO B  63 "
        pdb=" CD  PRO B  63 "
      ideal   model   delta    sigma   weight residual
     112.00   94.97   17.03 1.40e+00 5.10e-01 1.48e+02
  angle pdb=" N   PRO B  63 "
        pdb=" CD  PRO B  63 "
        pdb=" CG  PRO B  63 "
      ideal   model   delta    sigma   weight residual
     103.20   93.67    9.53 1.50e+00 4.44e-01 4.04e+01
  angle pdb=" C   ALA A 841 "
        pdb=" CA  ALA A 841 "
        pdb=" CB  ALA A 841 "
      ideal   model   delta    sigma   weight residual
     115.79  109.24    6.55 1.19e+00 7.06e-01 3.03e+01
  angle pdb=" N   PRO B  63 "
        pdb=" CA  PRO B  63 "
        pdb=" CB  PRO B  63 "
      ideal   model   delta    sigma   weight residual
     103.52   98.80    4.72 1.06e+00 8.90e-01 1.99e+01
  angle pdb=" CB  TPO E 286 "
        pdb=" OG1 TPO E 286 "
        pdb=" P   TPO E 286 "
      ideal   model   delta    sigma   weight residual
     119.31  106.82   12.49 3.00e+00 1.11e-01 1.73e+01
  ... (remaining 11993 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 4487
       17.87 -    35.74: 530
       35.74 -    53.61: 140
       53.61 -    71.48: 20
       71.48 -    89.35: 8
  Dihedral angle restraints: 5185
    sinusoidal: 1840
      harmonic: 3345
  Sorted by residual:
  dihedral pdb=" CA  ALA B 157 "
           pdb=" C   ALA B 157 "
           pdb=" N   ASN B 158 "
           pdb=" CA  ASN B 158 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.39  -27.61     0      5.00e+00 4.00e-02 3.05e+01
  dihedral pdb=" CA  ARG B  65 "
           pdb=" C   ARG B  65 "
           pdb=" N   THR B  66 "
           pdb=" CA  THR B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.19  -26.81     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  SER A1075 "
           pdb=" C   SER A1075 "
           pdb=" N   PHE A1076 "
           pdb=" CA  PHE A1076 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.28   23.72     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 5182 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 1263
       0.077 -    0.155: 159
       0.155 -    0.232: 1
       0.232 -    0.310: 0
       0.310 -    0.387: 1
  Chirality restraints: 1424
  Sorted by residual:
  chirality pdb=" CA  PRO B  63 "
            pdb=" N   PRO B  63 "
            pdb=" C   PRO B  63 "
            pdb=" CB  PRO B  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.33    0.39 2.00e-01 2.50e+01 3.75e+00
  chirality pdb=" CA  MET B 991 "
            pdb=" N   MET B 991 "
            pdb=" C   MET B 991 "
            pdb=" CB  MET B 991 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.23e-01
  chirality pdb=" CA  LEU A 926 "
            pdb=" N   LEU A 926 "
            pdb=" C   LEU A 926 "
            pdb=" CB  LEU A 926 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.92e-01
  ... (remaining 1421 not shown)

  Planarity restraints: 1519
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  62 "    0.112 5.00e-02 4.00e+02   1.53e-01 3.77e+01
        pdb=" N   PRO B  63 "   -0.265 5.00e-02 4.00e+02
        pdb=" CA  PRO B  63 "    0.073 5.00e-02 4.00e+02
        pdb=" CD  PRO B  63 "    0.079 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 184 "    0.034 5.00e-02 4.00e+02   5.21e-02 4.34e+00
        pdb=" N   PRO A 185 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 185 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 185 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 104 "   -0.030 5.00e-02 4.00e+02   4.55e-02 3.32e+00
        pdb=" N   PRO B 105 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO B 105 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 105 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1516 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 218
        2.68 -     3.24: 7582
        3.24 -     3.79: 11857
        3.79 -     4.35: 15007
        4.35 -     4.90: 26151
  Nonbonded interactions: 60815
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 178 "
            pdb=" OE2 GLU B 181 "
     model   vdw
     2.128 3.040
  nonbonded pdb=" O   SER A 886 "
            pdb=" OG  SER A 886 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   TYR A 812 "
            pdb=" OG1 THR A 833 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   SER B  52 "
            pdb=" OG  SER B  52 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   GLY A1010 "
            pdb=" OG  SER A1027 "
     model   vdw
     2.251 3.040
  ... (remaining 60810 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.160
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.184   8807  Z= 0.180
  Angle     :  0.719  17.026  12000  Z= 0.399
  Chirality :  0.046   0.387   1424
  Planarity :  0.005   0.153   1519
  Dihedral  : 16.740  89.349   3020
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 11.13 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 29.98 %
    Favored  : 69.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.72 (0.23), residues: 1132
  helix: -1.72 (0.60), residues: 66
  sheet: -1.45 (0.28), residues: 379
  loop : -3.34 (0.20), residues: 687

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B1016 
 HIS   0.004   0.001   HIS A 905 
 PHE   0.012   0.001   PHE A 829 
 TYR   0.009   0.001   TYR A 906 
 ARG   0.007   0.000   ARG B1015 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29891 (  189)
  hydrogen bonds       : angle       9.70147 (  564)
  SS BOND              : bond        0.00018 (    1)
  SS BOND              : angle       0.34412 (    2)
  covalent geometry    : bond        0.00414 ( 8806)
  covalent geometry    : angle       0.71878 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 1.025 
Fit side-chains
REVERT: A  835 MET cc_start: 0.8431 (mtp) cc_final: 0.8221 (mtm)
  outliers start: 2
  outliers final: 1
  residues processed: 57
  average time/residue: 0.2084
  time to fit residues: 17.2997
Evaluate side-chains
  58 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  292 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    9.9990
   chunk 87 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 90 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0370
   chunk 67 optimal weight:    6.9990
   chunk 104 optimal weight:    0.5980
   overall best weight:    1.2462

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

Flipped N/Q/H residues before XYZ refinement:
B 977 GLN
** A 950 ASN ** 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 = 0.2992 r_free = 0.2992 target = 0.057333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.046573 restraints weight = 34876.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.048256 restraints weight = 16523.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.049475 restraints weight = 10274.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.0784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8807  Z= 0.119
  Angle     :  0.616  14.603  12000  Z= 0.320
  Chirality :  0.045   0.164   1424
  Planarity :  0.004   0.058   1519
  Dihedral  :  4.741  33.731   1236
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 11.57 %
    Favored  : 87.99 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 27.78 %
    Favored  : 68.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.55 (0.23), residues: 1132
  helix: -0.98 (0.64), residues: 64
  sheet: -1.34 (0.26), residues: 407
  loop : -3.34 (0.20), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1016 
 HIS   0.005   0.001   HIS A 905 
 PHE   0.009   0.001   PHE A 829 
 TYR   0.012   0.001   TYR A 906 
 ARG   0.005   0.000   ARG B1015 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03867 (  189)
  hydrogen bonds       : angle       6.22571 (  564)
  SS BOND              : bond        0.00263 (    1)
  SS BOND              : angle       2.08160 (    2)
  covalent geometry    : bond        0.00273 ( 8806)
  covalent geometry    : angle       0.61571 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 58
  time to evaluate  : 0.907 
Fit side-chains
REVERT: E  289 ASP cc_start: 0.8164 (t0) cc_final: 0.7892 (t0)
REVERT: B  176 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8439 (p)
REVERT: A  792 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9048 (pp)
  outliers start: 29
  outliers final: 9
  residues processed: 83
  average time/residue: 0.1722
  time to fit residues: 21.5514
Evaluate side-chains
  63 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  875 ILE
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  906 TYR
Chi-restraints excluded: chain A residue 1036 MET
Chi-restraints excluded: chain A residue 1133 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 94 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 98 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 111 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 38 optimal weight:    8.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.054264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.043379 restraints weight = 36076.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.044969 restraints weight = 17362.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.046140 restraints weight = 10969.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8807  Z= 0.217
  Angle     :  0.655  13.475  12000  Z= 0.343
  Chirality :  0.046   0.167   1424
  Planarity :  0.004   0.057   1519
  Dihedral  :  5.088  36.580   1234
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 13.69 %
    Favored  : 85.87 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 27.66 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.23), residues: 1132
  helix: -0.88 (0.62), residues: 69
  sheet: -1.22 (0.26), residues: 423
  loop : -3.42 (0.20), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  42 
 HIS   0.007   0.001   HIS A 905 
 PHE   0.012   0.001   PHE A 829 
 TYR   0.012   0.001   TYR B1026 
 ARG   0.004   0.000   ARG B1015 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03940 (  189)
  hydrogen bonds       : angle       5.60820 (  564)
  SS BOND              : bond        0.00272 (    1)
  SS BOND              : angle       1.69486 (    2)
  covalent geometry    : bond        0.00493 ( 8806)
  covalent geometry    : angle       0.65423 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 53
  time to evaluate  : 0.912 
Fit side-chains
REVERT: E  289 ASP cc_start: 0.8466 (t0) cc_final: 0.8123 (t0)
REVERT: B  150 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8798 (tt0)
REVERT: B  176 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8570 (p)
REVERT: B 1041 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7305 (tt)
REVERT: A  350 MET cc_start: 0.9608 (ptt) cc_final: 0.9270 (ptp)
REVERT: A  792 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9138 (pp)
REVERT: A  870 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8886 (m)
REVERT: A 1036 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8525 (ptm)
  outliers start: 36
  outliers final: 19
  residues processed: 85
  average time/residue: 0.1763
  time to fit residues: 22.1164
Evaluate side-chains
  75 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 50
  time to evaluate  : 0.904 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  150 GLN
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  875 ILE
Chi-restraints excluded: chain B residue  895 CYS
Chi-restraints excluded: chain B residue  947 VAL
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain A residue   19 VAL
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  906 TYR
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  966 LEU
Chi-restraints excluded: chain A residue 1036 MET
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1133 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 48 optimal weight:    3.9990
   chunk 99 optimal weight:    0.8980
   chunk 98 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 72 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.054764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.043894 restraints weight = 35723.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.045509 restraints weight = 16994.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.046579 restraints weight = 10700.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8807  Z= 0.144
  Angle     :  0.601  13.699  12000  Z= 0.311
  Chirality :  0.045   0.158   1424
  Planarity :  0.004   0.057   1519
  Dihedral  :  4.982  36.829   1234
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 11.75 %
    Favored  : 87.81 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 27.78 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.24), residues: 1132
  helix: -0.58 (0.64), residues: 69
  sheet: -1.24 (0.26), residues: 415
  loop : -3.27 (0.21), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1016 
 HIS   0.006   0.001   HIS A 905 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.010   0.001   TYR B1026 
 ARG   0.002   0.000   ARG A 739 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03003 (  189)
  hydrogen bonds       : angle       5.23817 (  564)
  SS BOND              : bond        0.00188 (    1)
  SS BOND              : angle       1.50713 (    2)
  covalent geometry    : bond        0.00336 ( 8806)
  covalent geometry    : angle       0.60062 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 54
  time to evaluate  : 0.952 
Fit side-chains
REVERT: E  289 ASP cc_start: 0.8535 (t0) cc_final: 0.8145 (t0)
REVERT: B  176 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8519 (p)
REVERT: B  957 MET cc_start: 0.9154 (ttp) cc_final: 0.8713 (ttm)
REVERT: B  974 MET cc_start: 0.8096 (mmm) cc_final: 0.7069 (ttm)
REVERT: B 1041 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7403 (tt)
REVERT: A  350 MET cc_start: 0.9584 (ptt) cc_final: 0.9245 (ptp)
REVERT: A  870 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8778 (m)
REVERT: A 1036 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8515 (ptm)
  outliers start: 38
  outliers final: 21
  residues processed: 88
  average time/residue: 0.1919
  time to fit residues: 24.6514
Evaluate side-chains
  77 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 52
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  103 PHE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  875 ILE
Chi-restraints excluded: chain B residue  895 CYS
Chi-restraints excluded: chain B residue  947 VAL
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  873 MET
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  906 TYR
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  963 ASP
Chi-restraints excluded: chain A residue  966 LEU
Chi-restraints excluded: chain A residue 1036 MET
Chi-restraints excluded: chain A residue 1043 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 34 optimal weight:    0.0270
   chunk 3 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 108 optimal weight:    0.0980
   chunk 51 optimal weight:    0.4980
   chunk 85 optimal weight:    0.9980
   chunk 106 optimal weight:    5.9990
   overall best weight:    0.7240

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

Flipped N/Q/H residues before XYZ refinement:
A  36 ASN
A 790 ASN
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.056025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.045310 restraints weight = 35244.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.046981 restraints weight = 16686.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.048181 restraints weight = 10418.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8807  Z= 0.092
  Angle     :  0.572  14.128  12000  Z= 0.293
  Chirality :  0.045   0.151   1424
  Planarity :  0.004   0.057   1519
  Dihedral  :  4.704  36.620   1234
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 11.48 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 28.59 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.24), residues: 1132
  helix: -0.39 (0.66), residues: 70
  sheet: -1.03 (0.27), residues: 410
  loop : -3.15 (0.21), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1016 
 HIS   0.003   0.001   HIS A 905 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.008   0.001   TYR A 906 
 ARG   0.002   0.000   ARG B 993 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02493 (  189)
  hydrogen bonds       : angle       4.89572 (  564)
  SS BOND              : bond        0.00118 (    1)
  SS BOND              : angle       1.41447 (    2)
  covalent geometry    : bond        0.00215 ( 8806)
  covalent geometry    : angle       0.57150 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 59
  time to evaluate  : 0.916 
Fit side-chains
REVERT: E  289 ASP cc_start: 0.8497 (t0) cc_final: 0.8052 (t0)
REVERT: E  292 ASP cc_start: 0.8938 (p0) cc_final: 0.8672 (p0)
REVERT: B   86 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8512 (mtmm)
REVERT: B  103 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.8891 (t80)
REVERT: B  176 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8485 (p)
REVERT: B  896 ASP cc_start: 0.8940 (t0) cc_final: 0.8701 (t0)
REVERT: B  957 MET cc_start: 0.9161 (ttp) cc_final: 0.8767 (ttm)
REVERT: A  218 MET cc_start: 0.8683 (mtp) cc_final: 0.8470 (ttt)
REVERT: A  350 MET cc_start: 0.9524 (ptt) cc_final: 0.9179 (ptp)
REVERT: A  870 VAL cc_start: 0.9030 (OUTLIER) cc_final: 0.8504 (m)
  outliers start: 27
  outliers final: 16
  residues processed: 82
  average time/residue: 0.1722
  time to fit residues: 21.0060
Evaluate side-chains
  72 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 53
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  103 PHE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  875 ILE
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  790 ASN
Chi-restraints excluded: chain A residue  866 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  906 TYR
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  966 LEU
Chi-restraints excluded: chain A residue 1043 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0870
   chunk 106 optimal weight:    8.9990
   chunk 74 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0270
   chunk 40 optimal weight:    6.9990
   chunk 113 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 93 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 790 ASN
** A 950 ASN ** 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 = 0.2946 r_free = 0.2946 target = 0.056508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.045835 restraints weight = 34935.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.047558 restraints weight = 15815.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.048778 restraints weight = 9629.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8807  Z= 0.089
  Angle     :  0.578  14.021  12000  Z= 0.293
  Chirality :  0.045   0.248   1424
  Planarity :  0.004   0.056   1519
  Dihedral  :  4.602  35.982   1234
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 10.95 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 29.51 %
    Favored  : 67.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.24), residues: 1132
  helix: -0.09 (0.68), residues: 68
  sheet: -0.92 (0.27), residues: 410
  loop : -3.08 (0.21), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 165 
 HIS   0.005   0.001   HIS A 789 
 PHE   0.007   0.001   PHE B  61 
 TYR   0.008   0.001   TYR A 906 
 ARG   0.002   0.000   ARG A 739 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02361 (  189)
  hydrogen bonds       : angle       4.70539 (  564)
  SS BOND              : bond        0.00127 (    1)
  SS BOND              : angle       1.26342 (    2)
  covalent geometry    : bond        0.00210 ( 8806)
  covalent geometry    : angle       0.57791 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.934 
Fit side-chains
REVERT: E  289 ASP cc_start: 0.8393 (t0) cc_final: 0.7932 (t0)
REVERT: E  292 ASP cc_start: 0.8908 (p0) cc_final: 0.8659 (p0)
REVERT: B   41 LYS cc_start: 0.8914 (ttpp) cc_final: 0.8710 (ttpp)
REVERT: B  103 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8868 (t80)
REVERT: B  176 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8403 (p)
REVERT: B  896 ASP cc_start: 0.8959 (t0) cc_final: 0.8723 (t0)
REVERT: B  957 MET cc_start: 0.9198 (ttp) cc_final: 0.8660 (ttm)
REVERT: B 1041 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7388 (tt)
REVERT: A  350 MET cc_start: 0.9441 (ptt) cc_final: 0.9071 (ptp)
REVERT: A  835 MET cc_start: 0.8181 (mtp) cc_final: 0.7930 (mtm)
  outliers start: 28
  outliers final: 17
  residues processed: 81
  average time/residue: 0.1794
  time to fit residues: 21.4659
Evaluate side-chains
  71 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 51
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue  103 PHE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  875 ILE
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  906 TYR
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  966 LEU
Chi-restraints excluded: chain A residue 1036 MET
Chi-restraints excluded: chain A residue 1043 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 98 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 106 optimal weight:    2.9990
   chunk 7 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 108 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.055155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.043951 restraints weight = 36507.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.045638 restraints weight = 16351.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.046829 restraints weight = 10001.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8807  Z= 0.178
  Angle     :  0.619  13.376  12000  Z= 0.318
  Chirality :  0.046   0.230   1424
  Planarity :  0.004   0.056   1519
  Dihedral  :  4.765  35.330   1234
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 12.63 %
    Favored  : 86.93 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 28.94 %
    Favored  : 66.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.24), residues: 1132
  helix: -0.43 (0.65), residues: 74
  sheet: -0.91 (0.26), residues: 430
  loop : -3.21 (0.21), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  42 
 HIS   0.005   0.001   HIS A 905 
 PHE   0.007   0.001   PHE B 103 
 TYR   0.010   0.001   TYR B1026 
 ARG   0.002   0.000   ARG A 847 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02886 (  189)
  hydrogen bonds       : angle       4.82774 (  564)
  SS BOND              : bond        0.00107 (    1)
  SS BOND              : angle       1.01392 (    2)
  covalent geometry    : bond        0.00413 ( 8806)
  covalent geometry    : angle       0.61924 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 50
  time to evaluate  : 1.055 
Fit side-chains
REVERT: E  289 ASP cc_start: 0.8402 (t0) cc_final: 0.7931 (t0)
REVERT: E  292 ASP cc_start: 0.8930 (p0) cc_final: 0.8662 (p0)
REVERT: B  150 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8687 (tt0)
REVERT: B  176 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8439 (p)
REVERT: B  883 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9196 (tt)
REVERT: B  896 ASP cc_start: 0.9074 (t0) cc_final: 0.8850 (t0)
REVERT: B  934 MET cc_start: 0.8972 (tpp) cc_final: 0.8705 (tpp)
REVERT: B  957 MET cc_start: 0.9250 (ttp) cc_final: 0.8733 (ttm)
REVERT: B  960 LEU cc_start: 0.9468 (mp) cc_final: 0.9212 (mm)
REVERT: B 1041 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7356 (tt)
REVERT: A  350 MET cc_start: 0.9475 (ptt) cc_final: 0.9109 (ptp)
  outliers start: 36
  outliers final: 26
  residues processed: 81
  average time/residue: 0.1635
  time to fit residues: 20.4786
Evaluate side-chains
  79 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 49
  time to evaluate  : 1.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 PHE
Chi-restraints excluded: chain B residue  150 GLN
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  875 ILE
Chi-restraints excluded: chain B residue  883 LEU
Chi-restraints excluded: chain B residue  895 CYS
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue  178 ILE
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  906 TYR
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  963 ASP
Chi-restraints excluded: chain A residue  966 LEU
Chi-restraints excluded: chain A residue 1043 LEU
Chi-restraints excluded: chain A residue 1133 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    0.2980
   chunk 12 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 113 optimal weight:    0.0370
   chunk 76 optimal weight:    0.0020
   chunk 61 optimal weight:    9.9990
   chunk 79 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    2.0670

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

Flipped N/Q/H residues before XYZ refinement:
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.055494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.044349 restraints weight = 36407.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.046030 restraints weight = 16148.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.047106 restraints weight = 9925.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8807  Z= 0.139
  Angle     :  0.600  13.452  12000  Z= 0.306
  Chirality :  0.046   0.201   1424
  Planarity :  0.004   0.055   1519
  Dihedral  :  4.793  37.281   1234
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 11.57 %
    Favored  : 87.99 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 28.82 %
    Favored  : 67.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.24), residues: 1132
  helix: -0.30 (0.65), residues: 74
  sheet: -0.87 (0.26), residues: 422
  loop : -3.18 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1016 
 HIS   0.005   0.001   HIS A 803 
 PHE   0.010   0.001   PHE B 995 
 TYR   0.009   0.001   TYR B1026 
 ARG   0.002   0.000   ARG A 739 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02649 (  189)
  hydrogen bonds       : angle       4.62197 (  564)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       1.09882 (    2)
  covalent geometry    : bond        0.00326 ( 8806)
  covalent geometry    : angle       0.59982 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 50
  time to evaluate  : 1.069 
Fit side-chains
REVERT: E  289 ASP cc_start: 0.8390 (t0) cc_final: 0.7933 (t0)
REVERT: E  292 ASP cc_start: 0.8906 (p0) cc_final: 0.8624 (p0)
REVERT: B  176 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8328 (p)
REVERT: B  861 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6476 (mtm-85)
REVERT: B  883 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9178 (tt)
REVERT: B  896 ASP cc_start: 0.9058 (t0) cc_final: 0.8848 (t0)
REVERT: B  934 MET cc_start: 0.8851 (tpp) cc_final: 0.8582 (tpp)
REVERT: B  957 MET cc_start: 0.9216 (ttp) cc_final: 0.8710 (ttm)
REVERT: B  960 LEU cc_start: 0.9457 (mp) cc_final: 0.9154 (mm)
REVERT: B 1041 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7430 (tt)
REVERT: A  870 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8770 (m)
  outliers start: 33
  outliers final: 23
  residues processed: 81
  average time/residue: 0.1702
  time to fit residues: 20.6225
Evaluate side-chains
  78 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 50
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 PHE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  861 ARG
Chi-restraints excluded: chain B residue  875 ILE
Chi-restraints excluded: chain B residue  883 LEU
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  870 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  906 TYR
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  963 ASP
Chi-restraints excluded: chain A residue  966 LEU
Chi-restraints excluded: chain A residue 1043 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 80 optimal weight:    7.9990
   chunk 104 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 48 optimal weight:    7.9990
   chunk 75 optimal weight:    0.6980
   chunk 58 optimal weight:    8.9990
   chunk 63 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    4.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 973 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.051981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2545 r_free = 0.2545 target = 0.041229 restraints weight = 36711.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.042734 restraints weight = 17498.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.043722 restraints weight = 11109.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   8807  Z= 0.290
  Angle     :  0.713  12.017  12000  Z= 0.366
  Chirality :  0.047   0.198   1424
  Planarity :  0.004   0.056   1519
  Dihedral  :  5.194  39.137   1234
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 15.64 %
    Favored  : 83.92 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 28.94 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.24), residues: 1132
  helix: -0.45 (0.63), residues: 75
  sheet: -0.98 (0.26), residues: 430
  loop : -3.32 (0.21), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  42 
 HIS   0.009   0.001   HIS A 803 
 PHE   0.009   0.001   PHE B 103 
 TYR   0.016   0.002   TYR B1026 
 ARG   0.005   0.000   ARG B  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03476 (  189)
  hydrogen bonds       : angle       5.08357 (  564)
  SS BOND              : bond        0.00243 (    1)
  SS BOND              : angle       1.16622 (    2)
  covalent geometry    : bond        0.00663 ( 8806)
  covalent geometry    : angle       0.71281 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 50
  time to evaluate  : 1.232 
Fit side-chains
REVERT: E  289 ASP cc_start: 0.8551 (t0) cc_final: 0.8271 (t0)
REVERT: B   86 LYS cc_start: 0.8908 (mtmm) cc_final: 0.8207 (pttm)
REVERT: B  150 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8734 (tt0)
REVERT: B  176 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8444 (p)
REVERT: B  861 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6926 (mtm-85)
REVERT: B  883 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9240 (tt)
REVERT: B  896 ASP cc_start: 0.9119 (t0) cc_final: 0.8876 (t0)
REVERT: B  957 MET cc_start: 0.9209 (ttp) cc_final: 0.8721 (ttm)
REVERT: B 1041 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7413 (tt)
  outliers start: 34
  outliers final: 27
  residues processed: 80
  average time/residue: 0.1923
  time to fit residues: 22.9826
Evaluate side-chains
  81 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 49
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 PHE
Chi-restraints excluded: chain B residue  150 GLN
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  199 ILE
Chi-restraints excluded: chain B residue  861 ARG
Chi-restraints excluded: chain B residue  875 ILE
Chi-restraints excluded: chain B residue  883 LEU
Chi-restraints excluded: chain B residue  895 CYS
Chi-restraints excluded: chain B residue  908 ILE
Chi-restraints excluded: chain B residue  923 VAL
Chi-restraints excluded: chain B residue  947 VAL
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue   63 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  906 TYR
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  963 ASP
Chi-restraints excluded: chain A residue  966 LEU
Chi-restraints excluded: chain A residue 1133 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 109 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 106 optimal weight:    7.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.055657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.044378 restraints weight = 35819.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.046074 restraints weight = 15915.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.047286 restraints weight = 9861.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8807  Z= 0.098
  Angle     :  0.612  12.778  12000  Z= 0.308
  Chirality :  0.046   0.209   1424
  Planarity :  0.004   0.053   1519
  Dihedral  :  4.962  42.331   1234
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.44 %
    Allowed  : 10.78 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 30.21 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.24), residues: 1132
  helix:  0.15 (0.68), residues: 69
  sheet: -0.91 (0.27), residues: 418
  loop : -3.13 (0.21), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1016 
 HIS   0.003   0.001   HIS A 803 
 PHE   0.012   0.001   PHE B 995 
 TYR   0.008   0.001   TYR A 718 
 ARG   0.002   0.000   ARG E 291 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02485 (  189)
  hydrogen bonds       : angle       4.55564 (  564)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       1.20140 (    2)
  covalent geometry    : bond        0.00230 ( 8806)
  covalent geometry    : angle       0.61165 (11998)

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

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

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2264 Ramachandran restraints generated.
    1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.974 
Fit side-chains
REVERT: E  289 ASP cc_start: 0.8565 (t0) cc_final: 0.7953 (t0)
REVERT: B  176 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8170 (p)
REVERT: B  861 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6396 (mtm-85)
REVERT: B  896 ASP cc_start: 0.9085 (t0) cc_final: 0.8825 (t0)
REVERT: B  957 MET cc_start: 0.9179 (ttp) cc_final: 0.8637 (ttm)
REVERT: B  960 LEU cc_start: 0.9404 (mp) cc_final: 0.9141 (mm)
REVERT: B 1041 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7513 (tt)
  outliers start: 23
  outliers final: 19
  residues processed: 76
  average time/residue: 0.1958
  time to fit residues: 21.7697
Evaluate side-chains
  75 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 53
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   62 SER
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 PHE
Chi-restraints excluded: chain B residue  176 THR
Chi-restraints excluded: chain B residue  861 ARG
Chi-restraints excluded: chain B residue  875 ILE
Chi-restraints excluded: chain B residue 1041 LEU
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   60 LYS
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  302 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  362 MET
Chi-restraints excluded: chain A residue  816 LEU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  906 TYR
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue  930 VAL
Chi-restraints excluded: chain A residue  966 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 94 optimal weight:    0.0070
   chunk 22 optimal weight:    0.0020
   chunk 78 optimal weight:    4.9990
   chunk 108 optimal weight:    8.9990
   chunk 33 optimal weight:    0.7980
   chunk 79 optimal weight:    8.9990
   chunk 110 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 112 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.8808

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

Flipped N/Q/H residues before XYZ refinement:
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.056256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.044963 restraints weight = 35991.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.046705 restraints weight = 16216.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.047952 restraints weight = 9948.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8807  Z= 0.096
  Angle     :  0.584  13.063  12000  Z= 0.295
  Chirality :  0.045   0.193   1424
  Planarity :  0.004   0.056   1519
  Dihedral  :  4.696  43.172   1234
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 11.57 %
    Favored  : 88.07 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 30.09 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.24), residues: 1132
  helix: -0.12 (0.65), residues: 75
  sheet: -0.82 (0.27), residues: 421
  loop : -3.05 (0.21), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1016 
 HIS   0.003   0.001   HIS A 905 
 PHE   0.008   0.001   PHE B  61 
 TYR   0.008   0.001   TYR A 906 
 ARG   0.008   0.000   ARG B1015 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02304 (  189)
  hydrogen bonds       : angle       4.32743 (  564)
  SS BOND              : bond        0.00151 (    1)
  SS BOND              : angle       1.14382 (    2)
  covalent geometry    : bond        0.00229 ( 8806)
  covalent geometry    : angle       0.58396 (11998)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2474.52 seconds
wall clock time: 44 minutes 11.59 seconds (2651.59 seconds total)