Starting phenix.real_space_refine
on Fri Jul 25 21:03:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8r7k_18978/07_2025/8r7k_18978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8r7k_18978/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8r7k_18978/07_2025/8r7k_18978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8r7k_18978/07_2025/8r7k_18978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8r7k_18978/07_2025/8r7k_18978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8r7k_18978/07_2025/8r7k_18978.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.022
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 4}
          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: {'GLN:plan1': 4, 'HIS:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 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: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP: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: {'PHE:plan': 1, 'GLU:plan': 3, 'HIS: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: 5.03, per 1000 atoms: 0.63
  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: 1.75
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.74
  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: 1.83

  Time building geometry restraints manager: 2.12 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:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.230
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.470
-------------------------------------------------------------------------------
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 : 4.72
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.055   0.004   TRP B 103 
 HIS   0.017   0.002   HIS H 121 
 PHE   0.070   0.004   PHE H  65 
 TYR   0.057   0.005   TYR A 607 
 ARG   0.015   0.002   ARG H 175 

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

*********************** 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  : 0.937 
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: 0.6580 (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: 0.7712 (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: 0.7204 (p90)
  outliers start: 13
  outliers final: 7
  residues processed: 198
  average time/residue: 0.2098
  time to fit residues: 55.5971
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  : 0.963 
-------------------------------------------------------------------------------
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 84 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 25 optimal weight:    0.0370
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 78 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0570
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.155066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.131275 restraints weight = 15029.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.135231 restraints weight = 7551.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.137933 restraints weight = 4752.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8145  Z= 0.160
  Angle     :  0.753  16.121  11015  Z= 0.386
  Chirality :  0.044   0.300   1239
  Planarity :  0.008   0.159   1412
  Dihedral  :  8.898 138.510   1134
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  4.95 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 14.01 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.23), residues: 990
  helix: -1.68 (0.19), residues: 566
  sheet: -0.39 (0.70), residues: 62
  loop : -2.57 (0.27), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 103 
 HIS   0.011   0.001   HIS H 121 
 PHE   0.031   0.002   PHE A 874 
 TYR   0.022   0.002   TYR A 720 
 ARG   0.006   0.001   ARG H 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04707 (  319)
  hydrogen bonds       : angle       4.85093 (  945)
  covalent geometry    : bond        0.00362 ( 8145)
  covalent geometry    : angle       0.75331 (11015)

*********************** 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
  181 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  652 ARG cc_start: 0.8197 (ptp-110) cc_final: 0.7724 (ttp-110)
REVERT: A  717 ARG cc_start: 0.7432 (tmt-80) cc_final: 0.5732 (mtp180)
REVERT: A  736 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7506 (tm-30)
REVERT: A  788 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6816 (mp0)
REVERT: B   27 GLU cc_start: 0.8667 (tp30) cc_final: 0.8434 (tp30)
REVERT: B  137 MET cc_start: 0.8235 (tpp) cc_final: 0.7891 (tpp)
REVERT: H   49 ASP cc_start: 0.7867 (p0) cc_final: 0.7660 (p0)
REVERT: H  201 MET cc_start: 0.5088 (mmt) cc_final: 0.4874 (mmt)
REVERT: H  245 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7189 (m-30)
  outliers start: 22
  outliers final: 13
  residues processed: 171
  average time/residue: 0.2514
  time to fit residues: 58.5628
Evaluate side-chains
  161 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 1.892 
-------------------------------------------------------------------------------
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  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  253 ILE
Chi-restraints excluded: chain B residue  298 LEU
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   85 VAL
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 27 optimal weight:    0.6980
   chunk 39 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0010
   chunk 5 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0170
   chunk 43 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.4224

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
H  67 HIS
H 106 GLN
H 192 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.157943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.133706 restraints weight = 15432.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.137806 restraints weight = 7798.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.140668 restraints weight = 4897.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8145  Z= 0.119
  Angle     :  0.650  14.792  11015  Z= 0.328
  Chirality :  0.042   0.284   1239
  Planarity :  0.008   0.153   1412
  Dihedral  :  7.549 137.196   1121
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  4.95 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.91 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.25), residues: 990
  helix: -0.78 (0.21), residues: 546
  sheet: -0.29 (0.71), residues: 62
  loop : -2.26 (0.28), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.007   0.001   HIS H 121 
 PHE   0.031   0.002   PHE H  99 
 TYR   0.018   0.001   TYR A 720 
 ARG   0.006   0.000   ARG H 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03593 (  319)
  hydrogen bonds       : angle       4.29891 (  945)
  covalent geometry    : bond        0.00262 ( 8145)
  covalent geometry    : angle       0.64963 (11015)

*********************** 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
  181 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 1.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7736 (t80) cc_final: 0.7334 (t80)
REVERT: A  645 GLU cc_start: 0.7491 (tp30) cc_final: 0.6996 (tp30)
REVERT: A  736 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7708 (tm-30)
REVERT: A  788 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6890 (mp0)
REVERT: B   27 GLU cc_start: 0.8558 (tp30) cc_final: 0.8313 (tp30)
REVERT: B  137 MET cc_start: 0.8130 (tpp) cc_final: 0.7784 (mmm)
REVERT: B  243 SER cc_start: 0.8737 (m) cc_final: 0.8308 (p)
REVERT: B  370 MET cc_start: 0.7328 (tpp) cc_final: 0.6877 (tpp)
REVERT: H  245 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7001 (m-30)
  outliers start: 17
  outliers final: 10
  residues processed: 173
  average time/residue: 0.2995
  time to fit residues: 70.0354
Evaluate side-chains
  159 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 1.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   69 SER
Chi-restraints excluded: chain H residue  245 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0870
   chunk 59 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   chunk 91 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.7160

-------------------------------------------------------------------------------
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 ** 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 = 0.4140 r_free = 0.4140 target = 0.162396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.138599 restraints weight = 14315.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.142529 restraints weight = 7205.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.145184 restraints weight = 4547.003|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   8145  Z= 0.122
  Angle     :  0.641  15.857  11015  Z= 0.321
  Chirality :  0.042   0.284   1239
  Planarity :  0.007   0.154   1412
  Dihedral  :  7.224 133.132   1119
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  5.25 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.87 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.26), residues: 990
  helix: -0.32 (0.22), residues: 547
  sheet: -0.33 (0.70), residues: 62
  loop : -2.02 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 103 
 HIS   0.007   0.001   HIS H 121 
 PHE   0.033   0.001   PHE H  99 
 TYR   0.018   0.001   TYR A 720 
 ARG   0.006   0.000   ARG H 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03458 (  319)
  hydrogen bonds       : angle       4.19502 (  945)
  covalent geometry    : bond        0.00284 ( 8145)
  covalent geometry    : angle       0.64052 (11015)

*********************** 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: 27
    poor density    : 147
  time to evaluate  : 2.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7864 (t80) cc_final: 0.7364 (t80)
REVERT: A  645 GLU cc_start: 0.7489 (tp30) cc_final: 0.7056 (tp30)
REVERT: A  687 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.7042 (tp)
REVERT: A  736 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: A  788 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6919 (mp0)
REVERT: A  911 ARG cc_start: 0.6857 (ptm-80) cc_final: 0.6538 (ptm-80)
REVERT: B   27 GLU cc_start: 0.8520 (tp30) cc_final: 0.8275 (tp30)
REVERT: B  137 MET cc_start: 0.8101 (tpp) cc_final: 0.7880 (mmm)
REVERT: B  195 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7156 (mm)
REVERT: C   25 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7903 (mp0)
REVERT: H   65 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7658 (m-80)
REVERT: H  175 ARG cc_start: 0.8596 (tpp-160) cc_final: 0.7919 (tpp80)
  outliers start: 27
  outliers final: 17
  residues processed: 164
  average time/residue: 0.2750
  time to fit residues: 62.9000
Evaluate side-chains
  157 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
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 B residue  195 ILE
Chi-restraints excluded: chain B residue  205 SER
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   50 PHE
Chi-restraints excluded: chain H residue   65 PHE
Chi-restraints excluded: chain H residue   69 SER
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 5 optimal weight:    0.0170
   chunk 15 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 59 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0470
   chunk 66 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   overall best weight:    0.4716

-------------------------------------------------------------------------------
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 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 361 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.162135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.138503 restraints weight = 14066.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.142432 restraints weight = 7130.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.145061 restraints weight = 4500.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
moved from start:          0.2832

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= 0.112
  Angle     :  0.612  12.797  11015  Z= 0.309
  Chirality :  0.041   0.234   1239
  Planarity :  0.006   0.128   1412
  Dihedral  :  6.986 130.801   1119
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.15 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 18.96 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.26), residues: 990
  helix: -0.10 (0.22), residues: 553
  sheet: -0.29 (0.69), residues: 62
  loop : -2.07 (0.29), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 103 
 HIS   0.006   0.001   HIS H 121 
 PHE   0.028   0.001   PHE H  99 
 TYR   0.020   0.001   TYR A 790 
 ARG   0.007   0.000   ARG H 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  319)
  hydrogen bonds       : angle       4.04879 (  945)
  covalent geometry    : bond        0.00263 ( 8145)
  covalent geometry    : angle       0.61157 (11015)

*********************** 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
  187 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7858 (t80) cc_final: 0.7212 (t80)
REVERT: A  645 GLU cc_start: 0.7503 (tp30) cc_final: 0.7066 (tp30)
REVERT: A  648 MET cc_start: 0.7886 (ttm) cc_final: 0.7433 (ttm)
REVERT: A  687 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7095 (tp)
REVERT: A  788 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6951 (mp0)
REVERT: B   15 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7863 (mm-30)
REVERT: B   27 GLU cc_start: 0.8530 (tp30) cc_final: 0.8276 (tp30)
REVERT: B  146 MET cc_start: 0.6445 (tpp) cc_final: 0.6230 (tpp)
REVERT: B  328 LYS cc_start: 0.8289 (tppt) cc_final: 0.8014 (mppt)
REVERT: C   25 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7861 (mp0)
REVERT: C   31 ASP cc_start: 0.6449 (t0) cc_final: 0.6047 (t0)
REVERT: H   65 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7695 (m-80)
REVERT: H  175 ARG cc_start: 0.8589 (tpp-160) cc_final: 0.7696 (tpp80)
  outliers start: 29
  outliers final: 17
  residues processed: 175
  average time/residue: 0.1945
  time to fit residues: 47.0847
Evaluate side-chains
  167 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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  691 LEU
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  205 SER
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  253 ILE
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  172 THR
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 21 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 82 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 192 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.160526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.136844 restraints weight = 14329.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.140642 restraints weight = 7486.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.143157 restraints weight = 4819.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7124
moved from start:          0.3034

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= 0.127
  Angle     :  0.633  11.763  11015  Z= 0.319
  Chirality :  0.041   0.219   1239
  Planarity :  0.006   0.118   1412
  Dihedral  :  6.922 127.353   1119
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.25 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 19.20 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.26), residues: 990
  helix:  0.17 (0.23), residues: 552
  sheet: -0.29 (0.67), residues: 64
  loop : -2.03 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 103 
 HIS   0.006   0.001   HIS H 121 
 PHE   0.027   0.001   PHE H  99 
 TYR   0.018   0.002   TYR A 720 
 ARG   0.006   0.000   ARG H 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03241 (  319)
  hydrogen bonds       : angle       4.05944 (  945)
  covalent geometry    : bond        0.00308 ( 8145)
  covalent geometry    : angle       0.63260 (11015)

*********************** 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
  185 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7803 (t80) cc_final: 0.7133 (t80)
REVERT: A  645 GLU cc_start: 0.7601 (tp30) cc_final: 0.7151 (tp30)
REVERT: A  648 MET cc_start: 0.7958 (ttm) cc_final: 0.7392 (ttm)
REVERT: A  687 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7005 (tp)
REVERT: A  788 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7020 (mp0)
REVERT: B   15 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7829 (mm-30)
REVERT: B   27 GLU cc_start: 0.8508 (tp30) cc_final: 0.8260 (tp30)
REVERT: B  137 MET cc_start: 0.8039 (mmm) cc_final: 0.7778 (mmm)
REVERT: C   25 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7858 (mp0)
REVERT: C   31 ASP cc_start: 0.6481 (t0) cc_final: 0.6004 (t0)
REVERT: C   32 GLU cc_start: 0.7765 (pm20) cc_final: 0.7187 (pm20)
REVERT: H   65 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7737 (m-80)
REVERT: H  101 LEU cc_start: 0.8139 (mm) cc_final: 0.7921 (mm)
  outliers start: 31
  outliers final: 21
  residues processed: 173
  average time/residue: 0.1901
  time to fit residues: 45.3422
Evaluate side-chains
  171 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 147
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  655 LEU
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 B residue  205 SER
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  360 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 62 optimal weight:    0.4980
   chunk 35 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 85 optimal weight:    0.3980
   chunk 39 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
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**
A 923 HIS
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.154713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.131017 restraints weight = 14627.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.134612 restraints weight = 7563.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.137051 restraints weight = 4889.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   8145  Z= 0.160
  Angle     :  0.680  12.633  11015  Z= 0.342
  Chirality :  0.044   0.204   1239
  Planarity :  0.006   0.111   1412
  Dihedral  :  6.967 123.854   1119
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  5.56 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 19.69 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.26), residues: 990
  helix:  0.22 (0.23), residues: 548
  sheet: -0.49 (0.66), residues: 64
  loop : -2.01 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 103 
 HIS   0.006   0.001   HIS H 121 
 PHE   0.024   0.002   PHE H  99 
 TYR   0.014   0.002   TYR A 720 
 ARG   0.005   0.000   ARG H 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03610 (  319)
  hydrogen bonds       : angle       4.25689 (  945)
  covalent geometry    : bond        0.00387 ( 8145)
  covalent geometry    : angle       0.68025 (11015)

*********************** 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
  176 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 147
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7808 (t80) cc_final: 0.7234 (t80)
REVERT: A  645 GLU cc_start: 0.7652 (tp30) cc_final: 0.7207 (tp30)
REVERT: A  648 MET cc_start: 0.7979 (ttm) cc_final: 0.7575 (ttm)
REVERT: A  788 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7067 (mp0)
REVERT: B   15 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7785 (mm-30)
REVERT: B   27 GLU cc_start: 0.8574 (tp30) cc_final: 0.8275 (tp30)
REVERT: B  137 MET cc_start: 0.8076 (mmm) cc_final: 0.7498 (mmm)
REVERT: C   25 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7906 (mp0)
REVERT: H   65 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7848 (m-80)
REVERT: H  175 ARG cc_start: 0.8455 (tpp-160) cc_final: 0.7984 (tpp80)
  outliers start: 29
  outliers final: 20
  residues processed: 166
  average time/residue: 0.1840
  time to fit residues: 42.2844
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  : 0.921 
-------------------------------------------------------------------------------
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  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  923 HIS
Chi-restraints excluded: chain B residue  205 SER
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  360 VAL
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  190 ILE
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 55 optimal weight:    0.5980
   chunk 87 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 99 optimal weight:    8.9990
   chunk 42 optimal weight:    0.0870
   chunk 65 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 31 optimal weight:    0.4980
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 689 HIS
** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.159741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.135932 restraints weight = 14632.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.139664 restraints weight = 7593.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.142200 restraints weight = 4917.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8145  Z= 0.125
  Angle     :  0.658  13.177  11015  Z= 0.328
  Chirality :  0.042   0.206   1239
  Planarity :  0.006   0.108   1412
  Dihedral  :  6.825 122.945   1119
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.56 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.26 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.27), residues: 990
  helix:  0.35 (0.23), residues: 553
  sheet: -0.31 (0.66), residues: 64
  loop : -1.95 (0.30), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 103 
 HIS   0.018   0.001   HIS A 923 
 PHE   0.020   0.001   PHE H  99 
 TYR   0.021   0.001   TYR B  81 
 ARG   0.006   0.000   ARG H 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03259 (  319)
  hydrogen bonds       : angle       4.03135 (  945)
  covalent geometry    : bond        0.00307 ( 8145)
  covalent geometry    : angle       0.65787 (11015)

*********************** 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: 25
    poor density    : 151
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7814 (t80) cc_final: 0.7267 (t80)
REVERT: A  645 GLU cc_start: 0.7586 (tp30) cc_final: 0.7136 (tp30)
REVERT: A  648 MET cc_start: 0.8039 (ttm) cc_final: 0.7695 (ttm)
REVERT: A  788 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7005 (mp0)
REVERT: B   15 GLU cc_start: 0.8467 (mm-30) cc_final: 0.7828 (mm-30)
REVERT: B   27 GLU cc_start: 0.8517 (tp30) cc_final: 0.8221 (tp30)
REVERT: B   99 LYS cc_start: 0.6792 (mptt) cc_final: 0.6414 (tttt)
REVERT: B  137 MET cc_start: 0.8003 (mmm) cc_final: 0.6974 (ttm)
REVERT: C   25 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7835 (mp0)
REVERT: C   31 ASP cc_start: 0.6470 (t0) cc_final: 0.6150 (t0)
REVERT: C   33 ASP cc_start: 0.8390 (p0) cc_final: 0.7997 (t0)
REVERT: H   65 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7775 (m-80)
  outliers start: 25
  outliers final: 20
  residues processed: 166
  average time/residue: 0.1918
  time to fit residues: 44.2569
Evaluate side-chains
  169 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
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  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  205 SER
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  360 VAL
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  147 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  190 ILE
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 64 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 94 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 56 optimal weight:    7.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.4096 r_free = 0.4096 target = 0.158760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.135179 restraints weight = 14641.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.138883 restraints weight = 7499.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.141382 restraints weight = 4809.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.3563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8145  Z= 0.136
  Angle     :  0.666  13.695  11015  Z= 0.330
  Chirality :  0.043   0.248   1239
  Planarity :  0.006   0.106   1412
  Dihedral  :  6.777 120.612   1119
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.56 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.53 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.27), residues: 990
  helix:  0.44 (0.23), residues: 551
  sheet: -0.37 (0.65), residues: 64
  loop : -1.95 (0.30), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 103 
 HIS   0.006   0.001   HIS H 121 
 PHE   0.022   0.001   PHE H  99 
 TYR   0.020   0.001   TYR A 720 
 ARG   0.007   0.000   ARG H 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03328 (  319)
  hydrogen bonds       : angle       4.05744 (  945)
  covalent geometry    : bond        0.00337 ( 8145)
  covalent geometry    : angle       0.66561 (11015)

*********************** 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
  174 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7828 (t80) cc_final: 0.7253 (t80)
REVERT: A  645 GLU cc_start: 0.7639 (tp30) cc_final: 0.7190 (tp30)
REVERT: A  648 MET cc_start: 0.8033 (ttm) cc_final: 0.7676 (ttm)
REVERT: A  708 ILE cc_start: 0.7949 (mp) cc_final: 0.7268 (mm)
REVERT: A  788 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7034 (mp0)
REVERT: B   15 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7779 (mm-30)
REVERT: B   27 GLU cc_start: 0.8476 (tp30) cc_final: 0.8183 (tp30)
REVERT: B   99 LYS cc_start: 0.6937 (mptt) cc_final: 0.6538 (tttt)
REVERT: B  137 MET cc_start: 0.8023 (mmm) cc_final: 0.6997 (ttm)
REVERT: C   25 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7841 (mp0)
REVERT: C   31 ASP cc_start: 0.6420 (t0) cc_final: 0.6066 (t0)
REVERT: H   65 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7816 (m-80)
REVERT: H  175 ARG cc_start: 0.8449 (tpp-160) cc_final: 0.7984 (mmt-90)
  outliers start: 26
  outliers final: 23
  residues processed: 165
  average time/residue: 0.1925
  time to fit residues: 44.5633
Evaluate side-chains
  173 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
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  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 B residue  205 SER
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  360 VAL
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  147 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  190 ILE
Chi-restraints excluded: chain H residue  218 THR
Chi-restraints excluded: chain H residue  224 VAL
Chi-restraints excluded: chain H residue  244 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0030
   chunk 69 optimal weight:    9.9990
   chunk 78 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0470
   chunk 63 optimal weight:    0.3980
   chunk 26 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.3888

-------------------------------------------------------------------------------
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 = 0.4127 r_free = 0.4127 target = 0.161559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.138017 restraints weight = 14386.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.141937 restraints weight = 7171.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.144604 restraints weight = 4507.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8145  Z= 0.116
  Angle     :  0.645  14.445  11015  Z= 0.318
  Chirality :  0.042   0.226   1239
  Planarity :  0.006   0.106   1412
  Dihedral  :  6.509 117.969   1119
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.25 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 21.50 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.27), residues: 990
  helix:  0.65 (0.23), residues: 548
  sheet: -0.09 (0.67), residues: 64
  loop : -1.85 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  39 
 HIS   0.006   0.001   HIS H 121 
 PHE   0.024   0.001   PHE H  99 
 TYR   0.021   0.001   TYR A 720 
 ARG   0.007   0.000   ARG H 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02969 (  319)
  hydrogen bonds       : angle       3.90459 (  945)
  covalent geometry    : bond        0.00280 ( 8145)
  covalent geometry    : angle       0.64518 (11015)

********************** 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
  180 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 158
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  607 TYR cc_start: 0.7801 (t80) cc_final: 0.7253 (t80)
REVERT: A  645 GLU cc_start: 0.7651 (tp30) cc_final: 0.7218 (tp30)
REVERT: A  648 MET cc_start: 0.8080 (ttm) cc_final: 0.7819 (ttm)
REVERT: A  674 LYS cc_start: 0.6168 (mtpp) cc_final: 0.5823 (ttpp)
REVERT: A  708 ILE cc_start: 0.7889 (mp) cc_final: 0.7137 (mm)
REVERT: A  763 CYS cc_start: 0.7506 (t) cc_final: 0.7090 (p)
REVERT: A  788 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7016 (mp0)
REVERT: B   27 GLU cc_start: 0.8425 (tp30) cc_final: 0.8146 (tp30)
REVERT: B   99 LYS cc_start: 0.6871 (mptt) cc_final: 0.6512 (tttt)
REVERT: B  137 MET cc_start: 0.8053 (mmm) cc_final: 0.6978 (ttm)
REVERT: B  370 MET cc_start: 0.7322 (tpp) cc_final: 0.6864 (tpp)
REVERT: C   25 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7784 (mp0)
REVERT: C   31 ASP cc_start: 0.6412 (t0) cc_final: 0.6054 (t0)
REVERT: C   33 ASP cc_start: 0.8303 (p0) cc_final: 0.7929 (t70)
REVERT: H   65 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7657 (m-80)
REVERT: H  175 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.7925 (mmt-90)
  outliers start: 22
  outliers final: 19
  residues processed: 172
  average time/residue: 0.2305
  time to fit residues: 54.5479
Evaluate side-chains
  167 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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  689 HIS
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  788 GLU
Chi-restraints excluded: chain A residue  858 LEU
Chi-restraints excluded: chain B residue  205 SER
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  368 ILE
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  147 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  179 LEU
Chi-restraints excluded: chain H residue  190 ILE
Chi-restraints excluded: chain H residue  218 THR
Chi-restraints excluded: chain H residue  224 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    0.0570
   chunk 17 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 91 optimal weight:    8.9990
   chunk 73 optimal weight:    0.3980
   chunk 11 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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**
** A 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  96 GLN
** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.161444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.137806 restraints weight = 14458.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.141747 restraints weight = 7235.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.144408 restraints weight = 4542.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.3868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074   8145  Z= 0.117
  Angle     :  0.645  14.300  11015  Z= 0.318
  Chirality :  0.042   0.259   1239
  Planarity :  0.006   0.105   1412
  Dihedral  :  6.385 115.648   1119
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.25 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.38 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.27), residues: 990
  helix:  0.80 (0.23), residues: 545
  sheet: -0.04 (0.68), residues: 64
  loop : -1.87 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  39 
 HIS   0.006   0.001   HIS H 121 
 PHE   0.023   0.001   PHE H  99 
 TYR   0.019   0.001   TYR A 720 
 ARG   0.008   0.000   ARG A 911 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03032 (  319)
  hydrogen bonds       : angle       3.91198 (  945)
  covalent geometry    : bond        0.00285 ( 8145)
  covalent geometry    : angle       0.64479 (11015)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3226.63 seconds
wall clock time: 58 minutes 39.25 seconds (3519.25 seconds total)