Starting phenix.real_space_refine
on Tue Nov 18 10:47:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6omv_20132/11_2025/6omv_20132.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6omv_20132/11_2025/6omv_20132.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6omv_20132/11_2025/6omv_20132.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6omv_20132/11_2025/6omv_20132.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6omv_20132/11_2025/6omv_20132.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6omv_20132/11_2025/6omv_20132.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      57      5.49       5
     Mg      2      5.21       5
     S      41      5.16       5
     C    8199      2.51       5
     N    2171      2.21       5
     O    2627      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13097
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "E"
      Number of atoms: 349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 349
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "F"
      Number of atoms: 242
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 242
          Classifications: {'DNA': 12}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 11}
    Chain: "A"
      Number of atoms: 951
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 951
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 7, 'TRANS': 107}
    Chain: "B"
      Number of atoms: 9985
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1208, 9985
          Classifications: {'peptide': 1208}
          Link IDs: {'PTRANS': 26, 'TRANS': 1181}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 620
          Classifications: {'RNA': 29}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 9}
          Link IDs: {'rna2p': 9, 'rna3p': 19}
    Chain: "C"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 942
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 7, 'TRANS': 106}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "G"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 2.90, per 1000 atoms: 0.22
  Number of scatterers: 13097
  At special positions: 0
  Unit cell: (132.184, 106.6, 127.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      41     16.00
     P      57     15.00
     Mg      2     11.99
     O    2627      8.00
     N    2171      7.00
     C    8199      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 488.0 milliseconds
  

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2754

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 13 sheets defined
      45.2% alpha, 10.6% beta
      19 base pairs and 34 stacking pairs defined.
    Time for finding SS restraints: 1.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 126
    Processing helix  chain 'A' and resid 127 through 148
      removed outlier: 3.599A  pdb=" N   ILE A 133 " --> pdb=" O   ARG A 129 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LYS A 134 " --> pdb=" O   ALA A 130 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A 138 " --> pdb=" O   LYS A 134 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   ILE A 146 " --> pdb=" O   GLN A 142 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   LYS A 148 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 155
      removed outlier: 3.640A  pdb=" N   ARG A 155 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 204
      removed outlier: 3.644A  pdb=" N   ARG A 203 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 233
      removed outlier: 3.597A  pdb=" N   HIS A 233 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 34
    Processing helix  chain 'B' and resid 36 through 66
      removed outlier: 4.247A  pdb=" N   ASP B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   GLU B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   LYS B  48 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   GLY B  49 " --> pdb=" O   GLU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 67 through 69
      No H-bonds generated for 'chain 'B' and resid 67 through 69'
    Processing helix  chain 'B' and resid 73 through 81
      removed outlier: 3.555A  pdb=" N   TYR B  77 " --> pdb=" O   ASN B  73 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   SER B  79 " --> pdb=" O   ASN B  75 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 84
      No H-bonds generated for 'chain 'B' and resid 82 through 84'
    Processing helix  chain 'B' and resid 90 through 112
      removed outlier: 3.524A  pdb=" N   LEU B  94 " --> pdb=" O   GLU B  90 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ALA B 106 " --> pdb=" O   ARG B 102 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ALA B 108 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   PHE B 109 " --> pdb=" O   ILE B 105 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN B 112 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 3.823A  pdb=" N   GLU B 125 " --> pdb=" O   LYS B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 131
    Processing helix  chain 'B' and resid 134 through 142
    Processing helix  chain 'B' and resid 147 through 150
      removed outlier: 3.711A  pdb=" N   ALA B 150 " --> pdb=" O   PHE B 147 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 147 through 150'
    Processing helix  chain 'B' and resid 151 through 157
    Processing helix  chain 'B' and resid 171 through 178
    Processing helix  chain 'B' and resid 179 through 193
      removed outlier: 3.603A  pdb=" N   VAL B 193 " --> pdb=" O   ILE B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 207
    Processing helix  chain 'B' and resid 230 through 242
    Processing helix  chain 'B' and resid 254 through 260
    Processing helix  chain 'B' and resid 296 through 308
      removed outlier: 3.796A  pdb=" N   VAL B 300 " --> pdb=" O   SER B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 312 through 327
    Processing helix  chain 'B' and resid 343 through 352
      removed outlier: 3.501A  pdb=" N   LYS B 349 " --> pdb=" O   SER B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 370
    Processing helix  chain 'B' and resid 378 through 392
    Processing helix  chain 'B' and resid 397 through 404
    Processing helix  chain 'B' and resid 410 through 431
    Processing helix  chain 'B' and resid 452 through 472
      removed outlier: 4.043A  pdb=" N   ALA B 472 " --> pdb=" O   ASN B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 498
      removed outlier: 4.047A  pdb=" N   ASP B 489 " --> pdb=" O   SER B 485 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   ILE B 496 " --> pdb=" O   LEU B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 512
      removed outlier: 4.116A  pdb=" N   HIS B 502 " --> pdb=" O   LEU B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 543
    Processing helix  chain 'B' and resid 588 through 598
      Proline residue:  B 594  - end of helix
      removed outlier: 3.595A  pdb=" N   PHE B 598 " --> pdb=" O   PRO B 594 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 601 through 606
    Processing helix  chain 'B' and resid 610 through 619
    Processing helix  chain 'B' and resid 630 through 643
      removed outlier: 3.920A  pdb=" N   LEU B 635 " --> pdb=" O   ASP B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 644 through 646
      No H-bonds generated for 'chain 'B' and resid 644 through 646'
    Processing helix  chain 'B' and resid 666 through 676
    Processing helix  chain 'B' and resid 687 through 697
    Processing helix  chain 'B' and resid 718 through 727
    Processing helix  chain 'B' and resid 786 through 790
    Processing helix  chain 'B' and resid 811 through 823
      removed outlier: 3.802A  pdb=" N   ARG B 817 " --> pdb=" O   ASN B 813 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   HIS B 822 " --> pdb=" O   VAL B 818 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 872 through 885
      removed outlier: 3.580A  pdb=" N   GLU B 885 " --> pdb=" O   LYS B 881 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 919
      removed outlier: 3.700A  pdb=" N   GLU B 894 " --> pdb=" O   TRP B 890 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   ASN B 895 " --> pdb=" O   THR B 891 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ILE B 896 " --> pdb=" O   SER B 892 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LYS B 897 " --> pdb=" O   ILE B 893 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   SER B 905 " --> pdb=" O   ALA B 901 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   GLN B 906 " --> pdb=" O   GLY B 902 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL B 907 " --> pdb=" O   TYR B 903 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   VAL B 908 " --> pdb=" O   ILE B 904 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   HIS B 909 " --> pdb=" O   SER B 905 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LYS B 910 " --> pdb=" O   GLN B 906 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLU B 916 " --> pdb=" O   CYS B 912 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 939 through 955
      removed outlier: 3.942A  pdb=" N   LYS B 945 " --> pdb=" O   GLN B 941 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ASP B 952 " --> pdb=" O   LYS B 948 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LYS B 953 " --> pdb=" O   MET B 949 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1020 through 1030
    Processing helix  chain 'B' and resid 1091 through 1103
    Processing helix  chain 'B' and resid 1111 through 1116
    Processing helix  chain 'B' and resid 1120 through 1135
      removed outlier: 3.860A  pdb=" N   TYR B1124 " --> pdb=" O   ASP B1120 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER B1126 " --> pdb=" O   ALA B1122 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA B1129 " --> pdb=" O   SER B1125 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU B1130 " --> pdb=" O   SER B1126 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU B1135 " --> pdb=" O   MET B1131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1164 through 1169
      removed outlier: 4.425A  pdb=" N   ALA B1169 " --> pdb=" O   ARG B1165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1178 through 1201
      removed outlier: 3.756A  pdb=" N   GLY B1183 " --> pdb=" O   ALA B1179 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LYS B1190 " --> pdb=" O   ASN B1186 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL B1191 " --> pdb=" O   ILE B1187 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS B1199 " --> pdb=" O   ILE B1195 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS B1200 " --> pdb=" O   GLY B1196 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA B1201 " --> pdb=" O   GLN B1197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1205 through 1209
      removed outlier: 3.902A  pdb=" N   VAL B1209 " --> pdb=" O   LEU B1206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1214 through 1224
    Processing helix  chain 'C' and resid 123 through 149
      removed outlier: 3.585A  pdb=" N   LEU C 127 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ILE C 133 " --> pdb=" O   ARG C 129 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   ASN C 145 " --> pdb=" O   GLU C 141 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   ILE C 146 " --> pdb=" O   GLN C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 155
      removed outlier: 3.577A  pdb=" N   ARG C 155 " --> pdb=" O   TYR C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 204
      removed outlier: 3.616A  pdb=" N   ARG C 203 " --> pdb=" O   SER C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 226 through 231
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 207
      removed outlier: 6.143A  pdb=" N   TYR A 197 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188
      removed outlier: 3.622A  pdb=" N   ARG A 187 " --> pdb=" O   VAL B 758 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL B 783 " --> pdb=" O   HIS B 759 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 520 through 522
      removed outlier: 3.723A  pdb=" N   HIS B 797 " --> pdb=" O   GLU B 743 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   TYR B 794 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE B 704 " --> pdb=" O   TYR B 553 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   TYR B 553 " --> pdb=" O   ILE B 704 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   ILE B 546 " --> pdb=" O   ILE B 581 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE B 581 " --> pdb=" O   ILE B 546 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 520 through 522
      removed outlier: 3.723A  pdb=" N   HIS B 797 " --> pdb=" O   GLU B 743 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 339
      removed outlier: 3.655A  pdb=" N   PHE B 395 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 764 through 766
    Processing sheet with id=AA7, first strand: chain 'B' and resid 850 through 855
      removed outlier: 7.035A  pdb=" N   VAL B 843 " --> pdb=" O   VAL B 851 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   GLN B 853 " --> pdb=" O   ILE B 841 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ILE B 841 " --> pdb=" O   GLN B 853 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 858 through 863
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1031 through 1037
      removed outlier: 6.681A  pdb=" N   PHE B1031 " --> pdb=" O   ASP B1048 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   ASP B1048 " --> pdb=" O   PHE B1031 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1070 through 1073
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1139 through 1140
    Processing sheet with id=AB3, first strand: chain 'C' and resid 157 through 158
      removed outlier: 4.547A  pdb=" N   ASN C 157 " --> pdb=" O   VAL C 213 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 182 through 187
      removed outlier: 5.371A  pdb=" N   TYR C 197 " --> pdb=" O   GLY C 183 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   CYS C 185 " --> pdb=" O   CYS C 195 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   CYS C 195 " --> pdb=" O   CYS C 185 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1305 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      44 hydrogen bonds
      84 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      34 stacking parallelities
  Total time for adding SS restraints: 2.43

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2861
        1.33 -     1.45: 3263
        1.45 -     1.57: 7178
        1.57 -     1.69: 111
        1.69 -     1.81: 67
  Bond restraints: 13480
  Sorted by residual:
  bond pdb=" O3'   U G   9 "
       pdb=" P     A G  10 "
    ideal  model  delta    sigma   weight residual
    1.607  1.538  0.069 1.50e-02 4.44e+03 2.09e+01
  bond pdb=" N   LEU B 132 "
       pdb=" CA  LEU B 132 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.038 1.29e-02 6.01e+03 8.73e+00
  bond pdb=" N   ASP B 572 "
       pdb=" CA  ASP B 572 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.29e-02 6.01e+03 8.01e+00
  bond pdb=" N   GLU B 479 "
       pdb=" CA  GLU B 479 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.29e-02 6.01e+03 7.90e+00
  bond pdb=" N   LYS B 265 "
       pdb=" CA  LYS B 265 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.27e-02 6.20e+03 7.75e+00
  ... (remaining 13475 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 17406
        2.08 -     4.16: 869
        4.16 -     6.24: 100
        6.24 -     8.32: 22
        8.32 -    10.41: 14
  Bond angle restraints: 18411
  Sorted by residual:
  angle pdb=" C   TYR B 214 "
        pdb=" N   ASP B 215 "
        pdb=" CA  ASP B 215 "
      ideal   model   delta    sigma   weight residual
     120.89  112.52    8.37 1.50e+00 4.44e-01 3.11e+01
  angle pdb=" N   PRO B 608 "
        pdb=" CA  PRO B 608 "
        pdb=" CB  PRO B 608 "
      ideal   model   delta    sigma   weight residual
     102.36   98.11    4.25 7.80e-01 1.64e+00 2.96e+01
  angle pdb=" N   SER B 609 "
        pdb=" CA  SER B 609 "
        pdb=" C   SER B 609 "
      ideal   model   delta    sigma   weight residual
     110.97  105.10    5.87 1.09e+00 8.42e-01 2.90e+01
  angle pdb=" N   GLY B 624 "
        pdb=" CA  GLY B 624 "
        pdb=" C   GLY B 624 "
      ideal   model   delta    sigma   weight residual
     114.69  108.51    6.18 1.19e+00 7.06e-01 2.70e+01
  angle pdb=" C   ASN C 169 "
        pdb=" N   LEU C 170 "
        pdb=" CA  LEU C 170 "
      ideal   model   delta    sigma   weight residual
     121.54  131.38   -9.84 1.91e+00 2.74e-01 2.66e+01
  ... (remaining 18406 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.20: 7717
       35.20 -    70.41: 385
       70.41 -   105.61: 19
      105.61 -   140.82: 0
      140.82 -   176.02: 1
  Dihedral angle restraints: 8122
    sinusoidal: 3849
      harmonic: 4273
  Sorted by residual:
  dihedral pdb=" O4'   U G  16 "
           pdb=" C1'   U G  16 "
           pdb=" N1    U G  16 "
           pdb=" C2    U G  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.02 -176.02     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" CA  GLU B 221 "
           pdb=" C   GLU B 221 "
           pdb=" N   GLY B 222 "
           pdb=" CA  GLY B 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.67   29.33     0      5.00e+00 4.00e-02 3.44e+01
  dihedral pdb=" CA  LYS B  84 "
           pdb=" C   LYS B  84 "
           pdb=" N   THR B  85 "
           pdb=" CA  THR B  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.76  -28.24     0      5.00e+00 4.00e-02 3.19e+01
  ... (remaining 8119 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1392
       0.055 -    0.111: 472
       0.111 -    0.166: 108
       0.166 -    0.221: 23
       0.221 -    0.277: 6
  Chirality restraints: 2001
  Sorted by residual:
  chirality pdb=" CA  ILE B1034 "
            pdb=" N   ILE B1034 "
            pdb=" C   ILE B1034 "
            pdb=" CB  ILE B1034 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C3'   C G  11 "
            pdb=" C4'   C G  11 "
            pdb=" O3'   C G  11 "
            pdb=" C2'   C G  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.73    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CB  VAL B 936 "
            pdb=" CA  VAL B 936 "
            pdb=" CG1 VAL B 936 "
            pdb=" CG2 VAL B 936 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1998 not shown)

  Planarity restraints: 2148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 128 "   -0.050 5.00e-02 4.00e+02   7.50e-02 9.00e+00
        pdb=" N   PRO B 129 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 600 "   -0.014 2.00e-02 2.50e+03   2.92e-02 8.53e+00
        pdb=" C   LYS B 600 "    0.050 2.00e-02 2.50e+03
        pdb=" O   LYS B 600 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LYS B 601 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 482 "   -0.013 2.00e-02 2.50e+03   2.66e-02 7.10e+00
        pdb=" C   ARG B 482 "    0.046 2.00e-02 2.50e+03
        pdb=" O   ARG B 482 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP B 483 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 2145 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 284
        2.62 -     3.19: 11456
        3.19 -     3.76: 22166
        3.76 -     4.33: 28838
        4.33 -     4.90: 44475
  Nonbonded interactions: 107219
  Sorted by model distance:
  nonbonded pdb="MG    MG A 301 "
            pdb=" O   HOH G 102 "
     model   vdw
     2.054 2.170
  nonbonded pdb="MG    MG A 301 "
            pdb=" O   HOH A 402 "
     model   vdw
     2.070 2.170
  nonbonded pdb="MG    MG A 301 "
            pdb=" O   HOH G 103 "
     model   vdw
     2.076 2.170
  nonbonded pdb=" O   GLN B1108 "
            pdb=" NE2 GLN B1108 "
     model   vdw
     2.079 3.120
  nonbonded pdb=" O   LYS B 571 "
            pdb=" OD1 ASP B 572 "
     model   vdw
     2.101 3.040
  ... (remaining 107214 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 120 through 233)
  selection = chain 'C'
}

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:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.910
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
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      :  0.008   0.069  13480  Z= 0.385
  Angle     :  1.053  10.406  18411  Z= 0.627
  Chirality :  0.060   0.277   2001
  Planarity :  0.006   0.075   2148
  Dihedral  : 18.637 176.023   5368
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  :  9.18 %
    Favored  : 90.19 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 10.91 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.46 (0.17), residues: 1427
  helix: -2.84 (0.15), residues: 590
  sheet: -2.41 (0.35), residues: 173
  loop : -3.18 (0.20), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 102 
 TYR   0.039   0.003   TYR A 188 
 PHE   0.020   0.003   PHE B  19 
 TRP   0.013   0.002   TRP B 999 
 HIS   0.010   0.002   HIS C 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00758 (13480)
  covalent geometry    : angle       1.05348 (18411)
  hydrogen bonds       : bond        0.18847 (  496)
  hydrogen bonds       : angle       8.23253 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 268
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.2066 (mtp) cc_final: 0.1295 (mmt)
REVERT: A  133 ILE cc_start: 0.9188 (mt) cc_final: 0.8798 (mm)
REVERT: A  135 GLU cc_start: 0.8961 (tp30) cc_final: 0.8616 (tp30)
REVERT: A  137 ASP cc_start: 0.9154 (m-30) cc_final: 0.8902 (m-30)
REVERT: A  142 GLN cc_start: 0.8795 (tt0) cc_final: 0.8368 (tp-100)
REVERT: A  144 TYR cc_start: 0.7948 (t80) cc_final: 0.7063 (t80)
REVERT: A  154 LYS cc_start: 0.9543 (mttp) cc_final: 0.9154 (mtpt)
REVERT: A  157 ASN cc_start: 0.9157 (m110) cc_final: 0.8859 (t0)
REVERT: A  193 GLN cc_start: 0.8778 (tt0) cc_final: 0.8307 (tm-30)
REVERT: A  202 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7858 (ptpp)
REVERT: A  232 LEU cc_start: 0.8683 (tt) cc_final: 0.8180 (mt)
REVERT: B  167 LYS cc_start: 0.7527 (pttt) cc_final: 0.7319 (pttt)
REVERT: B  308 LEU cc_start: 0.9037 (mm) cc_final: 0.8829 (mp)
REVERT: B  558 MET cc_start: 0.7671 (mpp) cc_final: 0.7426 (mpp)
REVERT: B  815 GLU cc_start: 0.8788 (tp30) cc_final: 0.8428 (tp30)
REVERT: B  840 TYR cc_start: 0.8986 (t80) cc_final: 0.8667 (t80)
REVERT: B  927 LEU cc_start: 0.8558 (mt) cc_final: 0.8117 (tt)
REVERT: B  940 LYS cc_start: 0.9209 (tttt) cc_final: 0.8778 (tttp)
REVERT: B  941 GLN cc_start: 0.8569 (tp40) cc_final: 0.8294 (tp40)
REVERT: B  944 GLN cc_start: 0.8401 (mt0) cc_final: 0.8020 (mt0)
REVERT: B  945 LYS cc_start: 0.9029 (tptm) cc_final: 0.8725 (ttpt)
REVERT: B 1003 LYS cc_start: 0.9350 (mttt) cc_final: 0.9025 (mttm)
REVERT: B 1128 MET cc_start: 0.8921 (tpt) cc_final: 0.8672 (tpp)
REVERT: B 1167 TYR cc_start: 0.8382 (m-80) cc_final: 0.7989 (m-80)
REVERT: C  142 GLN cc_start: 0.9200 (mt0) cc_final: 0.8979 (tm-30)
REVERT: C  154 LYS cc_start: 0.8757 (mttm) cc_final: 0.8492 (ttmm)
REVERT: C  165 LEU cc_start: 0.9300 (tp) cc_final: 0.9099 (tp)
REVERT: C  187 ARG cc_start: 0.7833 (tpp80) cc_final: 0.6979 (tpp80)
REVERT: C  192 ASP cc_start: 0.9072 (OUTLIER) cc_final: 0.8516 (p0)
REVERT: C  217 ARG cc_start: 0.6125 (tpt170) cc_final: 0.5806 (tpt170)
REVERT: C  219 GLU cc_start: 0.8753 (mp0) cc_final: 0.8386 (mp0)
REVERT: C  230 ARG cc_start: 0.7564 (mtt-85) cc_final: 0.7318 (mtt-85)
  outliers start: 21
  outliers final: 4
  residues processed: 283
  average time/residue: 0.1297
  time to fit residues: 50.5349
Evaluate side-chains
  198 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 193
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  478 LYS
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain C residue  192 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
A 145 ASN
A 157 ASN
A 168 ASN
A 181 GLN
A 231 ASN
B 100 ASN
B 160 ASN
** B 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 263 ASN
** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 449 ASN
B 613 GLN
B 706 ASN
B 797 HIS
B 861 ASN
B 873 HIS
B 889 ASN
B 895 ASN
B 978 ASN
B 989 GLN
** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1118 GLN
C 168 ASN

Total number of N/Q/H flips: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.107809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.079110 restraints weight = 44868.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.081683 restraints weight = 19984.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.083211 restraints weight = 12566.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.084113 restraints weight = 9758.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.084475 restraints weight = 8547.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13480  Z= 0.135
  Angle     :  0.658  11.676  18411  Z= 0.353
  Chirality :  0.043   0.280   2001
  Planarity :  0.004   0.062   2148
  Dihedral  : 16.997 177.908   2333
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.29 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.09 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.20), residues: 1427
  helix: -1.45 (0.19), residues: 602
  sheet: -1.82 (0.42), residues: 132
  loop : -2.77 (0.21), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  18 
 TYR   0.025   0.002   TYR C 209 
 PHE   0.020   0.001   PHE C 196 
 TRP   0.007   0.001   TRP B 602 
 HIS   0.005   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (13480)
  covalent geometry    : angle       0.65758 (18411)
  hydrogen bonds       : bond        0.04358 (  496)
  hydrogen bonds       : angle       5.59018 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 224
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.2336 (mtp) cc_final: 0.1565 (mmt)
REVERT: A  133 ILE cc_start: 0.9140 (mt) cc_final: 0.8791 (mm)
REVERT: A  135 GLU cc_start: 0.8824 (tp30) cc_final: 0.8611 (tp30)
REVERT: A  142 GLN cc_start: 0.8698 (tt0) cc_final: 0.8441 (tp-100)
REVERT: A  144 TYR cc_start: 0.7665 (t80) cc_final: 0.6827 (t80)
REVERT: A  154 LYS cc_start: 0.9435 (mttp) cc_final: 0.9027 (mtmt)
REVERT: A  181 GLN cc_start: 0.8367 (tt0) cc_final: 0.7893 (tp-100)
REVERT: A  193 GLN cc_start: 0.8565 (tt0) cc_final: 0.8342 (tm-30)
REVERT: A  202 LYS cc_start: 0.8039 (mmtp) cc_final: 0.7559 (ptpp)
REVERT: A  227 GLU cc_start: 0.9110 (mp0) cc_final: 0.8858 (mp0)
REVERT: A  230 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8611 (ttm110)
REVERT: A  232 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8052 (mt)
REVERT: B   28 GLN cc_start: 0.9021 (tp40) cc_final: 0.8805 (tm-30)
REVERT: B  495 ASP cc_start: 0.6666 (p0) cc_final: 0.6358 (p0)
REVERT: B  603 MET cc_start: 0.9308 (mpp) cc_final: 0.9087 (pmm)
REVERT: B  815 GLU cc_start: 0.8518 (tp30) cc_final: 0.8228 (tp30)
REVERT: B  840 TYR cc_start: 0.8877 (t80) cc_final: 0.8558 (t80)
REVERT: B  895 ASN cc_start: 0.7838 (m110) cc_final: 0.7610 (m-40)
REVERT: B  940 LYS cc_start: 0.8910 (tttt) cc_final: 0.8348 (ptmm)
REVERT: B  941 GLN cc_start: 0.8464 (tp40) cc_final: 0.7994 (tp40)
REVERT: B  944 GLN cc_start: 0.8241 (mt0) cc_final: 0.7886 (mt0)
REVERT: B  949 MET cc_start: 0.7980 (ttm) cc_final: 0.7677 (ttm)
REVERT: B 1003 LYS cc_start: 0.9250 (mttt) cc_final: 0.8959 (mttm)
REVERT: B 1216 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8274 (tppt)
REVERT: C  133 ILE cc_start: 0.8764 (mm) cc_final: 0.8437 (tp)
REVERT: C  137 ASP cc_start: 0.9237 (m-30) cc_final: 0.8968 (m-30)
REVERT: C  186 MET cc_start: 0.7528 (tpp) cc_final: 0.7289 (ttt)
REVERT: C  209 TYR cc_start: 0.8116 (m-80) cc_final: 0.7827 (m-80)
REVERT: C  222 ARG cc_start: 0.9116 (tpp-160) cc_final: 0.8831 (tpp80)
  outliers start: 36
  outliers final: 16
  residues processed: 245
  average time/residue: 0.1181
  time to fit residues: 41.7292
Evaluate side-chains
  213 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 196
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  320 LYS
Chi-restraints excluded: chain B residue  541 ASP
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  618 ASN
Chi-restraints excluded: chain B residue  823 ASP
Chi-restraints excluded: chain B residue  877 ASP
Chi-restraints excluded: chain B residue  996 ILE
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  223 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 127 optimal weight:    8.9990
   chunk 76 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 126 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 44 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 63 optimal weight:    6.9990
   chunk 105 optimal weight:    0.0980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 759 HIS
B 808 ASN
B1108 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.107715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.079024 restraints weight = 45609.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.081556 restraints weight = 20368.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.083131 restraints weight = 12937.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.083888 restraints weight = 10032.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.084217 restraints weight = 8891.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13480  Z= 0.142
  Angle     :  0.629  10.565  18411  Z= 0.335
  Chirality :  0.042   0.183   2001
  Planarity :  0.004   0.053   2148
  Dihedral  : 16.723 177.993   2325
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.64 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.46 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.21), residues: 1427
  helix: -0.73 (0.20), residues: 601
  sheet: -1.59 (0.44), residues: 130
  loop : -2.55 (0.22), residues: 696

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 155 
 TYR   0.023   0.001   TYR B 510 
 PHE   0.012   0.001   PHE B 490 
 TRP   0.009   0.001   TRP B 602 
 HIS   0.005   0.001   HIS C 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13480)
  covalent geometry    : angle       0.62878 (18411)
  hydrogen bonds       : bond        0.03840 (  496)
  hydrogen bonds       : angle       5.19988 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 221
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.2387 (mtp) cc_final: 0.1997 (mmt)
REVERT: A  135 GLU cc_start: 0.8774 (tp30) cc_final: 0.8545 (tp30)
REVERT: A  142 GLN cc_start: 0.8795 (tt0) cc_final: 0.8540 (tp-100)
REVERT: A  144 TYR cc_start: 0.7751 (t80) cc_final: 0.6824 (t80)
REVERT: A  154 LYS cc_start: 0.9457 (mttp) cc_final: 0.8994 (mtmt)
REVERT: A  181 GLN cc_start: 0.8321 (tt0) cc_final: 0.8026 (tp40)
REVERT: A  193 GLN cc_start: 0.8554 (tt0) cc_final: 0.8337 (tm-30)
REVERT: A  202 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7348 (ptpp)
REVERT: A  232 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8032 (mt)
REVERT: B  110 LYS cc_start: 0.8567 (pttm) cc_final: 0.8075 (pttm)
REVERT: B  167 LYS cc_start: 0.7509 (pttt) cc_final: 0.7303 (pttt)
REVERT: B  510 TYR cc_start: 0.7578 (t80) cc_final: 0.6607 (t80)
REVERT: B  513 GLN cc_start: 0.6045 (OUTLIER) cc_final: 0.4296 (pp30)
REVERT: B  614 LYS cc_start: 0.9686 (mmmt) cc_final: 0.9435 (pttp)
REVERT: B  815 GLU cc_start: 0.8555 (tp30) cc_final: 0.8277 (tp30)
REVERT: B  840 TYR cc_start: 0.8896 (t80) cc_final: 0.8608 (t80)
REVERT: B  940 LYS cc_start: 0.8964 (tttt) cc_final: 0.8401 (ptmm)
REVERT: B  941 GLN cc_start: 0.8372 (tp40) cc_final: 0.7733 (tp40)
REVERT: B  944 GLN cc_start: 0.8296 (mt0) cc_final: 0.8072 (mt0)
REVERT: B 1003 LYS cc_start: 0.9245 (mttt) cc_final: 0.8988 (mttm)
REVERT: B 1068 TYR cc_start: 0.9300 (t80) cc_final: 0.9059 (t80)
REVERT: B 1108 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7709 (mp10)
REVERT: B 1216 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8339 (tppt)
REVERT: C  133 ILE cc_start: 0.8900 (mm) cc_final: 0.8564 (tp)
REVERT: C  137 ASP cc_start: 0.9280 (m-30) cc_final: 0.8958 (m-30)
REVERT: C  148 LYS cc_start: 0.8998 (ttmm) cc_final: 0.8398 (mtmm)
REVERT: C  192 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8587 (m-30)
REVERT: C  209 TYR cc_start: 0.8356 (m-80) cc_final: 0.8028 (m-80)
REVERT: C  222 ARG cc_start: 0.9154 (tpp-160) cc_final: 0.8875 (tpp80)
REVERT: C  230 ARG cc_start: 0.7300 (mtt-85) cc_final: 0.6729 (ptp-170)
  outliers start: 42
  outliers final: 24
  residues processed: 242
  average time/residue: 0.1143
  time to fit residues: 39.5972
Evaluate side-chains
  227 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 199
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  513 GLN
Chi-restraints excluded: chain B residue  541 ASP
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  618 ASN
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  796 LEU
Chi-restraints excluded: chain B residue  823 ASP
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  877 ASP
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  951 ILE
Chi-restraints excluded: chain B residue  996 ILE
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain B residue 1108 GLN
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  192 ASP
Chi-restraints excluded: chain C residue  223 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 131 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 138 optimal weight:    8.9990
   chunk 124 optimal weight:    0.9980
   chunk 132 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 168 ASN
B  76 ASN
** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 449 ASN
B 895 ASN
** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 208 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.104351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.080159 restraints weight = 45778.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.079444 restraints weight = 26034.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.080398 restraints weight = 20696.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.080376 restraints weight = 15524.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.081498 restraints weight = 13964.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13480  Z= 0.197
  Angle     :  0.660   9.499  18411  Z= 0.352
  Chirality :  0.044   0.193   2001
  Planarity :  0.004   0.046   2148
  Dihedral  : 16.723 177.843   2325
  Min Nonbonded Distance : 1.888

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  8.62 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.06 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.11 (0.22), residues: 1427
  helix: -0.35 (0.21), residues: 608
  sheet: -1.41 (0.44), residues: 133
  loop : -2.41 (0.23), residues: 686

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 155 
 TYR   0.026   0.002   TYR B 562 
 PHE   0.016   0.001   PHE B 946 
 TRP   0.014   0.001   TRP B 602 
 HIS   0.005   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (13480)
  covalent geometry    : angle       0.66008 (18411)
  hydrogen bonds       : bond        0.03906 (  496)
  hydrogen bonds       : angle       5.16243 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 192
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.1961 (mtp) cc_final: 0.1431 (mmt)
REVERT: A  142 GLN cc_start: 0.8946 (tt0) cc_final: 0.8556 (tp-100)
REVERT: A  154 LYS cc_start: 0.9499 (mttp) cc_final: 0.9020 (mtmt)
REVERT: A  186 MET cc_start: 0.7484 (mmm) cc_final: 0.6835 (mmm)
REVERT: A  193 GLN cc_start: 0.8622 (tt0) cc_final: 0.8380 (tm-30)
REVERT: A  202 LYS cc_start: 0.8373 (mmtp) cc_final: 0.7883 (mtmm)
REVERT: A  227 GLU cc_start: 0.9172 (mp0) cc_final: 0.8961 (mp0)
REVERT: A  232 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8021 (mt)
REVERT: B  116 LYS cc_start: 0.9070 (mmtp) cc_final: 0.8266 (pttm)
REVERT: B  510 TYR cc_start: 0.7581 (t80) cc_final: 0.6419 (t80)
REVERT: B  513 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.4508 (pp30)
REVERT: B  614 LYS cc_start: 0.9689 (mmmt) cc_final: 0.9324 (mmmm)
REVERT: B  659 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7625 (mp0)
REVERT: B  815 GLU cc_start: 0.8700 (tp30) cc_final: 0.8402 (tp30)
REVERT: B  840 TYR cc_start: 0.8986 (t80) cc_final: 0.8606 (t80)
REVERT: B  895 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7729 (t0)
REVERT: B  919 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8134 (t0)
REVERT: B  940 LYS cc_start: 0.9079 (tttt) cc_final: 0.8401 (ptmm)
REVERT: B  941 GLN cc_start: 0.8497 (tp40) cc_final: 0.7887 (tp40)
REVERT: B  944 GLN cc_start: 0.8369 (mt0) cc_final: 0.8130 (mt0)
REVERT: B  949 MET cc_start: 0.7994 (ttm) cc_final: 0.7660 (ttm)
REVERT: B 1003 LYS cc_start: 0.9268 (mttt) cc_final: 0.9004 (mttm)
REVERT: B 1131 MET cc_start: 0.8921 (mmm) cc_final: 0.8521 (mmm)
REVERT: B 1216 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8354 (tppt)
REVERT: C  133 ILE cc_start: 0.8907 (mm) cc_final: 0.8464 (tp)
REVERT: C  137 ASP cc_start: 0.9298 (m-30) cc_final: 0.8824 (m-30)
REVERT: C  138 LEU cc_start: 0.8687 (tt) cc_final: 0.7342 (tp)
REVERT: C  148 LYS cc_start: 0.9055 (ttmm) cc_final: 0.8550 (mtmm)
REVERT: C  209 TYR cc_start: 0.8190 (m-80) cc_final: 0.7902 (m-80)
REVERT: C  222 ARG cc_start: 0.9165 (tpp-160) cc_final: 0.8897 (tpp80)
  outliers start: 49
  outliers final: 29
  residues processed: 221
  average time/residue: 0.1101
  time to fit residues: 35.6487
Evaluate side-chains
  212 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 179
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  513 GLN
Chi-restraints excluded: chain B residue  541 ASP
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  618 ASN
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  796 LEU
Chi-restraints excluded: chain B residue  823 ASP
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  877 ASP
Chi-restraints excluded: chain B residue  895 ASN
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  951 ILE
Chi-restraints excluded: chain B residue  996 ILE
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  150 LEU
Chi-restraints excluded: chain C residue  192 ASP
Chi-restraints excluded: chain C residue  223 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 116 optimal weight:    0.9990
   chunk 107 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 19 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 93 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 168 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 260 ASN
B 268 GLN
B 895 ASN
B1108 GLN
** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 208 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.108951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.079981 restraints weight = 45695.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.082535 restraints weight = 20565.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.084122 restraints weight = 13008.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.084975 restraints weight = 10116.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.085365 restraints weight = 8875.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  13480  Z= 0.118
  Angle     :  0.613   9.656  18411  Z= 0.321
  Chirality :  0.042   0.198   2001
  Planarity :  0.003   0.044   2148
  Dihedral  : 16.521 176.563   2325
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 21.51 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.22), residues: 1427
  helix: -0.05 (0.21), residues: 596
  sheet: -1.43 (0.42), residues: 136
  loop : -2.19 (0.23), residues: 695

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1189 
 TYR   0.018   0.001   TYR B 562 
 PHE   0.016   0.001   PHE B 173 
 TRP   0.009   0.001   TRP B 602 
 HIS   0.005   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (13480)
  covalent geometry    : angle       0.61312 (18411)
  hydrogen bonds       : bond        0.03537 (  496)
  hydrogen bonds       : angle       4.86690 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 220
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.2075 (mtp) cc_final: 0.1511 (mmt)
REVERT: A  142 GLN cc_start: 0.8927 (tt0) cc_final: 0.8605 (tp-100)
REVERT: A  144 TYR cc_start: 0.7744 (t80) cc_final: 0.6866 (t80)
REVERT: A  154 LYS cc_start: 0.9457 (mttp) cc_final: 0.8774 (mtmt)
REVERT: A  181 GLN cc_start: 0.8439 (tt0) cc_final: 0.8208 (tt0)
REVERT: A  184 GLU cc_start: 0.5442 (OUTLIER) cc_final: 0.5132 (mt-10)
REVERT: A  186 MET cc_start: 0.7432 (mmm) cc_final: 0.6812 (mmm)
REVERT: A  193 GLN cc_start: 0.8558 (tt0) cc_final: 0.8356 (tm-30)
REVERT: A  202 LYS cc_start: 0.7991 (mmtp) cc_final: 0.7464 (mtmm)
REVERT: B  110 LYS cc_start: 0.8670 (pttm) cc_final: 0.8367 (pttm)
REVERT: B  116 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8172 (pttm)
REVERT: B  167 LYS cc_start: 0.7503 (pttt) cc_final: 0.7260 (pttt)
REVERT: B  386 ARG cc_start: -0.0997 (OUTLIER) cc_final: -0.1455 (ptt180)
REVERT: B  510 TYR cc_start: 0.7475 (t80) cc_final: 0.6466 (t80)
REVERT: B  513 GLN cc_start: 0.6115 (OUTLIER) cc_final: 0.4590 (pp30)
REVERT: B  531 MET cc_start: 0.8804 (mmm) cc_final: 0.8157 (tpp)
REVERT: B  614 LYS cc_start: 0.9688 (mmmt) cc_final: 0.9271 (mmmm)
REVERT: B  659 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7544 (mp0)
REVERT: B  815 GLU cc_start: 0.8570 (tp30) cc_final: 0.8247 (tp30)
REVERT: B  840 TYR cc_start: 0.8842 (t80) cc_final: 0.8280 (t80)
REVERT: B  853 GLN cc_start: 0.8378 (pm20) cc_final: 0.8095 (pm20)
REVERT: B  895 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7459 (t0)
REVERT: B  919 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8303 (t0)
REVERT: B  940 LYS cc_start: 0.8955 (tttt) cc_final: 0.8300 (ptmm)
REVERT: B  941 GLN cc_start: 0.8403 (tp40) cc_final: 0.7922 (tp40)
REVERT: B 1003 LYS cc_start: 0.9223 (mttt) cc_final: 0.8880 (mttm)
REVERT: B 1054 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8357 (mtt-85)
REVERT: B 1068 TYR cc_start: 0.9268 (t80) cc_final: 0.8861 (t80)
REVERT: B 1108 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7897 (mp10)
REVERT: B 1131 MET cc_start: 0.8866 (mmm) cc_final: 0.8421 (mmm)
REVERT: B 1216 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8338 (tppt)
REVERT: C  133 ILE cc_start: 0.8889 (mm) cc_final: 0.8384 (tp)
REVERT: C  137 ASP cc_start: 0.9248 (m-30) cc_final: 0.8645 (m-30)
REVERT: C  148 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8583 (mtmm)
REVERT: C  163 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8104 (mm-40)
REVERT: C  209 TYR cc_start: 0.8350 (m-80) cc_final: 0.8006 (m-80)
  outliers start: 42
  outliers final: 27
  residues processed: 246
  average time/residue: 0.1188
  time to fit residues: 41.8711
Evaluate side-chains
  227 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 194
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  386 ARG
Chi-restraints excluded: chain B residue  513 GLN
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  618 ASN
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  796 LEU
Chi-restraints excluded: chain B residue  823 ASP
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  877 ASP
Chi-restraints excluded: chain B residue  895 ASN
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  996 ILE
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain B residue 1108 GLN
Chi-restraints excluded: chain B residue 1211 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  192 ASP
Chi-restraints excluded: chain C residue  223 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 103 optimal weight:    0.6980
   chunk 140 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 116 optimal weight:    2.9990
   chunk 129 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0870
   chunk 11 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
B 112 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 481 ASN
B 895 ASN
** B1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 208 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.108423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.079368 restraints weight = 45241.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.081995 restraints weight = 20283.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.083562 restraints weight = 12798.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.084343 restraints weight = 9921.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.084926 restraints weight = 8731.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13480  Z= 0.118
  Angle     :  0.624  11.092  18411  Z= 0.324
  Chirality :  0.042   0.214   2001
  Planarity :  0.003   0.049   2148
  Dihedral  : 16.441 176.903   2325
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 22.65 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.22), residues: 1427
  helix:  0.09 (0.22), residues: 593
  sheet: -1.43 (0.41), residues: 142
  loop : -2.13 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1189 
 TYR   0.025   0.001   TYR B 995 
 PHE   0.016   0.001   PHE B 521 
 TRP   0.008   0.001   TRP B 602 
 HIS   0.004   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (13480)
  covalent geometry    : angle       0.62361 (18411)
  hydrogen bonds       : bond        0.03447 (  496)
  hydrogen bonds       : angle       4.75388 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 206
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.2224 (mtp) cc_final: 0.1753 (mmt)
REVERT: A  142 GLN cc_start: 0.9069 (tt0) cc_final: 0.8571 (tp-100)
REVERT: A  144 TYR cc_start: 0.7674 (t80) cc_final: 0.6749 (t80)
REVERT: A  154 LYS cc_start: 0.9451 (mttp) cc_final: 0.9041 (mttt)
REVERT: A  181 GLN cc_start: 0.8419 (tt0) cc_final: 0.8166 (tt0)
REVERT: A  186 MET cc_start: 0.7486 (mmm) cc_final: 0.6777 (mmm)
REVERT: A  202 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7525 (mtmm)
REVERT: A  230 ARG cc_start: 0.9075 (ttm110) cc_final: 0.8557 (ptp-110)
REVERT: B  116 LYS cc_start: 0.8876 (mmtp) cc_final: 0.8186 (pttm)
REVERT: B  167 LYS cc_start: 0.7479 (pttt) cc_final: 0.7253 (pttt)
REVERT: B  247 GLU cc_start: 0.3851 (OUTLIER) cc_final: 0.3200 (mp0)
REVERT: B  386 ARG cc_start: -0.0854 (OUTLIER) cc_final: -0.1260 (ptt180)
REVERT: B  510 TYR cc_start: 0.7451 (t80) cc_final: 0.6427 (t80)
REVERT: B  513 GLN cc_start: 0.6191 (OUTLIER) cc_final: 0.4607 (pp30)
REVERT: B  531 MET cc_start: 0.8815 (mmm) cc_final: 0.8239 (tpp)
REVERT: B  614 LYS cc_start: 0.9676 (mmmt) cc_final: 0.9264 (mmmm)
REVERT: B  659 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7469 (mp0)
REVERT: B  815 GLU cc_start: 0.8644 (tp30) cc_final: 0.8293 (tp30)
REVERT: B  840 TYR cc_start: 0.8854 (t80) cc_final: 0.8299 (t80)
REVERT: B  853 GLN cc_start: 0.8382 (pm20) cc_final: 0.8167 (pm20)
REVERT: B  895 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7655 (t0)
REVERT: B  919 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8322 (t0)
REVERT: B  941 GLN cc_start: 0.8295 (tp40) cc_final: 0.8032 (tp40)
REVERT: B 1003 LYS cc_start: 0.9208 (mttt) cc_final: 0.8937 (mttm)
REVERT: B 1131 MET cc_start: 0.8972 (mmm) cc_final: 0.8584 (mmm)
REVERT: B 1216 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8336 (tppt)
REVERT: C  133 ILE cc_start: 0.8879 (mm) cc_final: 0.8396 (tp)
REVERT: C  137 ASP cc_start: 0.9224 (m-30) cc_final: 0.8645 (m-30)
REVERT: C  138 LEU cc_start: 0.9036 (tp) cc_final: 0.8785 (tp)
REVERT: C  148 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8661 (mtmm)
REVERT: C  163 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8110 (mm-40)
REVERT: C  209 TYR cc_start: 0.8401 (m-80) cc_final: 0.8064 (m-80)
  outliers start: 36
  outliers final: 26
  residues processed: 230
  average time/residue: 0.1197
  time to fit residues: 39.7795
Evaluate side-chains
  229 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 198
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  184 GLU
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  247 GLU
Chi-restraints excluded: chain B residue  386 ARG
Chi-restraints excluded: chain B residue  513 GLN
Chi-restraints excluded: chain B residue  541 ASP
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  618 ASN
Chi-restraints excluded: chain B residue  620 THR
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  796 LEU
Chi-restraints excluded: chain B residue  823 ASP
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  877 ASP
Chi-restraints excluded: chain B residue  895 ASN
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  996 ILE
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain B residue 1211 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  223 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9980
   chunk 137 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 136 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 803 ASN
B 895 ASN
B1108 GLN
C 208 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.104717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.080666 restraints weight = 45011.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.079903 restraints weight = 24382.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.081652 restraints weight = 18163.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.081641 restraints weight = 12808.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.081878 restraints weight = 12193.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13480  Z= 0.175
  Angle     :  0.670  12.564  18411  Z= 0.347
  Chirality :  0.043   0.182   2001
  Planarity :  0.004   0.045   2148
  Dihedral  : 16.478 177.288   2325
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.11 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.22), residues: 1427
  helix:  0.18 (0.21), residues: 600
  sheet: -1.55 (0.42), residues: 145
  loop : -2.13 (0.24), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1189 
 TYR   0.034   0.002   TYR B1185 
 PHE   0.016   0.001   PHE B 521 
 TRP   0.015   0.001   TRP A 178 
 HIS   0.004   0.001   HIS B 759 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (13480)
  covalent geometry    : angle       0.67039 (18411)
  hydrogen bonds       : bond        0.03605 (  496)
  hydrogen bonds       : angle       4.83840 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 194
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.2189 (OUTLIER) cc_final: 0.1804 (mmt)
REVERT: A  142 GLN cc_start: 0.8978 (tt0) cc_final: 0.8586 (tp-100)
REVERT: A  144 TYR cc_start: 0.7746 (t80) cc_final: 0.7058 (t80)
REVERT: A  154 LYS cc_start: 0.9459 (mttp) cc_final: 0.9026 (mtmt)
REVERT: A  181 GLN cc_start: 0.8382 (tt0) cc_final: 0.8100 (tt0)
REVERT: A  186 MET cc_start: 0.7639 (mmm) cc_final: 0.6924 (mmm)
REVERT: A  202 LYS cc_start: 0.8213 (mmtp) cc_final: 0.7772 (mtmm)
REVERT: A  230 ARG cc_start: 0.9144 (ttm110) cc_final: 0.8696 (ptp-110)
REVERT: B  116 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8238 (pttm)
REVERT: B  247 GLU cc_start: 0.3750 (OUTLIER) cc_final: 0.3017 (mp0)
REVERT: B  386 ARG cc_start: -0.0581 (OUTLIER) cc_final: -0.1138 (ptt180)
REVERT: B  458 ASP cc_start: 0.9228 (m-30) cc_final: 0.8731 (p0)
REVERT: B  510 TYR cc_start: 0.7556 (t80) cc_final: 0.6526 (t80)
REVERT: B  513 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.5904 (tp-100)
REVERT: B  614 LYS cc_start: 0.9679 (mmmt) cc_final: 0.9293 (mmmm)
REVERT: B  659 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7636 (mp0)
REVERT: B  815 GLU cc_start: 0.8814 (tp30) cc_final: 0.8474 (tp30)
REVERT: B  840 TYR cc_start: 0.9029 (t80) cc_final: 0.8470 (t80)
REVERT: B  895 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7545 (t0)
REVERT: B  919 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8284 (t0)
REVERT: B  941 GLN cc_start: 0.8486 (tp40) cc_final: 0.8085 (tp40)
REVERT: B  949 MET cc_start: 0.7946 (ttm) cc_final: 0.7633 (ttm)
REVERT: B 1003 LYS cc_start: 0.9267 (mttt) cc_final: 0.8993 (mttm)
REVERT: B 1054 ARG cc_start: 0.8961 (ttm170) cc_final: 0.8442 (mmt-90)
REVERT: B 1131 MET cc_start: 0.8976 (mmm) cc_final: 0.8543 (mmm)
REVERT: B 1216 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8423 (tppt)
REVERT: C  133 ILE cc_start: 0.8888 (mm) cc_final: 0.8380 (tp)
REVERT: C  137 ASP cc_start: 0.9245 (m-30) cc_final: 0.8568 (m-30)
REVERT: C  148 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8656 (mtmm)
REVERT: C  163 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8147 (mm-40)
REVERT: C  192 ASP cc_start: 0.8494 (m-30) cc_final: 0.8134 (m-30)
REVERT: C  209 TYR cc_start: 0.8372 (m-80) cc_final: 0.8027 (m-80)
  outliers start: 43
  outliers final: 30
  residues processed: 221
  average time/residue: 0.1179
  time to fit residues: 37.5528
Evaluate side-chains
  220 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 184
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  247 GLU
Chi-restraints excluded: chain B residue  386 ARG
Chi-restraints excluded: chain B residue  513 GLN
Chi-restraints excluded: chain B residue  541 ASP
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  618 ASN
Chi-restraints excluded: chain B residue  620 THR
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  796 LEU
Chi-restraints excluded: chain B residue  823 ASP
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  877 ASP
Chi-restraints excluded: chain B residue  882 GLU
Chi-restraints excluded: chain B residue  895 ASN
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  996 ILE
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain B residue 1189 ARG
Chi-restraints excluded: chain B residue 1211 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  223 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 107 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 108 optimal weight:    0.0020
   chunk 141 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 133 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 895 ASN
B1108 GLN
C 191 ASN
C 193 GLN
C 208 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.106546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.077184 restraints weight = 44605.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.079791 restraints weight = 20390.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.081421 restraints weight = 12973.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.082152 restraints weight = 10053.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.082762 restraints weight = 8931.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13480  Z= 0.124
  Angle     :  0.649  11.222  18411  Z= 0.331
  Chirality :  0.042   0.189   2001
  Planarity :  0.003   0.053   2148
  Dihedral  : 16.360 176.142   2325
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.42 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.23), residues: 1427
  helix:  0.34 (0.22), residues: 592
  sheet: -1.50 (0.41), residues: 145
  loop : -1.98 (0.24), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 102 
 TYR   0.029   0.001   TYR B1185 
 PHE   0.023   0.001   PHE C 196 
 TRP   0.009   0.001   TRP B 602 
 HIS   0.004   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13480)
  covalent geometry    : angle       0.64885 (18411)
  hydrogen bonds       : bond        0.03381 (  496)
  hydrogen bonds       : angle       4.72663 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 199
  time to evaluate  : 0.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.2448 (mtp) cc_final: 0.2159 (mmt)
REVERT: A  142 GLN cc_start: 0.9077 (tt0) cc_final: 0.8652 (tp-100)
REVERT: A  144 TYR cc_start: 0.7817 (t80) cc_final: 0.7142 (t80)
REVERT: A  154 LYS cc_start: 0.9482 (mttp) cc_final: 0.9065 (mtmt)
REVERT: A  181 GLN cc_start: 0.8432 (tt0) cc_final: 0.8145 (tt0)
REVERT: A  186 MET cc_start: 0.7554 (mmm) cc_final: 0.6875 (mmm)
REVERT: A  193 GLN cc_start: 0.8527 (tt0) cc_final: 0.8183 (tm-30)
REVERT: A  196 PHE cc_start: 0.8563 (m-80) cc_final: 0.8275 (m-80)
REVERT: A  202 LYS cc_start: 0.8039 (mmtp) cc_final: 0.7542 (mtmm)
REVERT: A  228 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8661 (mt-10)
REVERT: A  230 ARG cc_start: 0.9146 (ttm110) cc_final: 0.8822 (ptp-110)
REVERT: B  110 LYS cc_start: 0.8686 (pttm) cc_final: 0.8306 (pttm)
REVERT: B  116 LYS cc_start: 0.8919 (mmtp) cc_final: 0.8263 (pttm)
REVERT: B  167 LYS cc_start: 0.7406 (pttt) cc_final: 0.7166 (pttt)
REVERT: B  247 GLU cc_start: 0.3871 (OUTLIER) cc_final: 0.3168 (mp0)
REVERT: B  386 ARG cc_start: -0.0832 (OUTLIER) cc_final: -0.1256 (ptt180)
REVERT: B  458 ASP cc_start: 0.9160 (m-30) cc_final: 0.8704 (p0)
REVERT: B  510 TYR cc_start: 0.7464 (t80) cc_final: 0.6395 (t80)
REVERT: B  513 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.5982 (tp-100)
REVERT: B  614 LYS cc_start: 0.9678 (mmmt) cc_final: 0.9270 (mmmm)
REVERT: B  659 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7494 (mp0)
REVERT: B  815 GLU cc_start: 0.8845 (tp30) cc_final: 0.8461 (tp30)
REVERT: B  840 TYR cc_start: 0.8964 (t80) cc_final: 0.8320 (t80)
REVERT: B  895 ASN cc_start: 0.8069 (OUTLIER) cc_final: 0.7716 (t0)
REVERT: B  919 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8293 (t0)
REVERT: B  941 GLN cc_start: 0.8528 (tp40) cc_final: 0.8121 (tp40)
REVERT: B  949 MET cc_start: 0.7964 (ttm) cc_final: 0.7679 (ttm)
REVERT: B  986 MET cc_start: 0.8582 (mpp) cc_final: 0.8150 (mpp)
REVERT: B 1003 LYS cc_start: 0.9229 (mttt) cc_final: 0.8830 (mttm)
REVERT: B 1054 ARG cc_start: 0.8892 (ttm170) cc_final: 0.8389 (mmt-90)
REVERT: B 1131 MET cc_start: 0.9077 (mmm) cc_final: 0.8615 (mmm)
REVERT: B 1216 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8356 (tppt)
REVERT: C  133 ILE cc_start: 0.8859 (mm) cc_final: 0.8390 (tp)
REVERT: C  137 ASP cc_start: 0.9217 (m-30) cc_final: 0.8599 (m-30)
REVERT: C  148 LYS cc_start: 0.9129 (ttmm) cc_final: 0.8655 (mtmm)
REVERT: C  163 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8243 (mm-40)
REVERT: C  209 TYR cc_start: 0.8443 (m-80) cc_final: 0.8091 (m-80)
  outliers start: 39
  outliers final: 28
  residues processed: 227
  average time/residue: 0.1165
  time to fit residues: 37.9813
Evaluate side-chains
  229 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 196
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 ILE
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  247 GLU
Chi-restraints excluded: chain B residue  386 ARG
Chi-restraints excluded: chain B residue  513 GLN
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  618 ASN
Chi-restraints excluded: chain B residue  620 THR
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  796 LEU
Chi-restraints excluded: chain B residue  823 ASP
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  877 ASP
Chi-restraints excluded: chain B residue  895 ASN
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  996 ILE
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain B residue 1053 SER
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain B residue 1108 GLN
Chi-restraints excluded: chain B residue 1189 ARG
Chi-restraints excluded: chain B residue 1211 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  223 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 34 optimal weight:    0.0670
   chunk 12 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 59 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 72 optimal weight:    0.2980
   chunk 17 optimal weight:    0.8980
   chunk 29 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 97 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.2522

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 895 ASN
B1108 GLN
C 191 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.106272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.076853 restraints weight = 45047.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.079447 restraints weight = 20713.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.080933 restraints weight = 13240.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.081901 restraints weight = 10451.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.082351 restraints weight = 9099.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  13480  Z= 0.138
  Angle     :  0.656  10.867  18411  Z= 0.335
  Chirality :  0.042   0.181   2001
  Planarity :  0.004   0.059   2148
  Dihedral  : 16.344 176.558   2325
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 23.87 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.23), residues: 1427
  helix:  0.43 (0.22), residues: 592
  sheet: -1.48 (0.42), residues: 144
  loop : -1.94 (0.24), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 102 
 TYR   0.027   0.001   TYR B1185 
 PHE   0.023   0.001   PHE C 196 
 TRP   0.008   0.001   TRP A 178 
 HIS   0.004   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (13480)
  covalent geometry    : angle       0.65550 (18411)
  hydrogen bonds       : bond        0.03374 (  496)
  hydrogen bonds       : angle       4.72409 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 194
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.2292 (OUTLIER) cc_final: 0.2040 (mmt)
REVERT: A  142 GLN cc_start: 0.9134 (tt0) cc_final: 0.8716 (tp-100)
REVERT: A  144 TYR cc_start: 0.7770 (t80) cc_final: 0.7080 (t80)
REVERT: A  154 LYS cc_start: 0.9500 (mttp) cc_final: 0.9077 (mtpt)
REVERT: A  181 GLN cc_start: 0.8438 (tt0) cc_final: 0.8132 (tt0)
REVERT: A  186 MET cc_start: 0.7692 (mmm) cc_final: 0.7474 (mmm)
REVERT: A  193 GLN cc_start: 0.8475 (tt0) cc_final: 0.8094 (tm-30)
REVERT: A  196 PHE cc_start: 0.8619 (m-80) cc_final: 0.8392 (m-80)
REVERT: A  228 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8692 (mt-10)
REVERT: A  230 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8796 (ptp-110)
REVERT: B  116 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8273 (pttm)
REVERT: B  167 LYS cc_start: 0.7408 (pttt) cc_final: 0.7159 (pttt)
REVERT: B  247 GLU cc_start: 0.3924 (OUTLIER) cc_final: 0.3227 (mp0)
REVERT: B  386 ARG cc_start: -0.0970 (OUTLIER) cc_final: -0.1328 (ptt180)
REVERT: B  458 ASP cc_start: 0.9161 (m-30) cc_final: 0.8744 (p0)
REVERT: B  510 TYR cc_start: 0.7472 (t80) cc_final: 0.6344 (t80)
REVERT: B  513 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.6013 (tp-100)
REVERT: B  614 LYS cc_start: 0.9677 (mmmt) cc_final: 0.9286 (mmmm)
REVERT: B  659 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7540 (mp0)
REVERT: B  815 GLU cc_start: 0.8932 (tp30) cc_final: 0.8533 (tp30)
REVERT: B  840 TYR cc_start: 0.9004 (t80) cc_final: 0.8310 (t80)
REVERT: B  895 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7733 (t0)
REVERT: B  941 GLN cc_start: 0.8590 (tp40) cc_final: 0.8174 (tp40)
REVERT: B  949 MET cc_start: 0.7950 (ttm) cc_final: 0.7652 (ttm)
REVERT: B 1003 LYS cc_start: 0.9247 (mttt) cc_final: 0.8821 (mttm)
REVERT: B 1131 MET cc_start: 0.9114 (mmm) cc_final: 0.8665 (mmm)
REVERT: B 1216 LYS cc_start: 0.9048 (ttmm) cc_final: 0.8397 (tppt)
REVERT: C  129 ARG cc_start: 0.7986 (ptt180) cc_final: 0.7528 (ptp-170)
REVERT: C  133 ILE cc_start: 0.8845 (mm) cc_final: 0.8387 (tp)
REVERT: C  137 ASP cc_start: 0.9209 (m-30) cc_final: 0.8595 (m-30)
REVERT: C  163 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8228 (mm-40)
REVERT: C  209 TYR cc_start: 0.8411 (m-80) cc_final: 0.8059 (m-80)
  outliers start: 38
  outliers final: 28
  residues processed: 221
  average time/residue: 0.1087
  time to fit residues: 34.8460
Evaluate side-chains
  221 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 188
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  247 GLU
Chi-restraints excluded: chain B residue  386 ARG
Chi-restraints excluded: chain B residue  513 GLN
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  618 ASN
Chi-restraints excluded: chain B residue  620 THR
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  796 LEU
Chi-restraints excluded: chain B residue  823 ASP
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  877 ASP
Chi-restraints excluded: chain B residue  895 ASN
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain B residue 1053 SER
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain B residue 1108 GLN
Chi-restraints excluded: chain B residue 1189 ARG
Chi-restraints excluded: chain B residue 1211 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  191 ASN
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  223 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9980
   chunk 59 optimal weight:   10.0000
   chunk 71 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 27 optimal weight:    9.9990
   chunk 108 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 759 HIS
B 895 ASN
B1108 GLN
** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.107156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.083479 restraints weight = 45481.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.083376 restraints weight = 26025.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.084186 restraints weight = 19084.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.084120 restraints weight = 14889.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.085106 restraints weight = 13228.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.4003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13480  Z= 0.126
  Angle     :  0.660  10.891  18411  Z= 0.337
  Chirality :  0.042   0.186   2001
  Planarity :  0.004   0.051   2148
  Dihedral  : 16.303 176.155   2325
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 24.26 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.23), residues: 1427
  helix:  0.44 (0.22), residues: 591
  sheet: -1.39 (0.42), residues: 144
  loop : -1.91 (0.24), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 203 
 TYR   0.028   0.001   TYR B1185 
 PHE   0.019   0.001   PHE C 196 
 TRP   0.006   0.001   TRP B 602 
 HIS   0.008   0.001   HIS C 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (13480)
  covalent geometry    : angle       0.66026 (18411)
  hydrogen bonds       : bond        0.03359 (  496)
  hydrogen bonds       : angle       4.66838 ( 1389)

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

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

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2854 Ramachandran restraints generated.
    1427 Oldfield, 0 Emsley, 1427 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 194
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 GLN cc_start: 0.9060 (tt0) cc_final: 0.8691 (tp-100)
REVERT: A  144 TYR cc_start: 0.7803 (t80) cc_final: 0.7142 (t80)
REVERT: A  154 LYS cc_start: 0.9478 (mttp) cc_final: 0.9118 (mtpt)
REVERT: A  181 GLN cc_start: 0.8399 (tt0) cc_final: 0.8132 (tt0)
REVERT: A  193 GLN cc_start: 0.8508 (tt0) cc_final: 0.8191 (tm-30)
REVERT: A  196 PHE cc_start: 0.8554 (m-80) cc_final: 0.8347 (m-80)
REVERT: A  228 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8679 (mt-10)
REVERT: A  230 ARG cc_start: 0.9158 (ttm110) cc_final: 0.8871 (ptp-110)
REVERT: B  116 LYS cc_start: 0.8915 (mmtp) cc_final: 0.8268 (pttm)
REVERT: B  167 LYS cc_start: 0.7415 (pttt) cc_final: 0.7191 (pttt)
REVERT: B  247 GLU cc_start: 0.3876 (OUTLIER) cc_final: 0.3238 (mp0)
REVERT: B  386 ARG cc_start: -0.0644 (OUTLIER) cc_final: -0.1124 (ptt180)
REVERT: B  510 TYR cc_start: 0.7434 (t80) cc_final: 0.6374 (t80)
REVERT: B  513 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.6054 (tp-100)
REVERT: B  614 LYS cc_start: 0.9659 (mmmt) cc_final: 0.9292 (mmmm)
REVERT: B  815 GLU cc_start: 0.8853 (tp30) cc_final: 0.8461 (tp30)
REVERT: B  840 TYR cc_start: 0.8969 (t80) cc_final: 0.8259 (t80)
REVERT: B  941 GLN cc_start: 0.8559 (tp40) cc_final: 0.8176 (tp40)
REVERT: B  949 MET cc_start: 0.7891 (ttm) cc_final: 0.7606 (ttm)
REVERT: B 1003 LYS cc_start: 0.9222 (mttt) cc_final: 0.8828 (mttm)
REVERT: B 1131 MET cc_start: 0.9071 (mmm) cc_final: 0.8621 (mmm)
REVERT: B 1216 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8346 (tppt)
REVERT: C  129 ARG cc_start: 0.8119 (ptt180) cc_final: 0.7739 (ptp-170)
REVERT: C  133 ILE cc_start: 0.8866 (mm) cc_final: 0.8665 (tp)
REVERT: C  137 ASP cc_start: 0.9241 (m-30) cc_final: 0.8704 (m-30)
REVERT: C  163 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8135 (mm-40)
REVERT: C  209 TYR cc_start: 0.8472 (m-80) cc_final: 0.8125 (m-80)
  outliers start: 33
  outliers final: 26
  residues processed: 217
  average time/residue: 0.1158
  time to fit residues: 36.3132
Evaluate side-chains
  217 residues out of total 1311 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 188
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  233 HIS
Chi-restraints excluded: chain B residue   37 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  224 PHE
Chi-restraints excluded: chain B residue  247 GLU
Chi-restraints excluded: chain B residue  386 ARG
Chi-restraints excluded: chain B residue  513 GLN
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  601 LYS
Chi-restraints excluded: chain B residue  620 THR
Chi-restraints excluded: chain B residue  758 VAL
Chi-restraints excluded: chain B residue  796 LEU
Chi-restraints excluded: chain B residue  823 ASP
Chi-restraints excluded: chain B residue  870 THR
Chi-restraints excluded: chain B residue  877 ASP
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1004 ILE
Chi-restraints excluded: chain B residue 1089 VAL
Chi-restraints excluded: chain B residue 1108 GLN
Chi-restraints excluded: chain B residue 1189 ARG
Chi-restraints excluded: chain B residue 1211 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  182 VAL
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  207 VAL
Chi-restraints excluded: chain C residue  223 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 146
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 29 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0060
   chunk 139 optimal weight:    0.7980
   chunk 78 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 989 GLN
B1108 GLN
** C 191 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 = 0.3935 r_free = 0.3935 target = 0.107800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.078359 restraints weight = 45117.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.080984 restraints weight = 21002.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.082405 restraints weight = 13484.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.083426 restraints weight = 10648.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.083836 restraints weight = 9291.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13480  Z= 0.132
  Angle     :  0.680  10.581  18411  Z= 0.349
  Chirality :  0.043   0.183   2001
  Planarity :  0.004   0.050   2148
  Dihedral  : 16.266 176.202   2325
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 24.87 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.23), residues: 1427
  helix:  0.42 (0.22), residues: 591
  sheet: -1.42 (0.42), residues: 144
  loop : -1.90 (0.24), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 203 
 TYR   0.027   0.001   TYR B1185 
 PHE   0.020   0.001   PHE B 173 
 TRP   0.007   0.001   TRP B 602 
 HIS   0.004   0.001   HIS B 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (13480)
  covalent geometry    : angle       0.67962 (18411)
  hydrogen bonds       : bond        0.03420 (  496)
  hydrogen bonds       : angle       4.70262 ( 1389)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2588.07 seconds
wall clock time: 45 minutes 30.23 seconds (2730.23 seconds total)