Starting phenix.real_space_refine
on Tue Jul 29 21:33:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jy5_36720/07_2025/8jy5_36720.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jy5_36720/07_2025/8jy5_36720.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jy5_36720/07_2025/8jy5_36720.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jy5_36720/07_2025/8jy5_36720.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jy5_36720/07_2025/8jy5_36720.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jy5_36720/07_2025/8jy5_36720.cif"
  }
  resolution = 4.17
  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=   0.007 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    7448      2.51       5
     N    1908      2.21       5
     O    2097      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11511
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1457, 11511
          Classifications: {'peptide': 1457}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1412}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 58
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 31
  Time building chain proxies: 6.95, per 1000 atoms: 0.60
  Number of scatterers: 11511
  At special positions: 0
  Unit cell: (94.16, 123.05, 160.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    2097      8.00
     N    1908      7.00
     C    7448      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   6 " - pdb=" SG  CYS A  26 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.85
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2754

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 8 sheets defined
      69.5% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 7
      removed outlier: 3.567A  pdb=" N   PHE A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 17
    Processing helix  chain 'A' and resid 24 through 29
      removed outlier: 3.617A  pdb=" N   GLU A  28 " --> pdb=" O   PRO A  24 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 24 through 29'
    Processing helix  chain 'A' and resid 33 through 54
      removed outlier: 3.584A  pdb=" N   LEU A  43 " --> pdb=" O   TYR A  39 " (cutoff:3.500A)
      Proline residue:  A  45  - end of helix
      removed outlier: 3.700A  pdb=" N   SER A  54 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 90
      removed outlier: 3.653A  pdb=" N   VAL A  86 " --> pdb=" O   GLU A  82 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 97 through 121
      removed outlier: 3.976A  pdb=" N   TYR A 101 " --> pdb=" O   PRO A  97 " (cutoff:3.500A)
      Proline residue:  A 104  - end of helix
      removed outlier: 3.901A  pdb=" N   LEU A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 156
      removed outlier: 4.087A  pdb=" N   PHE A 135 " --> pdb=" O   PHE A 131 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   PHE A 145 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   GLN A 146 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 183
      removed outlier: 3.535A  pdb=" N   ILE A 176 " --> pdb=" O   TYR A 172 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 177 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 197
      removed outlier: 3.891A  pdb=" N   SER A 196 " --> pdb=" O   ASN A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 206
    Processing helix  chain 'A' and resid 209 through 219
      removed outlier: 3.538A  pdb=" N   ILE A 213 " --> pdb=" O   TYR A 209 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LYS A 218 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ARG A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 226
    Processing helix  chain 'A' and resid 234 through 256
      removed outlier: 3.981A  pdb=" N   HIS A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ARG A 248 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 352
      removed outlier: 6.932A  pdb=" N   MET A 320 " --> pdb=" O   LYS A 316 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   VAL A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS A 324 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER A 325 " --> pdb=" O   VAL A 321 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 328 " --> pdb=" O   LYS A 324 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU A 330 " --> pdb=" O   PHE A 326 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   SER A 339 " --> pdb=" O   PHE A 335 " (cutoff:3.500A)
      Proline residue:  A 340  - end of helix
      removed outlier: 4.023A  pdb=" N   ASP A 352 " --> pdb=" O   SER A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 405
      removed outlier: 4.220A  pdb=" N   GLY A 360 " --> pdb=" O   TYR A 356 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   TYR A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 384 " --> pdb=" O   CYS A 380 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG A 393 " --> pdb=" O   GLY A 389 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR A 401 " --> pdb=" O   MET A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 413
    Processing helix  chain 'A' and resid 416 through 426
      removed outlier: 3.672A  pdb=" N   LEU A 423 " --> pdb=" O   GLU A 419 " (cutoff:3.500A)
      removed outlier: 4.643A  pdb=" N   MET A 424 " --> pdb=" O   THR A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 437
      removed outlier: 3.768A  pdb=" N   MET A 432 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ASP A 433 " --> pdb=" O   GLN A 429 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL A 434 " --> pdb=" O   LYS A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 459
      removed outlier: 4.291A  pdb=" N   VAL A 445 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 508
      removed outlier: 4.067A  pdb=" N   GLY A 466 " --> pdb=" O   SER A 462 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   MET A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ILE A 474 " --> pdb=" O   MET A 470 " (cutoff:3.500A)
      Proline residue:  A 475  - end of helix
      removed outlier: 4.128A  pdb=" N   LYS A 493 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   ASN A 494 " --> pdb=" O   LYS A 490 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG A 498 " --> pdb=" O   ASN A 494 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU A 504 " --> pdb=" O   LYS A 500 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 516
      removed outlier: 3.548A  pdb=" N   PHE A 515 " --> pdb=" O   ILE A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 568
      removed outlier: 3.597A  pdb=" N   LYS A 531 " --> pdb=" O   ASN A 527 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASN A 535 " --> pdb=" O   LYS A 531 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ALA A 538 " --> pdb=" O   LYS A 534 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL A 545 " --> pdb=" O   GLN A 541 " (cutoff:3.500A)
      Proline residue:  A 554  - end of helix
      removed outlier: 3.549A  pdb=" N   TYR A 565 " --> pdb=" O   THR A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 595
      removed outlier: 4.126A  pdb=" N   THR A 581 " --> pdb=" O   GLN A 577 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   SER A 582 " --> pdb=" O   LYS A 578 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE A 583 " --> pdb=" O   ALA A 579 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR A 584 " --> pdb=" O   PHE A 580 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   PHE A 591 " --> pdb=" O   ASN A 587 " (cutoff:3.500A)
      Proline residue:  A 592  - end of helix
    Processing helix  chain 'A' and resid 595 through 618
      removed outlier: 3.500A  pdb=" N   MET A 599 " --> pdb=" O   MET A 595 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ILE A 600 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL A 608 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER A 609 " --> pdb=" O   GLN A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 686
      removed outlier: 3.786A  pdb=" N   ILE A 681 " --> pdb=" O   LYS A 677 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   SER A 682 " --> pdb=" O   SER A 678 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   MET A 684 " --> pdb=" O   LEU A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 721
    Processing helix  chain 'A' and resid 726 through 737
    Processing helix  chain 'A' and resid 739 through 746
    Processing helix  chain 'A' and resid 748 through 751
    Processing helix  chain 'A' and resid 755 through 759
    Processing helix  chain 'A' and resid 762 through 777
      removed outlier: 3.601A  pdb=" N   GLN A 767 " --> pdb=" O   GLY A 763 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG A 768 " --> pdb=" O   GLY A 764 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLN A 777 " --> pdb=" O   ARG A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 803
    Processing helix  chain 'A' and resid 824 through 828
    Processing helix  chain 'A' and resid 844 through 852
      removed outlier: 3.567A  pdb=" N   LYS A 852 " --> pdb=" O   LEU A 848 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 861
      removed outlier: 3.716A  pdb=" N   LYS A 860 " --> pdb=" O   ALA A 856 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR A 861 " --> pdb=" O   LYS A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 894
      removed outlier: 3.643A  pdb=" N   ILE A 894 " --> pdb=" O   VAL A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 914
      removed outlier: 3.581A  pdb=" N   MET A 903 " --> pdb=" O   ALA A 899 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU A 906 " --> pdb=" O   THR A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 974
      removed outlier: 3.519A  pdb=" N   ILE A 974 " --> pdb=" O   TYR A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 1005
      removed outlier: 3.625A  pdb=" N   PHE A 981 " --> pdb=" O   PHE A 977 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU A 984 " --> pdb=" O   PHE A 980 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ALA A 992 " --> pdb=" O   MET A 988 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER A1005 " --> pdb=" O   SER A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1010
    Processing helix  chain 'A' and resid 1022 through 1065
      removed outlier: 3.591A  pdb=" N   GLY A1035 " --> pdb=" O   GLY A1031 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   VAL A1038 " --> pdb=" O   GLN A1034 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ALA A1041 " --> pdb=" O   PHE A1037 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   PHE A1047 " --> pdb=" O   PHE A1043 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LEU A1065 " --> pdb=" O   LEU A1061 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1068 through 1075
      removed outlier: 3.522A  pdb=" N   PHE A1072 " --> pdb=" O   PRO A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1092
      removed outlier: 4.086A  pdb=" N   ILE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP A1087 " --> pdb=" O   ARG A1083 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   ILE A1088 " --> pdb=" O   PHE A1084 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ASP A1092 " --> pdb=" O   ILE A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1093 through 1120
      removed outlier: 4.150A  pdb=" N   GLN A1097 " --> pdb=" O   ASP A1093 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ARG A1100 " --> pdb=" O   PRO A1096 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER A1101 " --> pdb=" O   GLN A1097 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   MET A1118 " --> pdb=" O   VAL A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1168
      removed outlier: 3.818A  pdb=" N   ILE A1126 " --> pdb=" O   VAL A1122 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ILE A1128 " --> pdb=" O   THR A1124 " (cutoff:3.500A)
      Proline residue:  A1129  - end of helix
      removed outlier: 3.527A  pdb=" N   ARG A1146 " --> pdb=" O   VAL A1142 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   GLN A1147 " --> pdb=" O   SER A1143 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A1149 " --> pdb=" O   SER A1145 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ARG A1150 " --> pdb=" O   ARG A1146 " (cutoff:3.500A)
      Proline residue:  A1158  - end of helix
      removed outlier: 3.573A  pdb=" N   SER A1168 " --> pdb=" O   SER A1164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1169 through 1177
      removed outlier: 3.602A  pdb=" N   ALA A1175 " --> pdb=" O   PRO A1171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1178 through 1229
      removed outlier: 3.541A  pdb=" N   ASP A1191 " --> pdb=" O   GLU A1187 " (cutoff:3.500A)
      removed outlier: 4.532A  pdb=" N   CYS A1196 " --> pdb=" O   THR A1192 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A1197 " --> pdb=" O   ASN A1193 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   SER A1199 " --> pdb=" O   LYS A1195 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   THR A1202 " --> pdb=" O   PHE A1198 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER A1203 " --> pdb=" O   SER A1199 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A1207 " --> pdb=" O   SER A1203 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ALA A1208 " --> pdb=" O   ASN A1204 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE A1209 " --> pdb=" O   ARG A1205 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU A1213 " --> pdb=" O   ILE A1209 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   VAL A1214 " --> pdb=" O   ARG A1210 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A1217 " --> pdb=" O   LEU A1213 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL A1219 " --> pdb=" O   GLY A1215 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   SER A1222 " --> pdb=" O   THR A1218 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA A1223 " --> pdb=" O   VAL A1219 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU A1224 " --> pdb=" O   PHE A1220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1236 through 1244
      removed outlier: 4.016A  pdb=" N   PHE A1240 " --> pdb=" O   ASP A1236 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   VAL A1241 " --> pdb=" O   THR A1237 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A1242 " --> pdb=" O   VAL A1238 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASN A1244 " --> pdb=" O   PHE A1240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1247 through 1266
      removed outlier: 3.738A  pdb=" N   ASN A1253 " --> pdb=" O   THR A1249 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   TRP A1254 " --> pdb=" O   GLN A1250 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   VAL A1256 " --> pdb=" O   LEU A1252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1277
    Processing helix  chain 'A' and resid 1339 through 1348
      removed outlier: 3.581A  pdb=" N   THR A1344 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1369 through 1373
    Processing helix  chain 'A' and resid 1391 through 1396
    Processing helix  chain 'A' and resid 1402 through 1413
    Processing helix  chain 'A' and resid 1415 through 1422
    Processing helix  chain 'A' and resid 1424 through 1427
    Processing helix  chain 'A' and resid 1431 through 1435
    Processing helix  chain 'A' and resid 1438 through 1454
    Processing helix  chain 'A' and resid 1468 through 1483
      removed outlier: 3.570A  pdb=" N   ILE A1479 " --> pdb=" O   ILE A1475 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLN A1480 " --> pdb=" O   GLN A1476 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN A1481 " --> pdb=" O   THR A1477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1517 through 1524
    Processing helix  chain 'A' and resid 1526 through 1535
    Processing sheet with id=AA1, first strand: chain 'A' and resid 627 through 629
      removed outlier: 6.784A  pdb=" N   SER A 643 " --> pdb=" O   VAL A 691 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   GLY A 693 " --> pdb=" O   GLU A 641 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   GLU A 641 " --> pdb=" O   GLY A 693 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ILE A 695 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   PHE A 639 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE A 697 " --> pdb=" O   MET A 637 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   MET A 637 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
      removed outlier: 5.483A  pdb=" N   ALA A 642 " --> pdb=" O   ASP A 656 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 627 through 629
      removed outlier: 6.784A  pdb=" N   SER A 643 " --> pdb=" O   VAL A 691 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   GLY A 693 " --> pdb=" O   GLU A 641 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   GLU A 641 " --> pdb=" O   GLY A 693 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   ILE A 695 " --> pdb=" O   PHE A 639 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   PHE A 639 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   ILE A 697 " --> pdb=" O   MET A 637 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   MET A 637 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET A 637 " --> pdb=" O   ILE A 661 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 701 through 704
      removed outlier: 3.755A  pdb=" N   ASP A 785 " --> pdb=" O   VAL A 704 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   TYR A 782 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   VAL A 818 " --> pdb=" O   TYR A 782 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   LEU A 784 " --> pdb=" O   VAL A 818 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   VAL A 667 " --> pdb=" O   LEU A 817 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   LEU A 666 " --> pdb=" O   GLU A 830 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   VAL A 832 " --> pdb=" O   LEU A 666 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   ALA A 668 " --> pdb=" O   VAL A 832 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   LEU A 834 " --> pdb=" O   ALA A 668 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ILE A 670 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ILE A 831 " --> pdb=" O   LYS A 842 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   LYS A 842 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL A 833 " --> pdb=" O   VAL A 840 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 713 through 714
      removed outlier: 4.063A  pdb=" N   GLY A 713 " --> pdb=" O   ILE A 754 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1315 through 1320
      removed outlier: 5.781A  pdb=" N   ARG A1318 " --> pdb=" O   VAL A1307 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   VAL A1307 " --> pdb=" O   ARG A1318 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1315 through 1320
      removed outlier: 5.781A  pdb=" N   ARG A1318 " --> pdb=" O   VAL A1307 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   VAL A1307 " --> pdb=" O   ARG A1318 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   PHE A1302 " --> pdb=" O   ILE A1359 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ILE A1359 " --> pdb=" O   PHE A1302 " (cutoff:3.500A)
      removed outlier: 5.301A  pdb=" N   ASN A1304 " --> pdb=" O   GLN A1357 " (cutoff:3.500A)
      removed outlier: 4.810A  pdb=" N   GLN A1357 " --> pdb=" O   ASN A1304 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1377 through 1380
      removed outlier: 4.151A  pdb=" N   ASP A1461 " --> pdb=" O   ILE A1380 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   VAL A1504 " --> pdb=" O   CYS A1515 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   CYS A1515 " --> pdb=" O   VAL A1504 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   VAL A1506 " --> pdb=" O   ILE A1513 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1389 through 1390

    669 hydrogen bonds defined for protein.
    1941 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: 4.85

  Time building geometry restraints manager: 3.40 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3650
        1.34 -     1.46: 2731
        1.46 -     1.58: 5275
        1.58 -     1.70: 0
        1.70 -     1.82: 96
  Bond restraints: 11752
  Sorted by residual:
  bond pdb=" C   SER A 339 "
       pdb=" N   PRO A 340 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.024 1.28e-02 6.10e+03 3.45e+00
  bond pdb=" C   ASN A 103 "
       pdb=" N   PRO A 104 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.36e-02 5.41e+03 2.35e+00
  bond pdb=" N   ASP A 656 "
       pdb=" CA  ASP A 656 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.73e+00
  bond pdb=" CA  THR A 873 "
       pdb=" CB  THR A 873 "
    ideal  model  delta    sigma   weight residual
    1.528  1.546 -0.018 1.49e-02 4.50e+03 1.50e+00
  bond pdb=" CA  PRO A1384 "
       pdb=" C   PRO A1384 "
    ideal  model  delta    sigma   weight residual
    1.527  1.514  0.013 1.07e-02 8.73e+03 1.47e+00
  ... (remaining 11747 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 15544
        1.80 -     3.59: 316
        3.59 -     5.39: 62
        5.39 -     7.19: 15
        7.19 -     8.99: 3
  Bond angle restraints: 15940
  Sorted by residual:
  angle pdb=" C   ASP A  22 "
        pdb=" N   LEU A  23 "
        pdb=" CA  LEU A  23 "
      ideal   model   delta    sigma   weight residual
     120.65  125.99   -5.34 1.36e+00 5.41e-01 1.54e+01
  angle pdb=" C   VAL A 229 "
        pdb=" N   ASP A 230 "
        pdb=" CA  ASP A 230 "
      ideal   model   delta    sigma   weight residual
     121.54  128.38   -6.84 1.91e+00 2.74e-01 1.28e+01
  angle pdb=" N   SER A 462 "
        pdb=" CA  SER A 462 "
        pdb=" C   SER A 462 "
      ideal   model   delta    sigma   weight residual
     114.56  110.08    4.48 1.27e+00 6.20e-01 1.25e+01
  angle pdb=" CA  MET A 988 "
        pdb=" CB  MET A 988 "
        pdb=" CG  MET A 988 "
      ideal   model   delta    sigma   weight residual
     114.10  121.05   -6.95 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" C   SER A1199 "
        pdb=" N   TRP A1200 "
        pdb=" CA  TRP A1200 "
      ideal   model   delta    sigma   weight residual
     122.26  116.35    5.91 1.73e+00 3.34e-01 1.17e+01
  ... (remaining 15935 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 6349
       17.82 -    35.64: 542
       35.64 -    53.46: 91
       53.46 -    71.28: 17
       71.28 -    89.10: 8
  Dihedral angle restraints: 7007
    sinusoidal: 2760
      harmonic: 4247
  Sorted by residual:
  dihedral pdb=" CA  PHE A 437 "
           pdb=" C   PHE A 437 "
           pdb=" N   MET A 438 "
           pdb=" CA  MET A 438 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.50   20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CB  CYS A   6 "
           pdb=" SG  CYS A   6 "
           pdb=" SG  CYS A  26 "
           pdb=" CB  CYS A  26 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   63.78   29.22     1      1.00e+01 1.00e-02 1.22e+01
  dihedral pdb=" CA  ARG A1349 "
           pdb=" C   ARG A1349 "
           pdb=" N   ILE A1350 "
           pdb=" CA  ILE A1350 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.71   17.29     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 7004 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1596
       0.056 -    0.112: 241
       0.112 -    0.168: 26
       0.168 -    0.224: 2
       0.224 -    0.280: 1
  Chirality restraints: 1866
  Sorted by residual:
  chirality pdb=" CB  ILE A 894 "
            pdb=" CA  ILE A 894 "
            pdb=" CG1 ILE A 894 "
            pdb=" CG2 ILE A 894 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  THR A 553 "
            pdb=" N   THR A 553 "
            pdb=" C   THR A 553 "
            pdb=" CB  THR A 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CG  LEU A1170 "
            pdb=" CB  LEU A1170 "
            pdb=" CD1 LEU A1170 "
            pdb=" CD2 LEU A1170 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.22e-01
  ... (remaining 1863 not shown)

  Planarity restraints: 1988
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1383 "    0.048 5.00e-02 4.00e+02   7.34e-02 8.61e+00
        pdb=" N   PRO A1384 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A1384 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A1384 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 442 "   -0.007 2.00e-02 2.50e+03   1.26e-02 3.97e+00
        pdb=" CG  TRP A 442 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 442 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 442 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 442 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 442 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 442 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 442 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 442 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 442 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 474 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO A 475 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 475 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 475 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1985 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 189
        2.68 -     3.23: 12561
        3.23 -     3.79: 18320
        3.79 -     4.34: 24736
        4.34 -     4.90: 37678
  Nonbonded interactions: 93484
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 767 "
            pdb=" O   ASP A 786 "
     model   vdw
     2.119 3.120
  nonbonded pdb=" OG  SER A1234 "
            pdb=" OD1 ASP A1236 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OD2 ASP A 786 "
            pdb=" OG  SER A 789 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OH  TYR A 209 "
            pdb=" O   SER A1199 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" ND2 ASN A 409 "
            pdb=" O   GLU A 687 "
     model   vdw
     2.235 3.120
  ... (remaining 93479 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     30.360
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  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:3.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11753  Z= 0.136
  Angle     :  0.656   8.987  15942  Z= 0.361
  Chirality :  0.041   0.280   1866
  Planarity :  0.004   0.073   1988
  Dihedral  : 13.663  89.097   4250
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.41 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.22), residues: 1451
  helix:  0.20 (0.17), residues: 874
  sheet:  0.74 (0.53), residues: 86
  loop : -0.22 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 442 
 HIS   0.004   0.001   HIS A1496 
 PHE   0.014   0.001   PHE A 981 
 TYR   0.015   0.001   TYR A 319 
 ARG   0.006   0.000   ARG A1257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27538 (  664)
  hydrogen bonds       : angle       8.06349 ( 1941)
  SS BOND              : bond        0.00051 (    1)
  SS BOND              : angle       0.63809 (    2)
  covalent geometry    : bond        0.00270 (11752)
  covalent geometry    : angle       0.65610 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 1.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.9437 (tt) cc_final: 0.9093 (tp)
REVERT: A  140 ILE cc_start: 0.9445 (mt) cc_final: 0.9159 (tp)
REVERT: A  363 CYS cc_start: 0.8757 (m) cc_final: 0.7965 (t)
REVERT: A  446 LEU cc_start: 0.9388 (tp) cc_final: 0.9078 (tp)
REVERT: A  450 LEU cc_start: 0.9403 (tt) cc_final: 0.8876 (tp)
REVERT: A  559 VAL cc_start: 0.9589 (t) cc_final: 0.9122 (t)
REVERT: A  583 ILE cc_start: 0.9379 (pt) cc_final: 0.9174 (pt)
REVERT: A  603 MET cc_start: 0.8042 (tmm) cc_final: 0.7820 (tmm)
REVERT: A  685 LEU cc_start: 0.9159 (mt) cc_final: 0.8815 (tp)
REVERT: A  688 MET cc_start: 0.5618 (tpt) cc_final: 0.5384 (tpp)
REVERT: A  887 LEU cc_start: 0.6924 (mt) cc_final: 0.6140 (mt)
REVERT: A  905 ARG cc_start: 0.8855 (tpt170) cc_final: 0.8483 (tpt-90)
REVERT: A  906 GLU cc_start: 0.9136 (tp30) cc_final: 0.8768 (tm-30)
REVERT: A 1116 ILE cc_start: 0.9644 (mt) cc_final: 0.9435 (mt)
REVERT: A 1141 TYR cc_start: 0.8218 (t80) cc_final: 0.7968 (t80)
REVERT: A 1255 LEU cc_start: 0.9360 (tp) cc_final: 0.9109 (tp)
REVERT: A 1273 THR cc_start: 0.9549 (p) cc_final: 0.9124 (p)
REVERT: A 1314 ASP cc_start: 0.8851 (m-30) cc_final: 0.8572 (p0)
REVERT: A 1327 MET cc_start: 0.6781 (mmp) cc_final: 0.6469 (mmp)
REVERT: A 1351 LEU cc_start: 0.9217 (mt) cc_final: 0.8557 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.2181
  time to fit residues: 86.3570
Evaluate side-chains
  189 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   chunk 60 optimal weight:   20.0000
   chunk 37 optimal weight:    7.9990
   chunk 74 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   chunk 113 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 84 optimal weight:    6.9990
   chunk 131 optimal weight:    7.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN
A 128 ASN
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1179 GLN
** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.045120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.033440 restraints weight = 96851.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.034426 restraints weight = 67187.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.035156 restraints weight = 51755.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11753  Z= 0.209
  Angle     :  0.676  10.311  15942  Z= 0.362
  Chirality :  0.044   0.205   1866
  Planarity :  0.005   0.081   1988
  Dihedral  :  4.327  19.048   1553
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 16.22
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.83 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  5.02 %
    Favored  : 94.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.22), residues: 1451
  helix:  0.74 (0.17), residues: 903
  sheet:  0.38 (0.53), residues: 86
  loop : -0.35 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 136 
 HIS   0.006   0.001   HIS A1496 
 PHE   0.018   0.002   PHE A 135 
 TYR   0.013   0.002   TYR A 616 
 ARG   0.006   0.001   ARG A 393 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06116 (  664)
  hydrogen bonds       : angle       5.28447 ( 1941)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       0.53081 (    2)
  covalent geometry    : bond        0.00421 (11752)
  covalent geometry    : angle       0.67636 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 208
  time to evaluate  : 2.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.9336 (mm) cc_final: 0.9090 (mm)
REVERT: A   74 PHE cc_start: 0.9338 (m-10) cc_final: 0.9108 (m-80)
REVERT: A  145 PHE cc_start: 0.9248 (m-80) cc_final: 0.8987 (m-80)
REVERT: A  234 LYS cc_start: 0.9837 (tppp) cc_final: 0.9341 (mmmm)
REVERT: A  470 MET cc_start: 0.9583 (mmp) cc_final: 0.9197 (mmm)
REVERT: A  477 ASN cc_start: 0.9746 (m-40) cc_final: 0.9507 (m-40)
REVERT: A  583 ILE cc_start: 0.9834 (pt) cc_final: 0.9501 (pt)
REVERT: A  595 MET cc_start: 0.9614 (mmp) cc_final: 0.9345 (mmm)
REVERT: A  598 MET cc_start: 0.9255 (tmm) cc_final: 0.8911 (tmm)
REVERT: A  599 MET cc_start: 0.9516 (pmm) cc_final: 0.9252 (pmm)
REVERT: A  616 TYR cc_start: 0.9411 (t80) cc_final: 0.8885 (t80)
REVERT: A  617 LEU cc_start: 0.9801 (mt) cc_final: 0.9345 (tp)
REVERT: A  688 MET cc_start: 0.6580 (tpt) cc_final: 0.5700 (tpp)
REVERT: A  817 LEU cc_start: 0.9815 (tp) cc_final: 0.9457 (pp)
REVERT: A  905 ARG cc_start: 0.9244 (tpt170) cc_final: 0.8996 (tpt-90)
REVERT: A  906 GLU cc_start: 0.9542 (tp30) cc_final: 0.9160 (tm-30)
REVERT: A 1123 PHE cc_start: 0.9699 (t80) cc_final: 0.9252 (t80)
REVERT: A 1141 TYR cc_start: 0.9532 (t80) cc_final: 0.9145 (t80)
REVERT: A 1225 MET cc_start: 0.9664 (mpp) cc_final: 0.8967 (mtt)
REVERT: A 1246 LEU cc_start: 0.9760 (mm) cc_final: 0.9545 (mm)
REVERT: A 1249 THR cc_start: 0.9619 (p) cc_final: 0.9416 (p)
REVERT: A 1314 ASP cc_start: 0.9729 (m-30) cc_final: 0.9436 (t70)
REVERT: A 1351 LEU cc_start: 0.9437 (mt) cc_final: 0.8798 (tp)
  outliers start: 4
  outliers final: 0
  residues processed: 211
  average time/residue: 0.2900
  time to fit residues: 95.3537
Evaluate side-chains
  174 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 112 optimal weight:    0.9990
   chunk 111 optimal weight:    0.9980
   chunk 135 optimal weight:    0.1980
   chunk 0 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 82 optimal weight:   50.0000
   chunk 49 optimal weight:    2.9990
   chunk 143 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.046296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.034186 restraints weight = 94363.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.035239 restraints weight = 65325.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.036039 restraints weight = 50066.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  11753  Z= 0.142
  Angle     :  0.658  10.705  15942  Z= 0.335
  Chirality :  0.044   0.327   1866
  Planarity :  0.004   0.042   1988
  Dihedral  :  4.243  19.110   1553
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.27 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  5.10 %
    Favored  : 94.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.22), residues: 1451
  helix:  0.73 (0.17), residues: 900
  sheet:  0.33 (0.53), residues: 86
  loop : -0.35 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A1206 
 HIS   0.005   0.001   HIS A1496 
 PHE   0.026   0.002   PHE A 981 
 TYR   0.023   0.001   TYR A1275 
 ARG   0.005   0.000   ARG A1174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05310 (  664)
  hydrogen bonds       : angle       4.85111 ( 1941)
  SS BOND              : bond        0.00045 (    1)
  SS BOND              : angle       0.70083 (    2)
  covalent geometry    : bond        0.00288 (11752)
  covalent geometry    : angle       0.65817 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 215
  time to evaluate  : 1.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.9289 (mm) cc_final: 0.9018 (mm)
REVERT: A   74 PHE cc_start: 0.9264 (m-10) cc_final: 0.9006 (m-80)
REVERT: A  145 PHE cc_start: 0.9187 (m-80) cc_final: 0.8742 (m-80)
REVERT: A  181 PHE cc_start: 0.9245 (m-10) cc_final: 0.8997 (m-80)
REVERT: A  393 ARG cc_start: 0.9569 (ptt90) cc_final: 0.9298 (ttp80)
REVERT: A  397 MET cc_start: 0.9503 (mtm) cc_final: 0.8993 (mtm)
REVERT: A  440 MET cc_start: 0.9198 (mmp) cc_final: 0.8985 (mmm)
REVERT: A  450 LEU cc_start: 0.9876 (tt) cc_final: 0.9511 (tt)
REVERT: A  454 PHE cc_start: 0.9173 (m-80) cc_final: 0.8523 (m-80)
REVERT: A  470 MET cc_start: 0.9529 (mmp) cc_final: 0.9252 (mmm)
REVERT: A  477 ASN cc_start: 0.9750 (m-40) cc_final: 0.9519 (m-40)
REVERT: A  583 ILE cc_start: 0.9806 (pt) cc_final: 0.9455 (pt)
REVERT: A  598 MET cc_start: 0.9272 (tmm) cc_final: 0.8898 (tmm)
REVERT: A  616 TYR cc_start: 0.9359 (t80) cc_final: 0.8848 (t80)
REVERT: A  617 LEU cc_start: 0.9775 (mt) cc_final: 0.9408 (tp)
REVERT: A  688 MET cc_start: 0.6911 (tpt) cc_final: 0.6102 (tpp)
REVERT: A  817 LEU cc_start: 0.9803 (tp) cc_final: 0.9435 (pp)
REVERT: A  822 MET cc_start: 0.8645 (mtt) cc_final: 0.8012 (mtp)
REVERT: A  905 ARG cc_start: 0.9239 (tpt170) cc_final: 0.8937 (tpt-90)
REVERT: A  906 GLU cc_start: 0.9555 (tp30) cc_final: 0.9145 (tm-30)
REVERT: A 1060 LEU cc_start: 0.9633 (mp) cc_final: 0.9381 (mp)
REVERT: A 1123 PHE cc_start: 0.9725 (t80) cc_final: 0.9286 (t80)
REVERT: A 1141 TYR cc_start: 0.9577 (t80) cc_final: 0.9278 (t80)
REVERT: A 1193 ASN cc_start: 0.9606 (t0) cc_final: 0.9176 (t0)
REVERT: A 1225 MET cc_start: 0.9660 (mpp) cc_final: 0.8914 (mtp)
REVERT: A 1246 LEU cc_start: 0.9726 (mm) cc_final: 0.9517 (mm)
REVERT: A 1314 ASP cc_start: 0.9726 (m-30) cc_final: 0.9431 (t70)
REVERT: A 1351 LEU cc_start: 0.9356 (mt) cc_final: 0.8712 (tp)
  outliers start: 4
  outliers final: 2
  residues processed: 216
  average time/residue: 0.2175
  time to fit residues: 72.2377
Evaluate side-chains
  186 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 142 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 120 optimal weight:    5.9990
   chunk 127 optimal weight:    0.7980
   chunk 113 optimal weight:    8.9990
   chunk 93 optimal weight:    0.0670
   chunk 51 optimal weight:    0.9990
   chunk 135 optimal weight:   20.0000
   chunk 74 optimal weight:    5.9990
   chunk 92 optimal weight:    7.9990
   chunk 144 optimal weight:    6.9990
   overall best weight:    1.7522

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 GLN
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1034 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.045990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.033901 restraints weight = 95284.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.034963 restraints weight = 65561.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.035758 restraints weight = 50126.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11753  Z= 0.131
  Angle     :  0.623   6.948  15942  Z= 0.319
  Chirality :  0.043   0.219   1866
  Planarity :  0.004   0.038   1988
  Dihedral  :  4.158  18.170   1553
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.48 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.22), residues: 1451
  helix:  0.76 (0.17), residues: 911
  sheet:  0.40 (0.52), residues: 91
  loop : -0.45 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A1044 
 HIS   0.005   0.001   HIS A1496 
 PHE   0.018   0.001   PHE A 437 
 TYR   0.020   0.001   TYR A1275 
 ARG   0.007   0.001   ARG A1174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04568 (  664)
  hydrogen bonds       : angle       4.57249 ( 1941)
  SS BOND              : bond        0.00098 (    1)
  SS BOND              : angle       0.63663 (    2)
  covalent geometry    : bond        0.00273 (11752)
  covalent geometry    : angle       0.62265 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 1.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 LEU cc_start: 0.9459 (mp) cc_final: 0.9220 (mp)
REVERT: A   70 VAL cc_start: 0.9355 (p) cc_final: 0.8974 (m)
REVERT: A   74 PHE cc_start: 0.9307 (m-10) cc_final: 0.9011 (m-80)
REVERT: A  145 PHE cc_start: 0.9101 (m-80) cc_final: 0.8788 (m-80)
REVERT: A  181 PHE cc_start: 0.9218 (m-10) cc_final: 0.8951 (m-80)
REVERT: A  393 ARG cc_start: 0.9589 (ptt90) cc_final: 0.9322 (ttp80)
REVERT: A  397 MET cc_start: 0.9500 (mtm) cc_final: 0.9024 (mtm)
REVERT: A  432 MET cc_start: 0.9290 (mmm) cc_final: 0.9082 (tpt)
REVERT: A  440 MET cc_start: 0.9302 (mmp) cc_final: 0.9100 (mmm)
REVERT: A  470 MET cc_start: 0.9539 (mmp) cc_final: 0.9260 (mmm)
REVERT: A  598 MET cc_start: 0.9245 (tmm) cc_final: 0.8795 (tmm)
REVERT: A  616 TYR cc_start: 0.9382 (t80) cc_final: 0.8944 (t80)
REVERT: A  617 LEU cc_start: 0.9773 (mt) cc_final: 0.9405 (tp)
REVERT: A  688 MET cc_start: 0.6926 (tpt) cc_final: 0.5980 (tpp)
REVERT: A  817 LEU cc_start: 0.9790 (tp) cc_final: 0.9433 (pp)
REVERT: A  822 MET cc_start: 0.8842 (mtt) cc_final: 0.8228 (mtp)
REVERT: A  905 ARG cc_start: 0.9243 (tpt170) cc_final: 0.8896 (tpt-90)
REVERT: A  906 GLU cc_start: 0.9542 (tp30) cc_final: 0.9182 (tm-30)
REVERT: A 1060 LEU cc_start: 0.9676 (mp) cc_final: 0.9435 (mp)
REVERT: A 1123 PHE cc_start: 0.9771 (t80) cc_final: 0.9181 (t80)
REVERT: A 1141 TYR cc_start: 0.9579 (t80) cc_final: 0.9345 (t80)
REVERT: A 1193 ASN cc_start: 0.9601 (t0) cc_final: 0.9187 (t0)
REVERT: A 1225 MET cc_start: 0.9657 (mpp) cc_final: 0.9026 (ptp)
REVERT: A 1277 LYS cc_start: 0.9478 (ptpp) cc_final: 0.9233 (pttm)
REVERT: A 1314 ASP cc_start: 0.9731 (m-30) cc_final: 0.9435 (t70)
REVERT: A 1351 LEU cc_start: 0.9319 (mt) cc_final: 0.8652 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 209
  average time/residue: 0.2011
  time to fit residues: 64.1823
Evaluate side-chains
  169 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 117 optimal weight:    1.9990
   chunk 68 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 143 optimal weight:   10.0000
   chunk 83 optimal weight:   20.0000
   chunk 121 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 798 HIS
A1034 GLN
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.046268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.034139 restraints weight = 93097.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.035190 restraints weight = 64620.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.035975 restraints weight = 49640.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11753  Z= 0.121
  Angle     :  0.617   9.485  15942  Z= 0.309
  Chirality :  0.042   0.191   1866
  Planarity :  0.003   0.035   1988
  Dihedral  :  4.101  20.996   1553
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.27 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.22), residues: 1451
  helix:  0.84 (0.17), residues: 911
  sheet:  0.40 (0.57), residues: 81
  loop : -0.46 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A1044 
 HIS   0.005   0.001   HIS A1496 
 PHE   0.022   0.001   PHE A 586 
 TYR   0.017   0.001   TYR A1275 
 ARG   0.015   0.001   ARG A1174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04182 (  664)
  hydrogen bonds       : angle       4.33707 ( 1941)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.57754 (    2)
  covalent geometry    : bond        0.00252 (11752)
  covalent geometry    : angle       0.61699 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 VAL cc_start: 0.9301 (p) cc_final: 0.8944 (m)
REVERT: A   74 PHE cc_start: 0.9221 (m-10) cc_final: 0.9011 (m-80)
REVERT: A  145 PHE cc_start: 0.9104 (m-80) cc_final: 0.8765 (m-80)
REVERT: A  181 PHE cc_start: 0.9220 (m-10) cc_final: 0.8944 (m-80)
REVERT: A  393 ARG cc_start: 0.9606 (ptt90) cc_final: 0.9311 (ttp-110)
REVERT: A  397 MET cc_start: 0.9484 (mtm) cc_final: 0.9106 (mtm)
REVERT: A  470 MET cc_start: 0.9532 (mmp) cc_final: 0.9252 (mmm)
REVERT: A  583 ILE cc_start: 0.9822 (pt) cc_final: 0.9513 (pt)
REVERT: A  598 MET cc_start: 0.9224 (tmm) cc_final: 0.8726 (tmm)
REVERT: A  616 TYR cc_start: 0.9406 (t80) cc_final: 0.8995 (t80)
REVERT: A  617 LEU cc_start: 0.9766 (mt) cc_final: 0.9544 (mt)
REVERT: A  688 MET cc_start: 0.6749 (tpt) cc_final: 0.6033 (tpp)
REVERT: A  817 LEU cc_start: 0.9794 (tp) cc_final: 0.9435 (pp)
REVERT: A  822 MET cc_start: 0.8780 (mtt) cc_final: 0.8157 (mtp)
REVERT: A  905 ARG cc_start: 0.9207 (tpt170) cc_final: 0.8981 (tpt-90)
REVERT: A  906 GLU cc_start: 0.9557 (tp30) cc_final: 0.9156 (tm-30)
REVERT: A 1060 LEU cc_start: 0.9658 (mp) cc_final: 0.9414 (mp)
REVERT: A 1123 PHE cc_start: 0.9770 (t80) cc_final: 0.9221 (t80)
REVERT: A 1193 ASN cc_start: 0.9576 (t0) cc_final: 0.9165 (t0)
REVERT: A 1209 ILE cc_start: 0.9881 (tp) cc_final: 0.9613 (tp)
REVERT: A 1225 MET cc_start: 0.9635 (mpp) cc_final: 0.9037 (mtp)
REVERT: A 1277 LYS cc_start: 0.9460 (ptpp) cc_final: 0.9229 (pttm)
REVERT: A 1314 ASP cc_start: 0.9731 (m-30) cc_final: 0.9438 (t70)
REVERT: A 1351 LEU cc_start: 0.9294 (mt) cc_final: 0.8595 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.2190
  time to fit residues: 69.9657
Evaluate side-chains
  175 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 130 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 134 optimal weight:    0.0470
   chunk 114 optimal weight:   10.0000
   chunk 56 optimal weight:    9.9990
   chunk 137 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 82 optimal weight:   20.0000
   chunk 84 optimal weight:    3.9990
   chunk 115 optimal weight:    8.9990
   overall best weight:    4.0086

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1399 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.044873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.033105 restraints weight = 98138.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.034110 restraints weight = 68023.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.034865 restraints weight = 52355.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11753  Z= 0.176
  Angle     :  0.627   8.919  15942  Z= 0.327
  Chirality :  0.042   0.185   1866
  Planarity :  0.004   0.037   1988
  Dihedral  :  4.127  18.880   1553
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.10 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.73 %
    Favored  : 98.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.22), residues: 1451
  helix:  0.84 (0.17), residues: 921
  sheet:  0.21 (0.57), residues: 81
  loop : -0.39 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1044 
 HIS   0.005   0.001   HIS A1496 
 PHE   0.020   0.001   PHE A 586 
 TYR   0.021   0.001   TYR A1275 
 ARG   0.005   0.001   ARG A1174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04002 (  664)
  hydrogen bonds       : angle       4.47643 ( 1941)
  SS BOND              : bond        0.00102 (    1)
  SS BOND              : angle       0.54804 (    2)
  covalent geometry    : bond        0.00358 (11752)
  covalent geometry    : angle       0.62735 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 199
  time to evaluate  : 1.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 VAL cc_start: 0.9347 (p) cc_final: 0.8936 (m)
REVERT: A  145 PHE cc_start: 0.9186 (m-80) cc_final: 0.8814 (m-80)
REVERT: A  181 PHE cc_start: 0.9273 (m-10) cc_final: 0.9000 (m-80)
REVERT: A  393 ARG cc_start: 0.9651 (ptt90) cc_final: 0.9334 (ttp-110)
REVERT: A  397 MET cc_start: 0.9480 (mtm) cc_final: 0.9067 (mtm)
REVERT: A  432 MET cc_start: 0.9722 (mmm) cc_final: 0.9431 (mmm)
REVERT: A  470 MET cc_start: 0.9575 (mmp) cc_final: 0.9334 (mmm)
REVERT: A  583 ILE cc_start: 0.9837 (pt) cc_final: 0.9543 (pt)
REVERT: A  598 MET cc_start: 0.9225 (tmm) cc_final: 0.8716 (tmm)
REVERT: A  616 TYR cc_start: 0.9407 (t80) cc_final: 0.8897 (t80)
REVERT: A  817 LEU cc_start: 0.9789 (tp) cc_final: 0.9450 (pp)
REVERT: A  822 MET cc_start: 0.8878 (mtt) cc_final: 0.8240 (mtp)
REVERT: A  905 ARG cc_start: 0.9277 (tpt170) cc_final: 0.9024 (tpt-90)
REVERT: A  906 GLU cc_start: 0.9567 (tp30) cc_final: 0.9176 (tm-30)
REVERT: A 1193 ASN cc_start: 0.9528 (t0) cc_final: 0.9069 (t0)
REVERT: A 1209 ILE cc_start: 0.9817 (tp) cc_final: 0.9528 (tp)
REVERT: A 1225 MET cc_start: 0.9630 (mpp) cc_final: 0.9321 (mpp)
REVERT: A 1277 LYS cc_start: 0.9449 (ptpp) cc_final: 0.9214 (pttm)
REVERT: A 1314 ASP cc_start: 0.9724 (m-30) cc_final: 0.9440 (t70)
REVERT: A 1351 LEU cc_start: 0.9279 (mt) cc_final: 0.8608 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 200
  average time/residue: 0.2081
  time to fit residues: 62.4406
Evaluate side-chains
  162 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 37 optimal weight:    0.8980
   chunk 112 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 114 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 115 optimal weight:    8.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    4.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 128 ASN
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1399 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.044798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.033304 restraints weight = 99481.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.034317 restraints weight = 68680.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.035072 restraints weight = 52602.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11753  Z= 0.176
  Angle     :  0.643   9.533  15942  Z= 0.334
  Chirality :  0.043   0.178   1866
  Planarity :  0.004   0.061   1988
  Dihedral  :  4.236  19.807   1553
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.83 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.22), residues: 1451
  helix:  0.85 (0.17), residues: 922
  sheet:  0.01 (0.57), residues: 81
  loop : -0.53 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1044 
 HIS   0.005   0.001   HIS A1496 
 PHE   0.028   0.002   PHE A  74 
 TYR   0.021   0.002   TYR A1275 
 ARG   0.021   0.001   ARG A1289 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03891 (  664)
  hydrogen bonds       : angle       4.51510 ( 1941)
  SS BOND              : bond        0.00099 (    1)
  SS BOND              : angle       0.43750 (    2)
  covalent geometry    : bond        0.00358 (11752)
  covalent geometry    : angle       0.64314 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 VAL cc_start: 0.9305 (p) cc_final: 0.8965 (m)
REVERT: A   74 PHE cc_start: 0.9282 (m-80) cc_final: 0.8757 (m-80)
REVERT: A  136 TRP cc_start: 0.9628 (m100) cc_final: 0.9412 (m100)
REVERT: A  145 PHE cc_start: 0.9174 (m-80) cc_final: 0.8782 (m-80)
REVERT: A  181 PHE cc_start: 0.9245 (m-10) cc_final: 0.8954 (m-80)
REVERT: A  380 CYS cc_start: 0.9571 (t) cc_final: 0.9318 (p)
REVERT: A  393 ARG cc_start: 0.9674 (ptt90) cc_final: 0.9357 (ttp-110)
REVERT: A  397 MET cc_start: 0.9491 (mtm) cc_final: 0.9171 (mtm)
REVERT: A  432 MET cc_start: 0.9720 (mmm) cc_final: 0.9247 (mmm)
REVERT: A  438 MET cc_start: 0.8633 (mmt) cc_final: 0.8362 (mmt)
REVERT: A  470 MET cc_start: 0.9573 (mmp) cc_final: 0.9365 (mmm)
REVERT: A  583 ILE cc_start: 0.9849 (pt) cc_final: 0.9552 (pt)
REVERT: A  598 MET cc_start: 0.9187 (tmm) cc_final: 0.8691 (tmm)
REVERT: A  662 MET cc_start: 0.9617 (mmp) cc_final: 0.9341 (mmp)
REVERT: A  688 MET cc_start: 0.7531 (tpt) cc_final: 0.6470 (tpp)
REVERT: A  817 LEU cc_start: 0.9787 (tp) cc_final: 0.9442 (pp)
REVERT: A  822 MET cc_start: 0.8919 (mtt) cc_final: 0.8349 (mtp)
REVERT: A  905 ARG cc_start: 0.9274 (tpt170) cc_final: 0.9007 (tpt-90)
REVERT: A  906 GLU cc_start: 0.9574 (tp30) cc_final: 0.9153 (tm-30)
REVERT: A 1037 PHE cc_start: 0.9446 (m-10) cc_final: 0.9192 (m-10)
REVERT: A 1064 ILE cc_start: 0.8171 (pt) cc_final: 0.7893 (pt)
REVERT: A 1193 ASN cc_start: 0.9511 (t0) cc_final: 0.9024 (t0)
REVERT: A 1225 MET cc_start: 0.9609 (mpp) cc_final: 0.9292 (ptp)
REVERT: A 1277 LYS cc_start: 0.9445 (ptpp) cc_final: 0.9239 (pttm)
REVERT: A 1314 ASP cc_start: 0.9728 (m-30) cc_final: 0.9455 (t70)
REVERT: A 1351 LEU cc_start: 0.9218 (mt) cc_final: 0.8585 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.2090
  time to fit residues: 61.0865
Evaluate side-chains
  158 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 125 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   chunk 115 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 8 optimal weight:    0.6980
   chunk 116 optimal weight:    0.2980
   chunk 37 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 94 optimal weight:    5.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1063 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 = 0.3099 r_free = 0.3099 target = 0.045883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.034169 restraints weight = 95633.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.035199 restraints weight = 66508.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.035973 restraints weight = 51069.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11753  Z= 0.123
  Angle     :  0.643   7.862  15942  Z= 0.321
  Chirality :  0.043   0.179   1866
  Planarity :  0.004   0.046   1988
  Dihedral  :  4.169  18.005   1553
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.48 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.22), residues: 1451
  helix:  0.95 (0.17), residues: 918
  sheet:  0.10 (0.57), residues: 81
  loop : -0.52 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1044 
 HIS   0.005   0.001   HIS A1496 
 PHE   0.024   0.001   PHE A 586 
 TYR   0.018   0.001   TYR A  65 
 ARG   0.007   0.000   ARG A1174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 (  664)
  hydrogen bonds       : angle       4.32232 ( 1941)
  SS BOND              : bond        0.00104 (    1)
  SS BOND              : angle       0.41224 (    2)
  covalent geometry    : bond        0.00261 (11752)
  covalent geometry    : angle       0.64347 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 VAL cc_start: 0.9243 (p) cc_final: 0.8879 (m)
REVERT: A   74 PHE cc_start: 0.9190 (m-80) cc_final: 0.8780 (m-80)
REVERT: A  145 PHE cc_start: 0.9186 (m-80) cc_final: 0.8793 (m-80)
REVERT: A  181 PHE cc_start: 0.9217 (m-10) cc_final: 0.8901 (m-80)
REVERT: A  380 CYS cc_start: 0.9566 (t) cc_final: 0.9294 (p)
REVERT: A  393 ARG cc_start: 0.9629 (ptt90) cc_final: 0.9338 (ttp80)
REVERT: A  397 MET cc_start: 0.9505 (mtm) cc_final: 0.9176 (mtm)
REVERT: A  432 MET cc_start: 0.9718 (mmm) cc_final: 0.9386 (mmm)
REVERT: A  438 MET cc_start: 0.8628 (mmt) cc_final: 0.8347 (mmt)
REVERT: A  583 ILE cc_start: 0.9840 (pt) cc_final: 0.9568 (pt)
REVERT: A  598 MET cc_start: 0.9129 (tmm) cc_final: 0.8714 (tmm)
REVERT: A  616 TYR cc_start: 0.9440 (t80) cc_final: 0.9068 (t80)
REVERT: A  617 LEU cc_start: 0.9773 (mt) cc_final: 0.9505 (mt)
REVERT: A  662 MET cc_start: 0.9612 (mmp) cc_final: 0.9337 (mmp)
REVERT: A  688 MET cc_start: 0.7513 (tpt) cc_final: 0.6364 (tpp)
REVERT: A  817 LEU cc_start: 0.9781 (tp) cc_final: 0.9405 (pp)
REVERT: A  822 MET cc_start: 0.8864 (mtt) cc_final: 0.8319 (mtp)
REVERT: A  897 ASP cc_start: 0.8632 (m-30) cc_final: 0.8150 (m-30)
REVERT: A  905 ARG cc_start: 0.9273 (tpt170) cc_final: 0.9022 (tpt-90)
REVERT: A  906 GLU cc_start: 0.9569 (tp30) cc_final: 0.9148 (tm-30)
REVERT: A 1037 PHE cc_start: 0.9434 (m-10) cc_final: 0.9152 (m-10)
REVERT: A 1064 ILE cc_start: 0.8084 (pt) cc_final: 0.7770 (pt)
REVERT: A 1193 ASN cc_start: 0.9527 (t0) cc_final: 0.9080 (t0)
REVERT: A 1225 MET cc_start: 0.9610 (mpp) cc_final: 0.9277 (ptp)
REVERT: A 1254 TRP cc_start: 0.8293 (t-100) cc_final: 0.6805 (t-100)
REVERT: A 1258 MET cc_start: 0.8965 (mtp) cc_final: 0.8020 (mtp)
REVERT: A 1277 LYS cc_start: 0.9431 (ptpp) cc_final: 0.9211 (pttm)
REVERT: A 1314 ASP cc_start: 0.9734 (m-30) cc_final: 0.9460 (t70)
REVERT: A 1351 LEU cc_start: 0.9165 (mt) cc_final: 0.8505 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.2148
  time to fit residues: 65.8251
Evaluate side-chains
  167 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 116 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 120 optimal weight:    5.9990
   chunk 76 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 70 optimal weight:   30.0000
   chunk 105 optimal weight:    3.9990
   chunk 138 optimal weight:    0.0770
   chunk 7 optimal weight:    0.2980
   chunk 112 optimal weight:    1.9990
   overall best weight:    2.4744

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1063 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 = 0.3089 r_free = 0.3089 target = 0.045315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.033758 restraints weight = 97472.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.034795 restraints weight = 67218.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.035561 restraints weight = 51408.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11753  Z= 0.137
  Angle     :  0.644   8.606  15942  Z= 0.325
  Chirality :  0.043   0.186   1866
  Planarity :  0.004   0.076   1988
  Dihedral  :  4.148  17.368   1553
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.55 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.22), residues: 1451
  helix:  0.90 (0.17), residues: 917
  sheet:  0.08 (0.57), residues: 81
  loop : -0.46 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1044 
 HIS   0.004   0.001   HIS A1496 
 PHE   0.021   0.001   PHE A 586 
 TYR   0.027   0.001   TYR A1275 
 ARG   0.006   0.000   ARG A1174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03815 (  664)
  hydrogen bonds       : angle       4.39957 ( 1941)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.42916 (    2)
  covalent geometry    : bond        0.00290 (11752)
  covalent geometry    : angle       0.64364 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 VAL cc_start: 0.9241 (p) cc_final: 0.8796 (m)
REVERT: A   74 PHE cc_start: 0.9158 (m-80) cc_final: 0.8707 (m-80)
REVERT: A  145 PHE cc_start: 0.9196 (m-80) cc_final: 0.8811 (m-80)
REVERT: A  181 PHE cc_start: 0.9230 (m-10) cc_final: 0.8927 (m-80)
REVERT: A  380 CYS cc_start: 0.9579 (t) cc_final: 0.9321 (p)
REVERT: A  393 ARG cc_start: 0.9664 (ptt90) cc_final: 0.9342 (ttp-110)
REVERT: A  397 MET cc_start: 0.9545 (mtm) cc_final: 0.9248 (mtm)
REVERT: A  432 MET cc_start: 0.9709 (mmm) cc_final: 0.9232 (mmm)
REVERT: A  438 MET cc_start: 0.8710 (mmt) cc_final: 0.8454 (mmt)
REVERT: A  583 ILE cc_start: 0.9842 (pt) cc_final: 0.9563 (pt)
REVERT: A  586 PHE cc_start: 0.9803 (m-80) cc_final: 0.9602 (m-80)
REVERT: A  603 MET cc_start: 0.8806 (ppp) cc_final: 0.8593 (ppp)
REVERT: A  616 TYR cc_start: 0.9490 (t80) cc_final: 0.9077 (t80)
REVERT: A  617 LEU cc_start: 0.9792 (mt) cc_final: 0.9470 (mt)
REVERT: A  662 MET cc_start: 0.9668 (mmp) cc_final: 0.9422 (mmp)
REVERT: A  688 MET cc_start: 0.7692 (tpt) cc_final: 0.6475 (tpp)
REVERT: A  817 LEU cc_start: 0.9794 (tp) cc_final: 0.9422 (pp)
REVERT: A  822 MET cc_start: 0.8898 (mtt) cc_final: 0.8446 (mtp)
REVERT: A  906 GLU cc_start: 0.9547 (tp30) cc_final: 0.9128 (tm-30)
REVERT: A 1037 PHE cc_start: 0.9426 (m-10) cc_final: 0.9160 (m-10)
REVERT: A 1064 ILE cc_start: 0.8025 (pt) cc_final: 0.7712 (pt)
REVERT: A 1193 ASN cc_start: 0.9522 (t0) cc_final: 0.9048 (t0)
REVERT: A 1212 GLU cc_start: 0.9516 (mt-10) cc_final: 0.9312 (pt0)
REVERT: A 1225 MET cc_start: 0.9629 (mpp) cc_final: 0.9110 (mtp)
REVERT: A 1226 MET cc_start: 0.9620 (mpp) cc_final: 0.9391 (mpp)
REVERT: A 1258 MET cc_start: 0.8971 (mtp) cc_final: 0.8573 (mtp)
REVERT: A 1277 LYS cc_start: 0.9418 (ptpp) cc_final: 0.9202 (pttm)
REVERT: A 1314 ASP cc_start: 0.9763 (m-30) cc_final: 0.9512 (t70)
REVERT: A 1351 LEU cc_start: 0.9114 (mt) cc_final: 0.8549 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1934
  time to fit residues: 57.9249
Evaluate side-chains
  167 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 141 optimal weight:    5.9990
   chunk 126 optimal weight:    0.7980
   chunk 110 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 120 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 140 optimal weight:    5.9990
   chunk 18 optimal weight:    0.3980
   chunk 40 optimal weight:    6.9990
   chunk 71 optimal weight:   30.0000
   overall best weight:    2.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1063 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 = 0.3087 r_free = 0.3087 target = 0.045279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.033747 restraints weight = 97501.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.034777 restraints weight = 67350.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.035545 restraints weight = 51582.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11753  Z= 0.135
  Angle     :  0.672  15.192  15942  Z= 0.334
  Chirality :  0.044   0.279   1866
  Planarity :  0.004   0.034   1988
  Dihedral  :  4.135  20.871   1553
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.55 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.22), residues: 1451
  helix:  0.89 (0.17), residues: 917
  sheet:  0.07 (0.58), residues: 81
  loop : -0.46 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1044 
 HIS   0.005   0.001   HIS A1496 
 PHE   0.021   0.001   PHE A 586 
 TYR   0.026   0.001   TYR A1275 
 ARG   0.006   0.001   ARG A1289 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 (  664)
  hydrogen bonds       : angle       4.38355 ( 1941)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.41454 (    2)
  covalent geometry    : bond        0.00285 (11752)
  covalent geometry    : angle       0.67184 (15940)

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

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

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2902 Ramachandran restraints generated.
    1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 VAL cc_start: 0.9229 (p) cc_final: 0.8765 (m)
REVERT: A   74 PHE cc_start: 0.9169 (m-80) cc_final: 0.8704 (m-80)
REVERT: A  145 PHE cc_start: 0.9211 (m-80) cc_final: 0.8819 (m-80)
REVERT: A  181 PHE cc_start: 0.9240 (m-10) cc_final: 0.8920 (m-80)
REVERT: A  380 CYS cc_start: 0.9579 (t) cc_final: 0.9331 (p)
REVERT: A  393 ARG cc_start: 0.9668 (ptt90) cc_final: 0.9343 (ttp-110)
REVERT: A  397 MET cc_start: 0.9545 (mtm) cc_final: 0.9248 (mtm)
REVERT: A  432 MET cc_start: 0.9706 (mmm) cc_final: 0.9206 (mmm)
REVERT: A  438 MET cc_start: 0.8709 (mmt) cc_final: 0.8466 (mmt)
REVERT: A  470 MET cc_start: 0.9554 (mmp) cc_final: 0.9339 (mmm)
REVERT: A  583 ILE cc_start: 0.9839 (pt) cc_final: 0.9552 (pt)
REVERT: A  586 PHE cc_start: 0.9798 (m-80) cc_final: 0.9592 (m-80)
REVERT: A  603 MET cc_start: 0.8841 (ppp) cc_final: 0.8632 (ppp)
REVERT: A  616 TYR cc_start: 0.9498 (t80) cc_final: 0.9085 (t80)
REVERT: A  617 LEU cc_start: 0.9790 (mt) cc_final: 0.9475 (mt)
REVERT: A  662 MET cc_start: 0.9661 (mmp) cc_final: 0.9424 (mmp)
REVERT: A  688 MET cc_start: 0.7794 (tpt) cc_final: 0.6582 (tpp)
REVERT: A  817 LEU cc_start: 0.9796 (tp) cc_final: 0.9423 (pp)
REVERT: A  822 MET cc_start: 0.8962 (mtt) cc_final: 0.8517 (mtp)
REVERT: A  906 GLU cc_start: 0.9565 (tp30) cc_final: 0.9161 (tm-30)
REVERT: A 1037 PHE cc_start: 0.9421 (m-10) cc_final: 0.9156 (m-10)
REVERT: A 1064 ILE cc_start: 0.8014 (pt) cc_final: 0.7697 (pt)
REVERT: A 1193 ASN cc_start: 0.9513 (t0) cc_final: 0.9019 (t0)
REVERT: A 1212 GLU cc_start: 0.9582 (mt-10) cc_final: 0.9358 (pt0)
REVERT: A 1225 MET cc_start: 0.9618 (mpp) cc_final: 0.9078 (mtp)
REVERT: A 1226 MET cc_start: 0.9633 (mpp) cc_final: 0.9401 (mpp)
REVERT: A 1258 MET cc_start: 0.8961 (mtp) cc_final: 0.8742 (mtp)
REVERT: A 1277 LYS cc_start: 0.9445 (ptpp) cc_final: 0.9226 (pttm)
REVERT: A 1314 ASP cc_start: 0.9771 (m-30) cc_final: 0.9518 (t70)
REVERT: A 1351 LEU cc_start: 0.9085 (mt) cc_final: 0.8531 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2062
  time to fit residues: 62.5719
Evaluate side-chains
  163 residues out of total 1291 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 84 optimal weight:   30.0000
   chunk 15 optimal weight:    0.0010
   chunk 126 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 115 optimal weight:    0.7980
   chunk 22 optimal weight:    0.0870
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 114 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.5364

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

Flipped N/Q/H residues before XYZ refinement:
A 820 HIS
A 865 HIS
** A1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1063 ASN
** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.046817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.034590 restraints weight = 93273.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.035650 restraints weight = 65109.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.036457 restraints weight = 50135.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.4530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  11753  Z= 0.119
  Angle     :  0.677  11.481  15942  Z= 0.329
  Chirality :  0.044   0.187   1866
  Planarity :  0.004   0.034   1988
  Dihedral  :  4.068  20.417   1553
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.34 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.22), residues: 1451
  helix:  0.84 (0.17), residues: 924
  sheet:  0.20 (0.58), residues: 81
  loop : -0.52 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A1044 
 HIS   0.004   0.001   HIS A1496 
 PHE   0.021   0.001   PHE A 586 
 TYR   0.025   0.001   TYR A1275 
 ARG   0.017   0.001   ARG A1174 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03678 (  664)
  hydrogen bonds       : angle       4.20490 ( 1941)
  SS BOND              : bond        0.00173 (    1)
  SS BOND              : angle       0.36878 (    2)
  covalent geometry    : bond        0.00246 (11752)
  covalent geometry    : angle       0.67701 (15940)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4049.88 seconds
wall clock time: 72 minutes 21.70 seconds (4341.70 seconds total)