Starting phenix.real_space_refine
on Fri Aug 22 21:27:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r7k_18978/08_2025/8r7k_18978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r7k_18978/08_2025/8r7k_18978.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r7k_18978/08_2025/8r7k_18978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r7k_18978/08_2025/8r7k_18978.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r7k_18978/08_2025/8r7k_18978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r7k_18978/08_2025/8r7k_18978.map"
  }
  resolution = 3.5
  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=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 94 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      58      5.16       5
     C    5092      2.51       5
     N    1385      2.21       5
     O    1446      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7984
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 2943
          Classifications: {'peptide': 374}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 16, 'TRANS': 357}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 69
          Unresolved non-hydrogen angles: 86
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 28
    Chain: "B"
      Number of atoms: 2873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2873
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 11, 'TRANS': 354}
          Chain breaks: 4
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 127
          Unresolved non-hydrogen angles: 155
          Unresolved non-hydrogen dihedrals: 107
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'HIS:plan': 3, 'GLU:plan': 6, 'GLN:plan1': 4, 'ASP:plan': 5, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 78
    Chain: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 418
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 1, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "H"
      Number of atoms: 1719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 220, 1719
          Classifications: {'peptide': 220}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 10, 'TRANS': 209}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 3, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "H"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ANP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.11, per 1000 atoms: 0.26
  Number of scatterers: 7984
  At special positions: 0
  Unit cell: (80.684, 113.133, 111.379, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      58     16.00
     P       3     15.00
     O    1446      8.00
     N    1385      7.00
     C    5092      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 491.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 4 sheets defined
      58.2% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 602 through 619
      removed outlier: 3.920A  pdb=" N   LYS A 606 " --> pdb=" O   THR A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 693 through 707
      removed outlier: 3.585A  pdb=" N   LEU A 697 " --> pdb=" O   PRO A 693 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER A 698 " --> pdb=" O   LEU A 694 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ARG A 699 " --> pdb=" O   PRO A 695 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 704 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 738
      removed outlier: 3.830A  pdb=" N   ARG A 726 " --> pdb=" O   PHE A 722 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 729 " --> pdb=" O   ASN A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 762
      removed outlier: 3.589A  pdb=" N   LEU A 747 " --> pdb=" O   LEU A 743 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   HIS A 760 " --> pdb=" O   ILE A 756 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   MET A 762 " --> pdb=" O   CYS A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 797
      removed outlier: 4.119A  pdb=" N   ASN A 775 " --> pdb=" O   ASP A 771 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS A 781 " --> pdb=" O   GLU A 777 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ASP A 792 " --> pdb=" O   GLU A 788 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 814
      removed outlier: 4.097A  pdb=" N   PHE A 806 " --> pdb=" O   SER A 802 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER A 814 " --> pdb=" O   ASN A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 819 through 826
      removed outlier: 3.564A  pdb=" N   GLN A 825 " --> pdb=" O   LEU A 821 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLN A 826 " --> pdb=" O   ARG A 822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 833
    Processing helix  chain 'A' and resid 834 through 845
      removed outlier: 3.509A  pdb=" N   GLN A 842 " --> pdb=" O   LYS A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 851 through 861
      removed outlier: 3.959A  pdb=" N   GLN A 860 " --> pdb=" O   PHE A 856 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER A 861 " --> pdb=" O   LYS A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 871
      removed outlier: 3.511A  pdb=" N   ALA A 867 " --> pdb=" O   SER A 863 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   CYS A 868 " --> pdb=" O   TYR A 864 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU A 869 " --> pdb=" O   LEU A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 889
      removed outlier: 3.655A  pdb=" N   ILE A 877 " --> pdb=" O   TYR A 873 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ARG A 878 " --> pdb=" O   PHE A 874 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 908
    Processing helix  chain 'A' and resid 912 through 922
      removed outlier: 3.944A  pdb=" N   ALA A 916 " --> pdb=" O   ASP A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 951 through 956
      removed outlier: 4.028A  pdb=" N   THR A 955 " --> pdb=" O   SER A 951 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 968
    Processing helix  chain 'B' and resid 6 through 19
    Processing helix  chain 'B' and resid 21 through 30
      removed outlier: 3.531A  pdb=" N   CYS B  25 " --> pdb=" O   ASP B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'B' and resid 55 through 75
      removed outlier: 3.591A  pdb=" N   GLU B  60 " --> pdb=" O   PRO B  56 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE B  62 " --> pdb=" O   TYR B  58 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ALA B  63 " --> pdb=" O   ASP B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 97
      removed outlier: 3.703A  pdb=" N   TYR B  81 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   LYS B  82 " --> pdb=" O   ILE B  78 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   CYS B  83 " --> pdb=" O   GLU B  79 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL B  88 " --> pdb=" O   GLN B  84 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ALA B  97 " --> pdb=" O   ARG B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 125
      removed outlier: 3.950A  pdb=" N   MET B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   TYR B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ALA B 110 " --> pdb=" O   PRO B 106 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL B 111 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU B 113 " --> pdb=" O   TYR B 109 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   ASP B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   ARG B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   VAL B 117 " --> pdb=" O   LEU B 113 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA B 122 " --> pdb=" O   PHE B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 142
    Processing helix  chain 'B' and resid 144 through 155
      removed outlier: 3.858A  pdb=" N   ASP B 155 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 172
    Processing helix  chain 'B' and resid 175 through 180
      removed outlier: 3.658A  pdb=" N   PHE B 180 " --> pdb=" O   PHE B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 197
      removed outlier: 3.544A  pdb=" N   ILE B 195 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 223
      removed outlier: 3.851A  pdb=" N   LYS B 213 " --> pdb=" O   ARG B 209 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   TYR B 214 " --> pdb=" O   VAL B 210 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   TYR B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 239
      removed outlier: 3.617A  pdb=" N   ALA B 229 " --> pdb=" O   ASP B 225 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLU B 231 " --> pdb=" O   LYS B 227 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TYR B 232 " --> pdb=" O   GLN B 228 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   SER B 234 " --> pdb=" O   GLU B 230 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS B 239 " --> pdb=" O   PHE B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 259
      removed outlier: 3.637A  pdb=" N   LYS B 248 " --> pdb=" O   SER B 244 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE B 251 " --> pdb=" O   ASN B 247 " (cutoff:3.500A)
      Proline residue:  B 257  - end of helix
    Processing helix  chain 'B' and resid 267 through 274
      removed outlier: 3.773A  pdb=" N   LEU B 271 " --> pdb=" O   THR B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 286
      removed outlier: 4.537A  pdb=" N   VAL B 282 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 301
      removed outlier: 4.166A  pdb=" N   HIS B 301 " --> pdb=" O   ALA B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 315
    Processing helix  chain 'B' and resid 317 through 334
      removed outlier: 3.709A  pdb=" N   ARG B 323 " --> pdb=" O   ILE B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 351
      removed outlier: 3.849A  pdb=" N   MET B 350 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 371
      removed outlier: 3.507A  pdb=" N   GLY B 371 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 59
      removed outlier: 3.559A  pdb=" N   LEU C  56 " --> pdb=" O   PHE C  52 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 47 through 51
      removed outlier: 3.915A  pdb=" N   PHE H  50 " --> pdb=" O   PHE H  47 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LEU H  51 " --> pdb=" O   ARG H  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 47 through 51'
    Processing helix  chain 'H' and resid 54 through 59
      removed outlier: 3.846A  pdb=" N   ALA H  59 " --> pdb=" O   GLU H  55 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 69 through 80
      Proline residue:  H  77  - end of helix
    Processing helix  chain 'H' and resid 94 through 102
    Processing helix  chain 'H' and resid 102 through 107
    Processing helix  chain 'H' and resid 122 through 137
      removed outlier: 3.803A  pdb=" N   PHE H 127 " --> pdb=" O   ARG H 123 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU H 134 " --> pdb=" O   SER H 130 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 154 through 164
    Processing helix  chain 'H' and resid 172 through 181
      removed outlier: 4.057A  pdb=" N   ALA H 178 " --> pdb=" O   GLY H 174 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 197 through 203
      removed outlier: 3.731A  pdb=" N   MET H 201 " --> pdb=" O   GLU H 197 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 207 through 215
    Processing helix  chain 'H' and resid 235 through 240
      removed outlier: 3.624A  pdb=" N   CYS H 239 " --> pdb=" O   ILE H 235 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ARG H 240 " --> pdb=" O   ARG H 236 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 235 through 240'
    Processing helix  chain 'H' and resid 241 through 243
      No H-bonds generated for 'chain 'H' and resid 241 through 243'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 897 through 900
    Processing sheet with id=AA2, first strand: chain 'B' and resid 337 through 339
      removed outlier: 3.560A  pdb=" N   LYS B 383 " --> pdb=" O   SER B 378 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER B 378 " --> pdb=" O   LYS B 383 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL B 385 " --> pdb=" O   TYR B 376 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR B 376 " --> pdb=" O   VAL B 385 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 227 through 228
      removed outlier: 7.208A  pdb=" N   CYS H  87 " --> pdb=" O   SER H 228 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ILE H 249 " --> pdb=" O   LEU H  86 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 145 through 148
      removed outlier: 3.565A  pdb=" N   ALA H 146 " --> pdb=" O   ILE H 168 " (cutoff:3.500A)
      removed outlier: 6.139A  pdb=" N   VAL H 116 " --> pdb=" O   VAL H 169 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   GLY H 171 " --> pdb=" O   VAL H 116 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   VAL H 118 " --> pdb=" O   GLY H 171 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   LEU H 117 " --> pdb=" O   ILE H 194 " (cutoff:3.500A)

    319 hydrogen bonds defined for protein.
    945 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2260
        1.34 -     1.46: 1708
        1.46 -     1.58: 4080
        1.58 -     1.70: 8
        1.70 -     1.82: 89
  Bond restraints: 8145
  Sorted by residual:
  bond pdb=" O3A ANP H1000 "
       pdb=" PB  ANP H1000 "
    ideal  model  delta    sigma   weight residual
    1.700  1.555  0.145 2.00e-02 2.50e+03 5.22e+01
  bond pdb=" N3B ANP H1000 "
       pdb=" PG  ANP H1000 "
    ideal  model  delta    sigma   weight residual
    1.795  1.695  0.100 2.00e-02 2.50e+03 2.50e+01
  bond pdb=" O5' ANP H1000 "
       pdb=" PA  ANP H1000 "
    ideal  model  delta    sigma   weight residual
    1.655  1.576  0.079 2.00e-02 2.50e+03 1.58e+01
  bond pdb=" C   LEU A 687 "
       pdb=" N   PRO A 688 "
    ideal  model  delta    sigma   weight residual
    1.335  1.378 -0.042 1.30e-02 5.92e+03 1.06e+01
  bond pdb=" CA  LEU A 687 "
       pdb=" C   LEU A 687 "
    ideal  model  delta    sigma   weight residual
    1.524  1.563 -0.039 1.26e-02 6.30e+03 9.55e+00
  ... (remaining 8140 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.62: 10766
        4.62 -     9.24: 207
        9.24 -    13.87: 31
       13.87 -    18.49: 9
       18.49 -    23.11: 2
  Bond angle restraints: 11015
  Sorted by residual:
  angle pdb=" CA  GLU A 690 "
        pdb=" CB  GLU A 690 "
        pdb=" CG  GLU A 690 "
      ideal   model   delta    sigma   weight residual
     114.10  128.43  -14.33 2.00e+00 2.50e-01 5.13e+01
  angle pdb=" CA  LYS B 189 "
        pdb=" CB  LYS B 189 "
        pdb=" CG  LYS B 189 "
      ideal   model   delta    sigma   weight residual
     114.10  127.98  -13.88 2.00e+00 2.50e-01 4.82e+01
  angle pdb=" CB  LYS H 162 "
        pdb=" CG  LYS H 162 "
        pdb=" CD  LYS H 162 "
      ideal   model   delta    sigma   weight residual
     111.30  126.88  -15.58 2.30e+00 1.89e-01 4.59e+01
  angle pdb=" CA  MET B 260 "
        pdb=" CB  MET B 260 "
        pdb=" CG  MET B 260 "
      ideal   model   delta    sigma   weight residual
     114.10  127.28  -13.18 2.00e+00 2.50e-01 4.34e+01
  angle pdb=" C   LEU A 687 "
        pdb=" CA  LEU A 687 "
        pdb=" CB  LEU A 687 "
      ideal   model   delta    sigma   weight residual
     110.17  122.88  -12.71 1.97e+00 2.58e-01 4.16e+01
  ... (remaining 11010 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.81: 4736
       30.81 -    61.61: 187
       61.61 -    92.42: 17
       92.42 -   123.22: 0
      123.22 -   154.03: 1
  Dihedral angle restraints: 4941
    sinusoidal: 1952
      harmonic: 2989
  Sorted by residual:
  dihedral pdb=" CA  LYS B 189 "
           pdb=" C   LYS B 189 "
           pdb=" N   PRO B 190 "
           pdb=" CA  PRO B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.35   42.65     0      5.00e+00 4.00e-02 7.28e+01
  dihedral pdb=" CA  PHE H  50 "
           pdb=" C   PHE H  50 "
           pdb=" N   LEU H  51 "
           pdb=" CA  LEU H  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.36   36.64     0      5.00e+00 4.00e-02 5.37e+01
  dihedral pdb=" CA  LEU B 333 "
           pdb=" C   LEU B 333 "
           pdb=" N   LYS B 334 "
           pdb=" CA  LYS B 334 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.18   27.82     0      5.00e+00 4.00e-02 3.10e+01
  ... (remaining 4938 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.202: 1211
       0.202 -    0.403: 24
       0.403 -    0.605: 3
       0.605 -    0.806: 0
       0.806 -    1.008: 1
  Chirality restraints: 1239
  Sorted by residual:
  chirality pdb=" CG  LEU A 687 "
            pdb=" CB  LEU A 687 "
            pdb=" CD1 LEU A 687 "
            pdb=" CD2 LEU A 687 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.58   -1.01 2.00e-01 2.50e+01 2.54e+01
  chirality pdb=" CB  ILE A 730 "
            pdb=" CA  ILE A 730 "
            pdb=" CG1 ILE A 730 "
            pdb=" CG2 ILE A 730 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.11    0.54 2.00e-01 2.50e+01 7.28e+00
  chirality pdb=" CG  LEU H 177 "
            pdb=" CB  LEU H 177 "
            pdb=" CD1 LEU H 177 "
            pdb=" CD2 LEU H 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.13   -0.46 2.00e-01 2.50e+01 5.23e+00
  ... (remaining 1236 not shown)

  Planarity restraints: 1412
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 641 "   -0.111 5.00e-02 4.00e+02   1.72e-01 4.72e+01
        pdb=" N   PRO A 642 "    0.297 5.00e-02 4.00e+02
        pdb=" CA  PRO A 642 "   -0.107 5.00e-02 4.00e+02
        pdb=" CD  PRO A 642 "   -0.079 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 685 "    0.097 5.00e-02 4.00e+02   1.52e-01 3.68e+01
        pdb=" N   PRO A 686 "   -0.262 5.00e-02 4.00e+02
        pdb=" CA  PRO A 686 "    0.091 5.00e-02 4.00e+02
        pdb=" CD  PRO A 686 "    0.075 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 189 "   -0.079 5.00e-02 4.00e+02   1.20e-01 2.29e+01
        pdb=" N   PRO B 190 "    0.207 5.00e-02 4.00e+02
        pdb=" CA  PRO B 190 "   -0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO B 190 "   -0.066 5.00e-02 4.00e+02
  ... (remaining 1409 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1976
        2.80 -     3.33: 7146
        3.33 -     3.85: 12469
        3.85 -     4.37: 14133
        4.37 -     4.90: 23681
  Nonbonded interactions: 59405
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 702 "
            pdb=" OG1 THR A 706 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OE2 GLU A 659 "
            pdb=" OH  TYR A 703 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   VAL B 286 "
            pdb=" ND2 ASN B 324 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" O   SER A 849 "
            pdb=" ND2 ASN B 366 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" O   LEU A 743 "
            pdb=" OG  SER A 746 "
     model   vdw
     2.331 3.040
  ... (remaining 59400 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.850
  Find NCS groups from input model:        0.040
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
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   0.145   8145  Z= 0.376
  Angle     :  1.564  23.110  11015  Z= 0.793
  Chirality :  0.079   1.008   1239
  Planarity :  0.013   0.172   1412
  Dihedral  : 16.950 154.029   2985
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  6.57 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.08 %
    Favored  : 86.35 %
  Cbeta Deviations :  0.20 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.39 (0.20), residues: 990
  helix: -3.17 (0.15), residues: 553
  sheet: -0.62 (0.72), residues: 57
  loop : -2.62 (0.26), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG H 175 
 TYR   0.057   0.005   TYR A 607 
 PHE   0.070   0.004   PHE H  65 
 TRP   0.055   0.004   TRP B 103 
 HIS   0.017   0.002   HIS H 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00839 ( 8145)
  covalent geometry    : angle       1.56368 (11015)
  hydrogen bonds       : bond        0.19232 (  319)
  hydrogen bonds       : angle       7.89241 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 189
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  690 GLU cc_start: 0.7953 (tp30) cc_final: 0.6579 (mp0)
REVERT: A  702 ASP cc_start: 0.8452 (m-30) cc_final: 0.8226 (t0)
REVERT: B   17 ILE cc_start: 0.8837 (mm) cc_final: 0.8480 (pt)
REVERT: B  137 MET cc_start: 0.7863 (tpp) cc_final: 0.7537 (mpp)
REVERT: B  315 GLU cc_start: 0.8165 (tp30) cc_final: 0.7711 (mt-10)
REVERT: B  361 GLN cc_start: 0.7205 (OUTLIER) cc_final: 0.6995 (tm-30)
REVERT: H   99 PHE cc_start: 0.7412 (p90) cc_final: 0.7203 (p90)
  outliers start: 13
  outliers final: 7
  residues processed: 198
  average time/residue: 0.0964
  time to fit residues: 25.7588
Evaluate side-chains
  168 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain B residue  183 ASN
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    0.0470
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   overall best weight:    0.7680

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

Flipped N/Q/H residues before XYZ refinement:
** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 850 ASN
B 228 GLN
H 106 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.157503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.133724 restraints weight = 15506.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.137786 restraints weight = 7823.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.140544 restraints weight = 4925.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.142371 restraints weight = 3559.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.143747 restraints weight = 2836.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   8145  Z= 0.142
  Angle     :  0.730  16.047  11015  Z= 0.373
  Chirality :  0.043   0.297   1239
  Planarity :  0.008   0.159   1412
  Dihedral  :  8.851 139.034   1134
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  4.65 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 12.68 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.96 (0.23), residues: 990
  helix: -1.67 (0.19), residues: 566
  sheet: -0.32 (0.70), residues: 62
  loop : -2.55 (0.28), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 878 
 TYR   0.018   0.002   TYR A 720 
 PHE   0.033   0.002   PHE H  99 
 TRP   0.019   0.001   TRP B 103 
 HIS   0.011   0.001   HIS H 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8145)
  covalent geometry    : angle       0.72956 (11015)
  hydrogen bonds       : bond        0.04430 (  319)
  hydrogen bonds       : angle       4.78020 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  652 ARG cc_start: 0.8220 (ptp-110) cc_final: 0.7732 (ttp-110)
REVERT: A  675 GLU cc_start: 0.6999 (mp0) cc_final: 0.6635 (mp0)
REVERT: A  717 ARG cc_start: 0.7408 (tmt-80) cc_final: 0.5725 (mtp180)
REVERT: A  736 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7457 (tm-30)
REVERT: A  788 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6733 (mp0)
REVERT: B   27 GLU cc_start: 0.8645 (tp30) cc_final: 0.8419 (tp30)
REVERT: B  137 MET cc_start: 0.8212 (tpp) cc_final: 0.7876 (tpp)
REVERT: H  245 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7168 (m-30)
  outliers start: 21
  outliers final: 10
  residues processed: 176
  average time/residue: 0.0876
  time to fit residues: 20.8410
Evaluate side-chains
  162 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  634 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  245 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 6 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 98 optimal weight:    0.2980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 654 GLN
** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.154038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.129692 restraints weight = 15284.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133655 restraints weight = 7806.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.136308 restraints weight = 4964.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.138019 restraints weight = 3639.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.139398 restraints weight = 2948.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8145  Z= 0.143
  Angle     :  0.673  15.154  11015  Z= 0.342
  Chirality :  0.043   0.278   1239
  Planarity :  0.008   0.153   1412
  Dihedral  :  7.661 135.386   1121
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  5.35 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.67 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.04 (0.25), residues: 990
  helix: -0.83 (0.21), residues: 549
  sheet: -0.45 (0.69), residues: 64
  loop : -2.18 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H 181 
 TYR   0.016   0.002   TYR A 720 
 PHE   0.032   0.002   PHE H  99 
 TRP   0.016   0.001   TRP B 103 
 HIS   0.007   0.001   HIS H 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8145)
  covalent geometry    : angle       0.67323 (11015)
  hydrogen bonds       : bond        0.03930 (  319)
  hydrogen bonds       : angle       4.42159 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7699 (t80) cc_final: 0.7316 (t80)
REVERT: A  645 GLU cc_start: 0.7773 (tp30) cc_final: 0.7376 (tp30)
REVERT: A  652 ARG cc_start: 0.8167 (ptp-110) cc_final: 0.7963 (ttp-110)
REVERT: A  675 GLU cc_start: 0.6552 (mp0) cc_final: 0.6309 (mp0)
REVERT: A  687 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7391 (tp)
REVERT: A  717 ARG cc_start: 0.7242 (tmt-80) cc_final: 0.6933 (ptm160)
REVERT: A  732 LYS cc_start: 0.8585 (tttt) cc_final: 0.8339 (tttp)
REVERT: A  736 GLN cc_start: 0.7991 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: A  788 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6927 (mp0)
REVERT: B   27 GLU cc_start: 0.8592 (tp30) cc_final: 0.8332 (tp30)
REVERT: B  137 MET cc_start: 0.8154 (tpp) cc_final: 0.7783 (mmm)
REVERT: B  328 LYS cc_start: 0.7762 (mmpt) cc_final: 0.7548 (tppt)
REVERT: H  175 ARG cc_start: 0.8622 (tpp-160) cc_final: 0.7991 (tpp80)
  outliers start: 21
  outliers final: 14
  residues processed: 161
  average time/residue: 0.0787
  time to fit residues: 17.2811
Evaluate side-chains
  152 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   85 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  218 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 34 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.149047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.124525 restraints weight = 15652.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.128282 restraints weight = 7936.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.130866 restraints weight = 5073.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.132471 restraints weight = 3739.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.133768 restraints weight = 3055.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   8145  Z= 0.192
  Angle     :  0.700  14.641  11015  Z= 0.359
  Chirality :  0.044   0.313   1239
  Planarity :  0.007   0.149   1412
  Dihedral  :  7.568 130.541   1120
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  6.16 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 17.27 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.26), residues: 990
  helix: -0.50 (0.21), residues: 557
  sheet: -0.70 (0.67), residues: 64
  loop : -2.16 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H 181 
 TYR   0.015   0.002   TYR A 790 
 PHE   0.022   0.002   PHE A 887 
 TRP   0.015   0.002   TRP B 103 
 HIS   0.006   0.001   HIS B 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8145)
  covalent geometry    : angle       0.70043 (11015)
  hydrogen bonds       : bond        0.04219 (  319)
  hydrogen bonds       : angle       4.50950 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 143
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  607 TYR cc_start: 0.7732 (t80) cc_final: 0.7202 (t80)
REVERT: A  645 GLU cc_start: 0.7809 (tp30) cc_final: 0.7560 (tp30)
REVERT: A  648 MET cc_start: 0.8156 (ttm) cc_final: 0.7389 (ttm)
REVERT: A  687 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7306 (tp)
REVERT: A  717 ARG cc_start: 0.7365 (tmt-80) cc_final: 0.6941 (ptm160)
REVERT: A  732 LYS cc_start: 0.8645 (tttt) cc_final: 0.8334 (tttm)
REVERT: A  736 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: A  788 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7061 (mp0)
REVERT: B   15 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7839 (mm-30)
REVERT: B   27 GLU cc_start: 0.8657 (tp30) cc_final: 0.8368 (tp30)
REVERT: C   25 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7940 (mp0)
REVERT: C   39 TRP cc_start: 0.7972 (m100) cc_final: 0.7395 (m100)
REVERT: H  101 LEU cc_start: 0.8230 (mm) cc_final: 0.8026 (mm)
REVERT: H  175 ARG cc_start: 0.8626 (tpp-160) cc_final: 0.8084 (tpp80)
  outliers start: 31
  outliers final: 20
  residues processed: 165
  average time/residue: 0.0793
  time to fit residues: 18.0114
Evaluate side-chains
  156 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  859 VAL
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  341 ASP
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   85 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  218 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    0.0770
   chunk 17 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 85 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.7942

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

Flipped N/Q/H residues before XYZ refinement:
** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.157321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.133572 restraints weight = 14453.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.137273 restraints weight = 7449.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.139651 restraints weight = 4796.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.141391 restraints weight = 3579.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.142446 restraints weight = 2908.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8145  Z= 0.129
  Angle     :  0.648  12.428  11015  Z= 0.326
  Chirality :  0.042   0.223   1239
  Planarity :  0.007   0.125   1412
  Dihedral  :  7.317 129.916   1120
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  5.35 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.44 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.26), residues: 990
  helix: -0.14 (0.22), residues: 555
  sheet: -0.63 (0.67), residues: 64
  loop : -2.02 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 878 
 TYR   0.011   0.001   TYR B  14 
 PHE   0.016   0.001   PHE H  99 
 TRP   0.014   0.001   TRP B 103 
 HIS   0.007   0.001   HIS A 923 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8145)
  covalent geometry    : angle       0.64786 (11015)
  hydrogen bonds       : bond        0.03623 (  319)
  hydrogen bonds       : angle       4.22108 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7711 (t80) cc_final: 0.7045 (t80)
REVERT: A  648 MET cc_start: 0.7841 (ttm) cc_final: 0.7341 (ttm)
REVERT: A  687 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7332 (tp)
REVERT: A  717 ARG cc_start: 0.7189 (tmt-80) cc_final: 0.6798 (ptm160)
REVERT: A  736 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: A  788 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7028 (mp0)
REVERT: A  911 ARG cc_start: 0.6920 (ptm-80) cc_final: 0.6613 (ptm-80)
REVERT: B   15 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7795 (mm-30)
REVERT: B   27 GLU cc_start: 0.8569 (tp30) cc_final: 0.8261 (tp30)
REVERT: B  137 MET cc_start: 0.8038 (mmm) cc_final: 0.7636 (mmm)
REVERT: C   25 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7864 (mp0)
REVERT: C   31 ASP cc_start: 0.6646 (t0) cc_final: 0.6293 (t0)
REVERT: H   65 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7818 (m-80)
REVERT: H  101 LEU cc_start: 0.8248 (mm) cc_final: 0.8042 (mm)
REVERT: H  175 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8023 (tpp80)
REVERT: H  247 MET cc_start: 0.7489 (ppp) cc_final: 0.7269 (ppp)
  outliers start: 26
  outliers final: 19
  residues processed: 167
  average time/residue: 0.0751
  time to fit residues: 17.7226
Evaluate side-chains
  162 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   50 PHE
Chi-restraints excluded: chain H residue   65 PHE
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   85 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  218 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 82 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0980
   chunk 76 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 27 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.158442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.134558 restraints weight = 14485.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.138387 restraints weight = 7331.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140949 restraints weight = 4653.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.142715 restraints weight = 3428.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.143887 restraints weight = 2775.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8145  Z= 0.124
  Angle     :  0.639  13.163  11015  Z= 0.321
  Chirality :  0.042   0.238   1239
  Planarity :  0.006   0.115   1412
  Dihedral  :  7.137 127.927   1120
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  4.95 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 20.65 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.26), residues: 990
  helix:  0.10 (0.23), residues: 552
  sheet: -0.53 (0.68), residues: 64
  loop : -2.03 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 878 
 TYR   0.018   0.001   TYR A 720 
 PHE   0.021   0.001   PHE H  99 
 TRP   0.013   0.001   TRP B 103 
 HIS   0.006   0.001   HIS H 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8145)
  covalent geometry    : angle       0.63943 (11015)
  hydrogen bonds       : bond        0.03339 (  319)
  hydrogen bonds       : angle       4.11436 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7738 (t80) cc_final: 0.7121 (t80)
REVERT: A  645 GLU cc_start: 0.7819 (tp30) cc_final: 0.7361 (tp30)
REVERT: A  648 MET cc_start: 0.7906 (ttm) cc_final: 0.7448 (ttm)
REVERT: A  687 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7426 (tp)
REVERT: A  732 LYS cc_start: 0.8359 (tttt) cc_final: 0.8136 (tttp)
REVERT: A  736 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: A  788 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7039 (mp0)
REVERT: B   15 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7800 (mm-30)
REVERT: B   27 GLU cc_start: 0.8554 (tp30) cc_final: 0.8264 (tp30)
REVERT: B   99 LYS cc_start: 0.6812 (mptt) cc_final: 0.6429 (tttt)
REVERT: B  137 MET cc_start: 0.8117 (mmm) cc_final: 0.7435 (mmm)
REVERT: C   25 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7861 (mp0)
REVERT: C   31 ASP cc_start: 0.6612 (t0) cc_final: 0.6164 (t0)
REVERT: H   65 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7779 (m-80)
REVERT: H  140 MET cc_start: 0.5820 (mtt) cc_final: 0.5448 (mtt)
REVERT: H  247 MET cc_start: 0.7412 (ppp) cc_final: 0.7193 (ppp)
  outliers start: 28
  outliers final: 20
  residues processed: 164
  average time/residue: 0.0662
  time to fit residues: 15.2179
Evaluate side-chains
  164 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   65 PHE
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   85 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  218 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 75 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 84 optimal weight:    0.0170
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
** A 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.160312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.136910 restraints weight = 14420.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.140690 restraints weight = 7316.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.143236 restraints weight = 4659.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.144797 restraints weight = 3424.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.146029 restraints weight = 2804.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   8145  Z= 0.117
  Angle     :  0.625  13.252  11015  Z= 0.314
  Chirality :  0.042   0.212   1239
  Planarity :  0.006   0.110   1412
  Dihedral  :  6.983 125.638   1120
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.05 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 20.53 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.27), residues: 990
  helix:  0.30 (0.23), residues: 555
  sheet: -0.58 (0.67), residues: 64
  loop : -2.00 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 878 
 TYR   0.016   0.001   TYR A 720 
 PHE   0.023   0.001   PHE H  99 
 TRP   0.013   0.001   TRP B 103 
 HIS   0.005   0.001   HIS H 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8145)
  covalent geometry    : angle       0.62484 (11015)
  hydrogen bonds       : bond        0.03226 (  319)
  hydrogen bonds       : angle       4.01110 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 151
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7732 (t80) cc_final: 0.7163 (t80)
REVERT: A  648 MET cc_start: 0.7878 (ttm) cc_final: 0.7389 (ttm)
REVERT: A  687 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7511 (tp)
REVERT: A  708 ILE cc_start: 0.8051 (mp) cc_final: 0.7576 (mm)
REVERT: A  732 LYS cc_start: 0.8280 (tttt) cc_final: 0.8032 (tttp)
REVERT: A  736 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7649 (tm-30)
REVERT: A  788 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7005 (mp0)
REVERT: B   15 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7739 (mm-30)
REVERT: B   27 GLU cc_start: 0.8500 (tp30) cc_final: 0.8215 (tp30)
REVERT: B   99 LYS cc_start: 0.6843 (mptt) cc_final: 0.6448 (tttt)
REVERT: B  137 MET cc_start: 0.8086 (mmm) cc_final: 0.7423 (mmm)
REVERT: B  146 MET cc_start: 0.6435 (tpp) cc_final: 0.6194 (tpp)
REVERT: C   25 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7838 (mp0)
REVERT: C   31 ASP cc_start: 0.6501 (t0) cc_final: 0.6199 (t0)
REVERT: H   65 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7773 (m-80)
REVERT: H  140 MET cc_start: 0.5974 (mtt) cc_final: 0.5685 (mtt)
REVERT: H  247 MET cc_start: 0.7368 (ppp) cc_final: 0.7129 (ppp)
  outliers start: 32
  outliers final: 23
  residues processed: 171
  average time/residue: 0.0884
  time to fit residues: 21.0349
Evaluate side-chains
  169 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   65 PHE
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   85 VAL
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  218 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 45 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0870
   chunk 77 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
A 760 HIS
** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 106 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.159629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.136199 restraints weight = 14459.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.139943 restraints weight = 7371.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.142467 restraints weight = 4715.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.144165 restraints weight = 3488.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.145318 restraints weight = 2830.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7079
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   8145  Z= 0.121
  Angle     :  0.637  13.796  11015  Z= 0.317
  Chirality :  0.042   0.208   1239
  Planarity :  0.006   0.106   1412
  Dihedral  :  6.888 123.659   1120
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.15 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 21.26 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.27), residues: 990
  helix:  0.39 (0.23), residues: 552
  sheet: -0.58 (0.67), residues: 64
  loop : -2.03 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 911 
 TYR   0.012   0.001   TYR A 720 
 PHE   0.022   0.001   PHE H  99 
 TRP   0.011   0.001   TRP B 103 
 HIS   0.005   0.001   HIS H 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8145)
  covalent geometry    : angle       0.63705 (11015)
  hydrogen bonds       : bond        0.03201 (  319)
  hydrogen bonds       : angle       4.00521 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7751 (t80) cc_final: 0.7194 (t80)
REVERT: A  645 GLU cc_start: 0.7777 (tp30) cc_final: 0.7408 (tp30)
REVERT: A  648 MET cc_start: 0.7942 (ttm) cc_final: 0.7462 (ttm)
REVERT: A  687 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7542 (tp)
REVERT: A  732 LYS cc_start: 0.8346 (tttt) cc_final: 0.8080 (tttp)
REVERT: A  736 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: A  788 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7028 (mp0)
REVERT: B   15 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7793 (mm-30)
REVERT: B   27 GLU cc_start: 0.8498 (tp30) cc_final: 0.8207 (tp30)
REVERT: B   99 LYS cc_start: 0.6930 (mptt) cc_final: 0.6510 (tttt)
REVERT: B  137 MET cc_start: 0.8131 (mmm) cc_final: 0.7184 (mmm)
REVERT: B  146 MET cc_start: 0.6326 (tpp) cc_final: 0.6048 (tpp)
REVERT: B  265 MET cc_start: 0.7824 (mmm) cc_final: 0.7574 (mmm)
REVERT: C   25 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7853 (mp0)
REVERT: C   31 ASP cc_start: 0.6504 (t0) cc_final: 0.5972 (t0)
REVERT: C   33 ASP cc_start: 0.8294 (p0) cc_final: 0.7819 (t0)
REVERT: H   65 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7801 (m-80)
REVERT: H  247 MET cc_start: 0.7387 (ppp) cc_final: 0.7147 (ppp)
  outliers start: 28
  outliers final: 23
  residues processed: 166
  average time/residue: 0.0837
  time to fit residues: 19.6734
Evaluate side-chains
  170 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  657 VAL
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain B residue  395 LEU
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   65 PHE
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   85 VAL
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  218 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 10 optimal weight:    0.1980
   chunk 66 optimal weight:    0.8980
   chunk 91 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0000
   chunk 7 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.160723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.136979 restraints weight = 14430.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.140894 restraints weight = 7211.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.143514 restraints weight = 4571.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.145308 restraints weight = 3359.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.146378 restraints weight = 2713.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8145  Z= 0.116
  Angle     :  0.633  13.860  11015  Z= 0.315
  Chirality :  0.042   0.251   1239
  Planarity :  0.006   0.105   1412
  Dihedral  :  6.771 120.723   1120
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.05 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.01 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.78 (0.27), residues: 990
  helix:  0.47 (0.23), residues: 557
  sheet: -0.52 (0.67), residues: 64
  loop : -2.05 (0.30), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 242 
 TYR   0.012   0.001   TYR A 720 
 PHE   0.024   0.001   PHE H  99 
 TRP   0.010   0.001   TRP B 103 
 HIS   0.005   0.001   HIS H 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8145)
  covalent geometry    : angle       0.63297 (11015)
  hydrogen bonds       : bond        0.03096 (  319)
  hydrogen bonds       : angle       3.91591 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 153
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7794 (t80) cc_final: 0.7154 (t80)
REVERT: A  645 GLU cc_start: 0.7781 (tp30) cc_final: 0.7389 (tp30)
REVERT: A  648 MET cc_start: 0.8024 (ttm) cc_final: 0.7523 (ttm)
REVERT: A  717 ARG cc_start: 0.6822 (ptm160) cc_final: 0.5384 (mtp180)
REVERT: A  788 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7024 (mp0)
REVERT: B   15 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7750 (mm-30)
REVERT: B   27 GLU cc_start: 0.8469 (tp30) cc_final: 0.8188 (tp30)
REVERT: B   99 LYS cc_start: 0.6943 (mptt) cc_final: 0.6588 (tttt)
REVERT: B  137 MET cc_start: 0.8058 (mmm) cc_final: 0.6892 (ttm)
REVERT: B  146 MET cc_start: 0.6494 (tpp) cc_final: 0.6217 (tpp)
REVERT: B  335 THR cc_start: 0.7217 (p) cc_final: 0.6918 (t)
REVERT: C   25 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7761 (mp0)
REVERT: C   31 ASP cc_start: 0.6284 (t0) cc_final: 0.5884 (t0)
REVERT: H   65 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7629 (m-80)
REVERT: H   99 PHE cc_start: 0.7673 (p90) cc_final: 0.7352 (p90)
REVERT: H  175 ARG cc_start: 0.8388 (tpp-160) cc_final: 0.7928 (mmt-90)
REVERT: H  247 MET cc_start: 0.7337 (ppp) cc_final: 0.7087 (ppp)
  outliers start: 31
  outliers final: 24
  residues processed: 171
  average time/residue: 0.0767
  time to fit residues: 18.4356
Evaluate side-chains
  169 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  790 TYR
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   50 PHE
Chi-restraints excluded: chain H residue   65 PHE
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   85 VAL
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  218 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0980
   chunk 49 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0030
   chunk 9 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.159460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.135721 restraints weight = 14507.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.139543 restraints weight = 7308.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.142164 restraints weight = 4662.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.143768 restraints weight = 3414.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.145082 restraints weight = 2782.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073   8145  Z= 0.127
  Angle     :  0.661  14.076  11015  Z= 0.328
  Chirality :  0.043   0.277   1239
  Planarity :  0.006   0.107   1412
  Dihedral  :  6.693 118.485   1120
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  4.85 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.38 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.27), residues: 990
  helix:  0.57 (0.23), residues: 549
  sheet: -0.59 (0.67), residues: 64
  loop : -1.99 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 911 
 TYR   0.012   0.001   TYR A 720 
 PHE   0.023   0.001   PHE H  99 
 TRP   0.010   0.001   TRP B 103 
 HIS   0.005   0.001   HIS H 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8145)
  covalent geometry    : angle       0.66074 (11015)
  hydrogen bonds       : bond        0.03169 (  319)
  hydrogen bonds       : angle       3.96140 (  945)

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

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

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1980 Ramachandran restraints generated.
    990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7782 (t80) cc_final: 0.7089 (t80)
REVERT: A  645 GLU cc_start: 0.7775 (tp30) cc_final: 0.7407 (tp30)
REVERT: A  648 MET cc_start: 0.8053 (ttm) cc_final: 0.7608 (ttm)
REVERT: A  708 ILE cc_start: 0.7737 (mp) cc_final: 0.6994 (mm)
REVERT: A  717 ARG cc_start: 0.6824 (ptm160) cc_final: 0.5433 (mtp180)
REVERT: A  725 ASN cc_start: 0.8870 (t0) cc_final: 0.8524 (t0)
REVERT: A  788 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7061 (mp0)
REVERT: B   15 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7753 (mm-30)
REVERT: B   27 GLU cc_start: 0.8432 (tp30) cc_final: 0.8142 (tp30)
REVERT: B   99 LYS cc_start: 0.7028 (mptt) cc_final: 0.6659 (tttt)
REVERT: B  137 MET cc_start: 0.8081 (mmm) cc_final: 0.6923 (ttm)
REVERT: B  146 MET cc_start: 0.6524 (tpp) cc_final: 0.6244 (tpp)
REVERT: B  335 THR cc_start: 0.7240 (p) cc_final: 0.6924 (t)
REVERT: C   25 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7739 (mp0)
REVERT: H   65 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.7718 (m-80)
REVERT: H   84 ASP cc_start: 0.8051 (m-30) cc_final: 0.7599 (m-30)
REVERT: H   99 PHE cc_start: 0.7685 (p90) cc_final: 0.7382 (p90)
REVERT: H  247 MET cc_start: 0.7294 (ppp) cc_final: 0.7017 (ppp)
  outliers start: 26
  outliers final: 24
  residues processed: 160
  average time/residue: 0.0884
  time to fit residues: 19.9390
Evaluate side-chains
  166 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  664 THR
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  675 GLU
Chi-restraints excluded: chain A residue  689 HIS
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  790 TYR
Chi-restraints excluded: chain A residue  831 VAL
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  360 VAL
Chi-restraints excluded: chain C residue   37 HIS
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   50 PHE
Chi-restraints excluded: chain H residue   65 PHE
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue   85 VAL
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  218 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0170
   chunk 65 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 88 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.7622

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

Flipped N/Q/H residues before XYZ refinement:
** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.160317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.136428 restraints weight = 14499.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.140311 restraints weight = 7319.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.142938 restraints weight = 4661.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.144588 restraints weight = 3416.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.145848 restraints weight = 2790.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
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   0.073   8145  Z= 0.126
  Angle     :  0.661  14.195  11015  Z= 0.327
  Chirality :  0.043   0.282   1239
  Planarity :  0.006   0.109   1412
  Dihedral  :  6.624 116.792   1120
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  4.85 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 21.74 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.27), residues: 990
  helix:  0.56 (0.23), residues: 550
  sheet: -0.52 (0.68), residues: 64
  loop : -1.81 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 911 
 TYR   0.012   0.001   TYR A 720 
 PHE   0.023   0.001   PHE H  99 
 TRP   0.010   0.001   TRP B 103 
 HIS   0.005   0.001   HIS H 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8145)
  covalent geometry    : angle       0.66086 (11015)
  hydrogen bonds       : bond        0.03224 (  319)
  hydrogen bonds       : angle       4.02307 (  945)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1412.95 seconds
wall clock time: 25 minutes 6.01 seconds (1506.01 seconds total)