Starting phenix.real_space_refine
on Wed Jun 11 21:29:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yov_33988/06_2025/7yov_33988.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yov_33988/06_2025/7yov_33988.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.25
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yov_33988/06_2025/7yov_33988.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yov_33988/06_2025/7yov_33988.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yov_33988/06_2025/7yov_33988.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yov_33988/06_2025/7yov_33988.cif"
  }
  resolution = 3.25
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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      82      5.16       5
     C    8368      2.51       5
     N    2307      2.21       5
     O    2475      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13232
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 577
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 76, 572
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
      Conformer: "B"
        Number of residues, atoms: 76, 572
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          bond proxies already assigned to first conformer: 570
    Chain: "C"
      Number of atoms: 537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 537
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 2, 'TRANS': 68}
    Chain: "E"
      Number of atoms: 1186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 158, 1186
          Classifications: {'peptide': 158}
          Link IDs: {'PTRANS': 12, 'TRANS': 145}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 516
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 516
          Classifications: {'peptide': 68}
          Link IDs: {'PTRANS': 2, 'TRANS': 65}
    Chain: "A"
      Number of atoms: 10416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1310, 10416
          Classifications: {'peptide': 1310}
          Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1252}
          Chain breaks: 7
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AALA D 301 " occ=0.50
      ... (8 atoms not shown)
      pdb=" CB BALA D 301 " occ=0.50
  Time building chain proxies: 9.08, per 1000 atoms: 0.69
  Number of scatterers: 13232
  At special positions: 0
  Unit cell: (106.08, 159.12, 109.2, 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      82     16.00
     O    2475      8.00
     N    2307      7.00
     C    8368      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1112 " - pdb=" SG  CYS A1350 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1157 " - pdb=" SG  CYS A1160 " 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: 4.06
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3228

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 6 sheets defined
      57.2% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.56
  Creating SS restraints...
    Processing helix  chain 'D' and resid 238 through 280
      removed outlier: 4.277A  pdb=" N   ASP D 250 " --> pdb=" O   ASP D 246 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   LEU D 251 " --> pdb=" O   TYR D 247 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   VAL D 252 " --> pdb=" O   GLN D 248 " (cutoff:3.500A)
      Proline residue:  D 260  - end of helix
      removed outlier: 3.574A  pdb=" N   THR D 271 " --> pdb=" O   GLN D 267 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 296 through 303
    Processing helix  chain 'C' and resid 237 through 285
      removed outlier: 3.984A  pdb=" N   THR C 256 " --> pdb=" O   VAL C 252 " (cutoff:3.500A)
      Proline residue:  C 260  - end of helix
      removed outlier: 4.227A  pdb=" N   VAL C 275 " --> pdb=" O   THR C 271 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   MET C 276 " --> pdb=" O   SER C 272 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ILE C 285 " --> pdb=" O   GLY C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 304
    Processing helix  chain 'E' and resid 237 through 278
      removed outlier: 3.994A  pdb=" N   SER E 243 " --> pdb=" O   SER E 239 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR E 256 " --> pdb=" O   VAL E 252 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER E 257 " --> pdb=" O   LEU E 253 " (cutoff:3.500A)
      Proline residue:  E 260  - end of helix
      removed outlier: 3.867A  pdb=" N   SER E 264 " --> pdb=" O   PRO E 260 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL E 275 " --> pdb=" O   THR E 271 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   MET E 276 " --> pdb=" O   SER E 272 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 296 through 302
    Processing helix  chain 'E' and resid 316 through 320
      removed outlier: 3.581A  pdb=" N   VAL E 320 " --> pdb=" O   SER E 317 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 337 through 341
      removed outlier: 3.534A  pdb=" N   ASP E 340 " --> pdb=" O   HIS E 337 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU E 341 " --> pdb=" O   PRO E 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 337 through 341'
    Processing helix  chain 'E' and resid 352 through 366
    Processing helix  chain 'E' and resid 369 through 382
      removed outlier: 3.602A  pdb=" N   LEU E 380 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASP E 381 " --> pdb=" O   LEU E 377 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER E 382 " --> pdb=" O   SER E 378 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 388 through 397
      removed outlier: 3.522A  pdb=" N   ILE E 392 " --> pdb=" O   GLU E 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 274
      removed outlier: 3.921A  pdb=" N   ILE B 245 " --> pdb=" O   ARG B 241 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   THR B 256 " --> pdb=" O   VAL B 252 " (cutoff:3.500A)
      removed outlier: 4.762A  pdb=" N   SER B 257 " --> pdb=" O   LEU B 253 " (cutoff:3.500A)
      Proline residue:  B 260  - end of helix
      removed outlier: 3.593A  pdb=" N   VAL B 273 " --> pdb=" O   LEU B 269 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA B 274 " --> pdb=" O   LYS B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 279
    Processing helix  chain 'B' and resid 295 through 300
    Processing helix  chain 'A' and resid 8 through 12
    Processing helix  chain 'A' and resid 25 through 36
      removed outlier: 3.916A  pdb=" N   LEU A  29 " --> pdb=" O   VAL A  25 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   THR A  36 " --> pdb=" O   TYR A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 45
      removed outlier: 3.724A  pdb=" N   ASP A  45 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 59
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.855A  pdb=" N   ARG A  68 " --> pdb=" O   PRO A  64 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   MET A  69 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   HIS A  77 " --> pdb=" O   GLY A  73 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN A  78 " --> pdb=" O   ARG A  74 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   THR A  79 " --> pdb=" O   SER A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 100
      removed outlier: 3.672A  pdb=" N   GLY A 100 " --> pdb=" O   GLU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 141
      removed outlier: 4.120A  pdb=" N   ILE A 113 " --> pdb=" O   LYS A 109 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A 116 " --> pdb=" O   ARG A 112 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   GLU A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      Proline residue:  A 127  - end of helix
      removed outlier: 3.531A  pdb=" N   CYS A 132 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLU A 136 " --> pdb=" O   CYS A 132 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LYS A 137 " --> pdb=" O   SER A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 160
    Processing helix  chain 'A' and resid 169 through 192
      removed outlier: 3.717A  pdb=" N   ALA A 175 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   THR A 192 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 254
      removed outlier: 3.709A  pdb=" N   VAL A 234 " --> pdb=" O   SER A 230 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LEU A 235 " --> pdb=" O   GLN A 231 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLU A 242 " --> pdb=" O   ALA A 238 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   SER A 252 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 274
      removed outlier: 3.728A  pdb=" N   ALA A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLU A 262 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   LYS A 263 " --> pdb=" O   CYS A 259 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 279
    Processing helix  chain 'A' and resid 281 through 288
      removed outlier: 3.907A  pdb=" N   VAL A 285 " --> pdb=" O   GLN A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 299
      removed outlier: 3.518A  pdb=" N   PHE A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ALA A 293 " --> pdb=" O   MET A 289 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL A 297 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 323
      removed outlier: 3.557A  pdb=" N   SER A 312 " --> pdb=" O   GLY A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 342
    Processing helix  chain 'A' and resid 347 through 352
    Processing helix  chain 'A' and resid 353 through 356
      removed outlier: 3.518A  pdb=" N   LEU A 356 " --> pdb=" O   MET A 353 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 353 through 356'
    Processing helix  chain 'A' and resid 366 through 379
      removed outlier: 4.059A  pdb=" N   ALA A 373 " --> pdb=" O   ALA A 369 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   GLN A 377 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 408
      removed outlier: 3.619A  pdb=" N   GLN A 391 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE A 395 " --> pdb=" O   GLN A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 432
    Processing helix  chain 'A' and resid 436 through 443
    Processing helix  chain 'A' and resid 443 through 448
    Processing helix  chain 'A' and resid 479 through 484
      removed outlier: 3.522A  pdb=" N   PHE A 484 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 490 through 495
      removed outlier: 3.581A  pdb=" N   LYS A 495 " --> pdb=" O   GLU A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 512
      removed outlier: 3.704A  pdb=" N   PHE A 510 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 511 " --> pdb=" O   LEU A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 523
      removed outlier: 3.714A  pdb=" N   GLU A 523 " --> pdb=" O   TYR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 575
    Processing helix  chain 'A' and resid 576 through 581
    Processing helix  chain 'A' and resid 593 through 598
    Processing helix  chain 'A' and resid 599 through 603
      removed outlier: 3.869A  pdb=" N   SER A 603 " --> pdb=" O   SER A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 650 through 663
      removed outlier: 5.374A  pdb=" N   LEU A 656 " --> pdb=" O   GLN A 652 " (cutoff:3.500A)
      removed outlier: 4.809A  pdb=" N   PHE A 657 " --> pdb=" O   THR A 653 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ILE A 661 " --> pdb=" O   PHE A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 681
      removed outlier: 3.804A  pdb=" N   LEU A 676 " --> pdb=" O   GLU A 672 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ASP A 680 " --> pdb=" O   LEU A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 699 through 703
    Processing helix  chain 'A' and resid 721 through 740
      removed outlier: 3.714A  pdb=" N   TRP A 725 " --> pdb=" O   CYS A 721 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER A 740 " --> pdb=" O   ALA A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 791
      removed outlier: 3.832A  pdb=" N   HIS A 775 " --> pdb=" O   LEU A 771 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 823 through 830
      removed outlier: 3.746A  pdb=" N   ASN A 827 " --> pdb=" O   GLN A 823 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER A 829 " --> pdb=" O   LEU A 825 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LYS A 830 " --> pdb=" O   LYS A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 859
      removed outlier: 3.708A  pdb=" N   SER A 845 " --> pdb=" O   ASN A 841 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ILE A 849 " --> pdb=" O   SER A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 883
      removed outlier: 3.604A  pdb=" N   TYR A 868 " --> pdb=" O   ASP A 864 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   SER A 882 " --> pdb=" O   THR A 878 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLU A 883 " --> pdb=" O   TYR A 879 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 898
      removed outlier: 4.004A  pdb=" N   SER A 897 " --> pdb=" O   SER A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 901 through 909
    Processing helix  chain 'A' and resid 933 through 948
      removed outlier: 3.757A  pdb=" N   THR A 937 " --> pdb=" O   ASP A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 952 through 961
      removed outlier: 4.096A  pdb=" N   MET A 956 " --> pdb=" O   GLY A 952 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   THR A 957 " --> pdb=" O   PRO A 953 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 975
    Processing helix  chain 'A' and resid 986 through 1000
      removed outlier: 3.530A  pdb=" N   PHE A1000 " --> pdb=" O   GLN A 996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1029
      removed outlier: 3.763A  pdb=" N   GLU A1020 " --> pdb=" O   ASN A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1045
      removed outlier: 3.672A  pdb=" N   ALA A1038 " --> pdb=" O   HIS A1034 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1055
    Processing helix  chain 'A' and resid 1060 through 1070
      removed outlier: 3.840A  pdb=" N   ILE A1066 " --> pdb=" O   THR A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1075 through 1083
    Processing helix  chain 'A' and resid 1083 through 1096
    Processing helix  chain 'A' and resid 1112 through 1125
      removed outlier: 3.718A  pdb=" N   LEU A1116 " --> pdb=" O   CYS A1112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1130
    Processing helix  chain 'A' and resid 1141 through 1146
      removed outlier: 3.820A  pdb=" N   VAL A1146 " --> pdb=" O   THR A1142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1212 through 1230
    Processing helix  chain 'A' and resid 1232 through 1245
      removed outlier: 3.575A  pdb=" N   ALA A1238 " --> pdb=" O   ILE A1234 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS A1241 " --> pdb=" O   THR A1237 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER A1245 " --> pdb=" O   LYS A1241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1258
      removed outlier: 4.098A  pdb=" N   LEU A1256 " --> pdb=" O   GLU A1252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1287 through 1291
      removed outlier: 4.161A  pdb=" N   VAL A1291 " --> pdb=" O   SER A1288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1311 through 1328
      removed outlier: 3.704A  pdb=" N   LEU A1318 " --> pdb=" O   GLN A1314 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU A1325 " --> pdb=" O   LEU A1321 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   PHE A1328 " --> pdb=" O   ILE A1324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 309 through 310
      removed outlier: 3.502A  pdb=" N   VAL A 384 " --> pdb=" O   ILE B 285 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS A 382 " --> pdb=" O   ASP B 287 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 204
      removed outlier: 3.648A  pdb=" N   GLN A 208 " --> pdb=" O   THR A 219 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 556
    Processing sheet with id=AA4, first strand: chain 'A' and resid 743 through 744
      removed outlier: 4.367A  pdb=" N   ARG A 743 " --> pdb=" O   THR A 758 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 807 through 810
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1292 through 1294

    614 hydrogen bonds defined for protein.
    1765 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: 3.99

  Time building geometry restraints manager: 5.04 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3968
        1.33 -     1.45: 2289
        1.45 -     1.57: 7089
        1.57 -     1.69: 0
        1.69 -     1.81: 134
  Bond restraints: 13480
  Sorted by residual:
  bond pdb=" C   ILE E 259 "
       pdb=" N   PRO E 260 "
    ideal  model  delta    sigma   weight residual
    1.336  1.394 -0.058 1.25e-02 6.40e+03 2.17e+01
  bond pdb=" C   ALA A 474 "
       pdb=" N   HIS A 475 "
    ideal  model  delta    sigma   weight residual
    1.330  1.278  0.052 1.47e-02 4.63e+03 1.23e+01
  bond pdb=" CB  VAL A 748 "
       pdb=" CG1 VAL A 748 "
    ideal  model  delta    sigma   weight residual
    1.521  1.420  0.101 3.30e-02 9.18e+02 9.43e+00
  bond pdb=" CG  LEU A 647 "
       pdb=" CD1 LEU A 647 "
    ideal  model  delta    sigma   weight residual
    1.521  1.429  0.092 3.30e-02 9.18e+02 7.77e+00
  bond pdb=" CB  MET D 276 "
       pdb=" CG  MET D 276 "
    ideal  model  delta    sigma   weight residual
    1.520  1.440  0.080 3.00e-02 1.11e+03 7.12e+00
  ... (remaining 13475 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.50: 17908
        3.50 -     6.99: 300
        6.99 -    10.49: 35
       10.49 -    13.99: 4
       13.99 -    17.48: 3
  Bond angle restraints: 18250
  Sorted by residual:
  angle pdb=" CA  LEU A1008 "
        pdb=" CB  LEU A1008 "
        pdb=" CG  LEU A1008 "
      ideal   model   delta    sigma   weight residual
     116.30  133.78  -17.48 3.50e+00 8.16e-02 2.50e+01
  angle pdb=" C   GLY E 314 "
        pdb=" N   ASP E 315 "
        pdb=" CA  ASP E 315 "
      ideal   model   delta    sigma   weight residual
     121.61  128.48   -6.87 1.39e+00 5.18e-01 2.44e+01
  angle pdb=" C   ASP A 706 "
        pdb=" N   ASP A 707 "
        pdb=" CA  ASP A 707 "
      ideal   model   delta    sigma   weight residual
     121.54  130.91   -9.37 1.91e+00 2.74e-01 2.40e+01
  angle pdb=" C   PHE A 580 "
        pdb=" N   GLN A 581 "
        pdb=" CA  GLN A 581 "
      ideal   model   delta    sigma   weight residual
     121.54  130.27   -8.73 1.91e+00 2.74e-01 2.09e+01
  angle pdb=" CA  LEU E 286 "
        pdb=" CB  LEU E 286 "
        pdb=" CG  LEU E 286 "
      ideal   model   delta    sigma   weight residual
     116.30  131.51  -15.21 3.50e+00 8.16e-02 1.89e+01
  ... (remaining 18245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.42: 7701
       15.42 -    30.83: 449
       30.83 -    46.24: 103
       46.24 -    61.66: 13
       61.66 -    77.07: 14
  Dihedral angle restraints: 8280
    sinusoidal: 3335
      harmonic: 4945
  Sorted by residual:
  dihedral pdb=" CB  CYS A1157 "
           pdb=" SG  CYS A1157 "
           pdb=" SG  CYS A1160 "
           pdb=" CB  CYS A1160 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.59  -64.59     1      1.00e+01 1.00e-02 5.48e+01
  dihedral pdb=" CA  SER A1283 "
           pdb=" C   SER A1283 "
           pdb=" N   LEU A1284 "
           pdb=" CA  LEU A1284 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.13   26.87     0      5.00e+00 4.00e-02 2.89e+01
  dihedral pdb=" CA  ASN A 795 "
           pdb=" C   ASN A 795 "
           pdb=" N   LEU A 796 "
           pdb=" CA  LEU A 796 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.01   25.99     0      5.00e+00 4.00e-02 2.70e+01
  ... (remaining 8277 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1611
       0.068 -    0.137: 437
       0.137 -    0.205: 58
       0.205 -    0.273: 10
       0.273 -    0.342: 2
  Chirality restraints: 2118
  Sorted by residual:
  chirality pdb=" CB  VAL A 234 "
            pdb=" CA  VAL A 234 "
            pdb=" CG1 VAL A 234 "
            pdb=" CG2 VAL A 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.92e+00
  chirality pdb=" CB  ILE A 674 "
            pdb=" CA  ILE A 674 "
            pdb=" CG1 ILE A 674 "
            pdb=" CG2 ILE A 674 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CB  ILE D 238 "
            pdb=" CA  ILE D 238 "
            pdb=" CG1 ILE D 238 "
            pdb=" CG2 ILE D 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.92   -0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 2115 not shown)

  Planarity restraints: 2323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 395 "   -0.024 2.00e-02 2.50e+03   2.80e-02 1.38e+01
        pdb=" CG  PHE A 395 "    0.061 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 395 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 395 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 395 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 395 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 395 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  33 "    0.017 2.00e-02 2.50e+03   2.22e-02 1.23e+01
        pdb=" CG  TRP A  33 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  33 "    0.036 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  33 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  33 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  33 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  33 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  33 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  33 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  33 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 412 "    0.019 2.00e-02 2.50e+03   1.98e-02 9.76e+00
        pdb=" CG  TRP A 412 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 412 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 412 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 412 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 412 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 412 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 412 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 412 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 412 "    0.001 2.00e-02 2.50e+03
  ... (remaining 2320 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 240
        2.66 -     3.22: 12386
        3.22 -     3.78: 20834
        3.78 -     4.34: 28551
        4.34 -     4.90: 47088
  Nonbonded interactions: 109099
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN E 255 "
            pdb=" OD1 ASP B 250 "
     model   vdw
     2.102 3.120
  nonbonded pdb=" NH1 ARG E 263 "
            pdb=" OG1 THR B 261 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" OG  SER A 167 "
            pdb=" OD1 ASP A 245 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   GLU A 840 "
            pdb=" OG  SER A1085 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   ASP A1094 "
            pdb=" OG  SER A1099 "
     model   vdw
     2.279 3.040
  ... (remaining 109094 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 236 through 300)
  selection = (chain 'C' and resid 236 through 300)
  selection = (chain 'D' and resid 236 through 300)
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.630
  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:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     35.180
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
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      :  0.011   0.103  13482  Z= 0.459
  Angle     :  1.167  17.484  18254  Z= 0.615
  Chirality :  0.063   0.342   2118
  Planarity :  0.009   0.077   2323
  Dihedral  : 11.203  77.075   5046
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  3.28 %
    Favored  : 95.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.95 (0.16), residues: 1660
  helix: -2.73 (0.12), residues: 884
  sheet: -0.72 (0.64), residues: 71
  loop : -2.53 (0.21), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.005   TRP A  33 
 HIS   0.015   0.003   HIS A 475 
 PHE   0.061   0.005   PHE A 395 
 TYR   0.038   0.004   TYR A 908 
 ARG   0.015   0.002   ARG A 562 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15613 (  614)
  hydrogen bonds       : angle       6.75375 ( 1765)
  SS BOND              : bond        0.00490 (    2)
  SS BOND              : angle       2.14373 (    4)
  covalent geometry    : bond        0.01113 (13480)
  covalent geometry    : angle       1.16708 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  373 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 356
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  354 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7725 (mt)
REVERT: B  234 MET cc_start: 0.3778 (pmm) cc_final: 0.2844 (tpp)
REVERT: B  235 MET cc_start: 0.6910 (ppp) cc_final: 0.6531 (ttm)
REVERT: A  569 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6689 (mm-30)
REVERT: A 1216 LYS cc_start: 0.8173 (mttp) cc_final: 0.7717 (mtmm)
  outliers start: 17
  outliers final: 4
  residues processed: 369
  average time/residue: 0.3284
  time to fit residues: 162.5844
Evaluate side-chains
  205 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 200
  time to evaluate  : 1.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  354 ILE
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  824 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 140 optimal weight:    0.6980
   chunk 125 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 84 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 130 optimal weight:    2.9990
   chunk 50 optimal weight:    0.4980
   chunk 79 optimal weight:    0.9980
   chunk 96 optimal weight:    0.6980
   chunk 150 optimal weight:   10.0000
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
C 248 GLN
E 279 ASN
E 369 HIS
** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  27 HIS
A 222 ASN
A 316 GLN
A 328 GLN
A 565 GLN
A 575 GLN
A 648 ASN
A 662 ASN
A 749 GLN
A 775 HIS
A 827 ASN
A 870 ASN
A 896 GLN
A 906 HIS
A 914 GLN
A1088 HIS
A1375 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.169993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.136683 restraints weight = 36688.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 4.94
r_work: 0.3463 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3467
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3467 r_free = 0.3467    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3467
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13482  Z= 0.143
  Angle     :  0.646  10.272  18254  Z= 0.332
  Chirality :  0.043   0.248   2118
  Planarity :  0.005   0.058   2323
  Dihedral  :  5.751  49.274   1817
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.11 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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: -2.19 (0.19), residues: 1660
  helix: -0.99 (0.16), residues: 879
  sheet: -0.73 (0.60), residues: 73
  loop : -2.04 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 176 
 HIS   0.006   0.001   HIS A 178 
 PHE   0.017   0.001   PHE A 163 
 TYR   0.021   0.002   TYR E 247 
 ARG   0.005   0.001   ARG A 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04544 (  614)
  hydrogen bonds       : angle       4.71878 ( 1765)
  SS BOND              : bond        0.00429 (    2)
  SS BOND              : angle       2.24811 (    4)
  covalent geometry    : bond        0.00316 (13480)
  covalent geometry    : angle       0.64564 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 234
  time to evaluate  : 1.668 
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: C  276 MET cc_start: 0.7525 (mmt) cc_final: 0.7007 (mmt)
REVERT: E  283 MET cc_start: 0.8187 (mmt) cc_final: 0.7918 (mmt)
REVERT: E  354 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8520 (mt)
REVERT: B  234 MET cc_start: 0.3656 (pmm) cc_final: 0.2254 (tpp)
REVERT: B  235 MET cc_start: 0.7607 (ppp) cc_final: 0.7397 (ttt)
REVERT: A   57 LYS cc_start: 0.8539 (tttp) cc_final: 0.8319 (tptt)
REVERT: A   62 SER cc_start: 0.7513 (m) cc_final: 0.7254 (p)
REVERT: A  136 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7963 (mt-10)
REVERT: A  861 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8441 (mm)
  outliers start: 33
  outliers final: 14
  residues processed: 262
  average time/residue: 0.2990
  time to fit residues: 109.0898
Evaluate side-chains
  209 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 192
  time to evaluate  : 1.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain E residue  354 ILE
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  861 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue 1321 LEU
Chi-restraints excluded: chain A residue 1346 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 141 optimal weight:    0.0870
   chunk 73 optimal weight:    2.9990
   chunk 134 optimal weight:    1.9990
   chunk 94 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0270
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.3618

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

Flipped N/Q/H residues before XYZ refinement:
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 267 GLN
** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 328 GLN
A 652 GLN
** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1185 ASN
A1315 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.171285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.133049 restraints weight = 36897.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 3.23
r_work: 0.3553 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3556
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3556 r_free = 0.3556    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3556
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050  13482  Z= 0.117
  Angle     :  0.588  10.926  18254  Z= 0.295
  Chirality :  0.041   0.203   2118
  Planarity :  0.004   0.044   2323
  Dihedral  :  4.966  34.795   1816
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.59 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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: -1.37 (0.20), residues: 1660
  helix: -0.21 (0.17), residues: 881
  sheet: -0.36 (0.65), residues: 67
  loop : -1.83 (0.22), residues: 712

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 176 
 HIS   0.005   0.001   HIS A1344 
 PHE   0.019   0.001   PHE A 163 
 TYR   0.019   0.001   TYR E 247 
 ARG   0.005   0.001   ARG E 300 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03881 (  614)
  hydrogen bonds       : angle       4.25582 ( 1765)
  SS BOND              : bond        0.00336 (    2)
  SS BOND              : angle       1.96369 (    4)
  covalent geometry    : bond        0.00244 (13480)
  covalent geometry    : angle       0.58726 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 221
  time to evaluate  : 1.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  277 GLU cc_start: 0.7750 (pt0) cc_final: 0.7496 (tm-30)
REVERT: E  247 TYR cc_start: 0.4968 (t80) cc_final: 0.4466 (m-10)
REVERT: B  234 MET cc_start: 0.2936 (pmm) cc_final: 0.2353 (tpp)
REVERT: B  235 MET cc_start: 0.7685 (ppp) cc_final: 0.7223 (ttm)
REVERT: B  267 GLN cc_start: 0.6813 (OUTLIER) cc_final: 0.6456 (tt0)
REVERT: B  270 LYS cc_start: 0.8529 (tppp) cc_final: 0.8083 (tmmt)
REVERT: A   35 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7617 (mp)
REVERT: A   62 SER cc_start: 0.7522 (m) cc_final: 0.7224 (p)
REVERT: A  101 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7860 (tt)
REVERT: A  111 ARG cc_start: 0.7844 (mtt-85) cc_final: 0.7607 (mmt90)
REVERT: A  241 MET cc_start: 0.8805 (mmm) cc_final: 0.8494 (mmm)
REVERT: A  956 MET cc_start: 0.7876 (tpt) cc_final: 0.7487 (tpt)
REVERT: A 1317 MET cc_start: 0.7967 (ttm) cc_final: 0.7585 (ttm)
  outliers start: 34
  outliers final: 13
  residues processed: 248
  average time/residue: 0.2868
  time to fit residues: 101.0360
Evaluate side-chains
  199 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 GLN
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue 1311 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 129 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
C 279 ASN
A  11 HIS
** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
A 827 ASN
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1375 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.167039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.125599 restraints weight = 33892.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 3.03
r_work: 0.3502 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3510
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3510 r_free = 0.3510    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3510 r_free = 0.3510    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3510
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  13482  Z= 0.158
  Angle     :  0.618  10.524  18254  Z= 0.308
  Chirality :  0.043   0.221   2118
  Planarity :  0.004   0.039   2323
  Dihedral  :  4.864  41.127   1814
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.79 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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: -1.01 (0.20), residues: 1660
  helix:  0.05 (0.17), residues: 892
  sheet: -0.24 (0.65), residues: 67
  loop : -1.63 (0.23), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 169 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.019   0.001   PHE A1360 
 TYR   0.021   0.002   TYR E 247 
 ARG   0.005   0.000   ARG C 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03814 (  614)
  hydrogen bonds       : angle       4.18041 ( 1765)
  SS BOND              : bond        0.00277 (    2)
  SS BOND              : angle       1.83887 (    4)
  covalent geometry    : bond        0.00367 (13480)
  covalent geometry    : angle       0.61744 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 198
  time to evaluate  : 1.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  276 MET cc_start: 0.7412 (mtp) cc_final: 0.7001 (mtp)
REVERT: E  247 TYR cc_start: 0.5011 (t80) cc_final: 0.4504 (m-10)
REVERT: B  234 MET cc_start: 0.2776 (pmm) cc_final: 0.2381 (tpp)
REVERT: B  267 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6736 (tt0)
REVERT: B  270 LYS cc_start: 0.8516 (tppp) cc_final: 0.8097 (tmmt)
REVERT: A   35 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7806 (mp)
REVERT: A   62 SER cc_start: 0.7589 (m) cc_final: 0.7311 (p)
REVERT: A  101 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7763 (tt)
REVERT: A  762 ARG cc_start: 0.6497 (OUTLIER) cc_final: 0.6227 (tmm-80)
REVERT: A  804 SER cc_start: 0.8935 (t) cc_final: 0.8679 (m)
REVERT: A  956 MET cc_start: 0.7801 (tpt) cc_final: 0.7385 (tpt)
REVERT: A 1016 ASN cc_start: 0.6563 (p0) cc_final: 0.6198 (p0)
REVERT: A 1313 TYR cc_start: 0.6803 (p90) cc_final: 0.6590 (p90)
  outliers start: 37
  outliers final: 25
  residues processed: 225
  average time/residue: 0.2841
  time to fit residues: 91.6954
Evaluate side-chains
  215 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 186
  time to evaluate  : 1.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 GLN
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain E residue  395 LEU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  749 GLN
Chi-restraints excluded: chain A residue  762 ARG
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1222 SER
Chi-restraints excluded: chain A residue 1311 VAL
Chi-restraints excluded: chain A residue 1321 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 89 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 157 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 115 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B 267 GLN
** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 348 ASN
** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 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 = 0.4169 r_free = 0.4169 target = 0.166649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.133652 restraints weight = 32242.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 4.41
r_work: 0.3440 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3448
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3448 r_free = 0.3448    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3448
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13482  Z= 0.147
  Angle     :  0.606  10.250  18254  Z= 0.299
  Chirality :  0.042   0.204   2118
  Planarity :  0.004   0.041   2323
  Dihedral  :  4.755  41.376   1814
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 13.13 %
    Favored  : 84.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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: -0.74 (0.20), residues: 1660
  helix:  0.29 (0.17), residues: 891
  sheet: -0.22 (0.64), residues: 67
  loop : -1.50 (0.23), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 169 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.022   0.001   PHE A 163 
 TYR   0.024   0.002   TYR E 247 
 ARG   0.011   0.000   ARG C 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03742 (  614)
  hydrogen bonds       : angle       4.10638 ( 1765)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       1.77147 (    4)
  covalent geometry    : bond        0.00347 (13480)
  covalent geometry    : angle       0.60548 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 197
  time to evaluate  : 1.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  276 MET cc_start: 0.7598 (mtp) cc_final: 0.7240 (mtp)
REVERT: E  247 TYR cc_start: 0.5106 (t80) cc_final: 0.4508 (m-10)
REVERT: E  272 SER cc_start: 0.8044 (m) cc_final: 0.7693 (t)
REVERT: B  234 MET cc_start: 0.2878 (pmm) cc_final: 0.2585 (tpt)
REVERT: B  235 MET cc_start: 0.7904 (ppp) cc_final: 0.7419 (ttp)
REVERT: B  267 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6589 (tt0)
REVERT: B  268 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7545 (tp-100)
REVERT: B  270 LYS cc_start: 0.8568 (tppp) cc_final: 0.8102 (tmmt)
REVERT: B  298 ASP cc_start: 0.7686 (m-30) cc_final: 0.7479 (m-30)
REVERT: A   35 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7859 (mp)
REVERT: A   62 SER cc_start: 0.7695 (m) cc_final: 0.7400 (p)
REVERT: A   65 ASP cc_start: 0.8388 (m-30) cc_final: 0.7941 (p0)
REVERT: A  101 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7782 (tt)
REVERT: A  241 MET cc_start: 0.8895 (mmm) cc_final: 0.8551 (mmm)
REVERT: A  804 SER cc_start: 0.8953 (t) cc_final: 0.8693 (m)
REVERT: A  833 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7292 (mp)
REVERT: A  956 MET cc_start: 0.7819 (tpt) cc_final: 0.7400 (tpt)
REVERT: A 1016 ASN cc_start: 0.6482 (p0) cc_final: 0.6153 (p0)
REVERT: A 1220 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7545 (ptm-80)
  outliers start: 36
  outliers final: 24
  residues processed: 226
  average time/residue: 0.2702
  time to fit residues: 88.8686
Evaluate side-chains
  214 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 186
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 GLN
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain E residue  395 LEU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  456 ILE
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  833 LEU
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1222 SER
Chi-restraints excluded: chain A residue 1321 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 105 optimal weight:    0.2980
   chunk 114 optimal weight:    0.7980
   chunk 142 optimal weight:    0.9990
   chunk 131 optimal weight:    0.0070
   chunk 95 optimal weight:    2.9990
   chunk 165 optimal weight:    1.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
B 267 GLN
** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1375 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.168249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.136142 restraints weight = 29604.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 3.93
r_work: 0.3503 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3507
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3507
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  13482  Z= 0.112
  Angle     :  0.567   9.953  18254  Z= 0.282
  Chirality :  0.041   0.207   2118
  Planarity :  0.004   0.039   2323
  Dihedral  :  4.555  40.485   1814
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 12.93 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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: -0.42 (0.21), residues: 1660
  helix:  0.54 (0.17), residues: 892
  sheet: -0.06 (0.64), residues: 67
  loop : -1.34 (0.23), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 176 
 HIS   0.006   0.001   HIS A1034 
 PHE   0.026   0.001   PHE A 163 
 TYR   0.021   0.001   TYR E 247 
 ARG   0.007   0.000   ARG C 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03499 (  614)
  hydrogen bonds       : angle       3.99047 ( 1765)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       1.72624 (    4)
  covalent geometry    : bond        0.00250 (13480)
  covalent geometry    : angle       0.56687 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 203
  time to evaluate  : 1.519 
Fit side-chains
   revert: symmetry clash
REVERT: E  247 TYR cc_start: 0.4928 (t80) cc_final: 0.4404 (m-10)
REVERT: B  235 MET cc_start: 0.7891 (ppp) cc_final: 0.7291 (ttm)
REVERT: B  267 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6806 (tt0)
REVERT: B  270 LYS cc_start: 0.8514 (tppp) cc_final: 0.8139 (tmmt)
REVERT: A   35 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7792 (mp)
REVERT: A   56 LYS cc_start: 0.8350 (pptt) cc_final: 0.7891 (mppt)
REVERT: A   62 SER cc_start: 0.7596 (m) cc_final: 0.7337 (p)
REVERT: A   65 ASP cc_start: 0.8401 (m-30) cc_final: 0.7940 (p0)
REVERT: A  101 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7790 (tt)
REVERT: A  762 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6351 (tmm-80)
REVERT: A  804 SER cc_start: 0.8890 (t) cc_final: 0.8630 (m)
REVERT: A  805 ASP cc_start: 0.7557 (m-30) cc_final: 0.7282 (m-30)
REVERT: A  956 MET cc_start: 0.7814 (tpt) cc_final: 0.7409 (tpt)
REVERT: A 1220 ARG cc_start: 0.8063 (ptm160) cc_final: 0.7462 (ptm-80)
REVERT: A 1229 TYR cc_start: 0.7903 (m-80) cc_final: 0.7656 (m-80)
REVERT: A 1318 LEU cc_start: 0.7692 (mt) cc_final: 0.7439 (mp)
  outliers start: 43
  outliers final: 25
  residues processed: 238
  average time/residue: 0.2584
  time to fit residues: 90.2831
Evaluate side-chains
  212 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 183
  time to evaluate  : 1.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 GLN
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  117 ILE
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  762 ARG
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1222 SER
Chi-restraints excluded: chain A residue 1321 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 104 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 48 optimal weight:   10.0000
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 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 = 0.4178 r_free = 0.4178 target = 0.168856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.136873 restraints weight = 30831.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 4.05
r_work: 0.3480 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3484
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13482  Z= 0.118
  Angle     :  0.572  10.176  18254  Z= 0.283
  Chirality :  0.041   0.194   2118
  Planarity :  0.004   0.038   2323
  Dihedral  :  4.471  42.114   1814
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.53 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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: -0.26 (0.21), residues: 1660
  helix:  0.66 (0.17), residues: 892
  sheet:  0.08 (0.65), residues: 67
  loop : -1.27 (0.23), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 169 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.028   0.001   PHE A 163 
 TYR   0.022   0.001   TYR E 247 
 ARG   0.003   0.000   ARG A 813 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 (  614)
  hydrogen bonds       : angle       3.96084 ( 1765)
  SS BOND              : bond        0.00231 (    2)
  SS BOND              : angle       1.69035 (    4)
  covalent geometry    : bond        0.00271 (13480)
  covalent geometry    : angle       0.57154 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 190
  time to evaluate  : 2.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  247 TYR cc_start: 0.4945 (t80) cc_final: 0.4383 (m-10)
REVERT: B  235 MET cc_start: 0.7892 (ppp) cc_final: 0.7356 (ttm)
REVERT: B  267 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7092 (tp40)
REVERT: B  270 LYS cc_start: 0.8591 (tppp) cc_final: 0.8080 (tmmt)
REVERT: A   35 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7938 (mp)
REVERT: A   62 SER cc_start: 0.7683 (m) cc_final: 0.7417 (p)
REVERT: A   65 ASP cc_start: 0.8441 (m-30) cc_final: 0.7951 (p0)
REVERT: A  101 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7818 (tt)
REVERT: A  241 MET cc_start: 0.8876 (mmm) cc_final: 0.8556 (mmm)
REVERT: A  762 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6377 (tmm-80)
REVERT: A  804 SER cc_start: 0.8922 (t) cc_final: 0.8679 (m)
REVERT: A  805 ASP cc_start: 0.7743 (m-30) cc_final: 0.7491 (m-30)
REVERT: A 1017 GLU cc_start: 0.6881 (mp0) cc_final: 0.6606 (mp0)
REVERT: A 1220 ARG cc_start: 0.7966 (ptm160) cc_final: 0.7371 (ptm-80)
REVERT: A 1318 LEU cc_start: 0.7760 (mt) cc_final: 0.7503 (mp)
  outliers start: 39
  outliers final: 27
  residues processed: 220
  average time/residue: 0.3077
  time to fit residues: 100.6189
Evaluate side-chains
  215 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 184
  time to evaluate  : 1.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 GLN
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  101 LEU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  762 ARG
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain A residue 1034 HIS
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1321 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 116 optimal weight:    0.7980
   chunk 155 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 129 optimal weight:    0.3980
   chunk 133 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 135 optimal weight:    1.9990
   chunk 149 optimal weight:    0.0770
   chunk 51 optimal weight:    1.9990
   chunk 143 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 166 HIS
** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 HIS
A 749 GLN
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1375 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.169334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.135792 restraints weight = 27224.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 3.34
r_work: 0.3528 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13482  Z= 0.112
  Angle     :  0.565  10.312  18254  Z= 0.280
  Chirality :  0.040   0.193   2118
  Planarity :  0.004   0.043   2323
  Dihedral  :  4.385  42.164   1814
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 14.07 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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: -0.12 (0.21), residues: 1660
  helix:  0.78 (0.17), residues: 893
  sheet:  0.16 (0.65), residues: 67
  loop : -1.22 (0.23), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 164 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.030   0.001   PHE A 163 
 TYR   0.019   0.001   TYR E 247 
 ARG   0.004   0.000   ARG C 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03394 (  614)
  hydrogen bonds       : angle       3.92352 ( 1765)
  SS BOND              : bond        0.00223 (    2)
  SS BOND              : angle       1.67000 (    4)
  covalent geometry    : bond        0.00252 (13480)
  covalent geometry    : angle       0.56402 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 194
  time to evaluate  : 1.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  247 TYR cc_start: 0.4824 (t80) cc_final: 0.4377 (m-10)
REVERT: B  283 MET cc_start: 0.8503 (tpp) cc_final: 0.8011 (tpt)
REVERT: A   35 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7938 (mp)
REVERT: A   56 LYS cc_start: 0.8378 (pptt) cc_final: 0.7908 (mppt)
REVERT: A   62 SER cc_start: 0.7664 (m) cc_final: 0.7411 (p)
REVERT: A   65 ASP cc_start: 0.8491 (m-30) cc_final: 0.7977 (p0)
REVERT: A  241 MET cc_start: 0.8875 (mmm) cc_final: 0.8555 (mmm)
REVERT: A  294 TYR cc_start: 0.8635 (m-10) cc_final: 0.8385 (m-10)
REVERT: A  332 ASP cc_start: 0.7896 (t0) cc_final: 0.7690 (t0)
REVERT: A  593 THR cc_start: 0.7996 (m) cc_final: 0.7745 (t)
REVERT: A  749 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7531 (pm20)
REVERT: A  804 SER cc_start: 0.8875 (t) cc_final: 0.8621 (m)
REVERT: A  805 ASP cc_start: 0.7603 (m-30) cc_final: 0.7370 (m-30)
REVERT: A 1220 ARG cc_start: 0.7887 (ptm160) cc_final: 0.7322 (ptm-80)
REVERT: A 1229 TYR cc_start: 0.7797 (m-80) cc_final: 0.7454 (m-80)
REVERT: A 1318 LEU cc_start: 0.7672 (mt) cc_final: 0.7429 (mp)
  outliers start: 36
  outliers final: 28
  residues processed: 220
  average time/residue: 0.2693
  time to fit residues: 86.7788
Evaluate side-chains
  214 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 1.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain E residue  267 GLN
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  749 GLN
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain A residue 1034 HIS
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1222 SER
Chi-restraints excluded: chain A residue 1321 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 139 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 155 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
D 240 GLN
D 279 ASN
A  11 HIS
** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 749 GLN
** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1235 ASN
A1375 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.168539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.136134 restraints weight = 27737.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 3.55
r_work: 0.3491 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3499
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3499 r_free = 0.3499    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3499
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13482  Z= 0.126
  Angle     :  0.583  10.239  18254  Z= 0.290
  Chirality :  0.041   0.195   2118
  Planarity :  0.004   0.038   2323
  Dihedral  :  4.404  43.568   1814
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.47 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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: -0.06 (0.21), residues: 1660
  helix:  0.80 (0.17), residues: 899
  sheet:  0.12 (0.66), residues: 67
  loop : -1.15 (0.24), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 169 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.029   0.001   PHE A 163 
 TYR   0.021   0.001   TYR E 247 
 ARG   0.004   0.000   ARG C 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03449 (  614)
  hydrogen bonds       : angle       3.94037 ( 1765)
  SS BOND              : bond        0.00204 (    2)
  SS BOND              : angle       1.64654 (    4)
  covalent geometry    : bond        0.00291 (13480)
  covalent geometry    : angle       0.58224 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 195
  time to evaluate  : 2.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  247 TYR cc_start: 0.4835 (t80) cc_final: 0.4401 (m-10)
REVERT: B  283 MET cc_start: 0.8568 (tpp) cc_final: 0.8040 (tpt)
REVERT: A   35 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7972 (mp)
REVERT: A   62 SER cc_start: 0.7681 (m) cc_final: 0.7428 (p)
REVERT: A   65 ASP cc_start: 0.8485 (m-30) cc_final: 0.7945 (p0)
REVERT: A  294 TYR cc_start: 0.8635 (m-10) cc_final: 0.8415 (m-10)
REVERT: A  332 ASP cc_start: 0.7956 (t0) cc_final: 0.7732 (t0)
REVERT: A  593 THR cc_start: 0.7996 (m) cc_final: 0.7746 (t)
REVERT: A  804 SER cc_start: 0.8943 (t) cc_final: 0.8707 (m)
REVERT: A  871 TYR cc_start: 0.7939 (t80) cc_final: 0.7367 (t80)
REVERT: A 1017 GLU cc_start: 0.6839 (mp0) cc_final: 0.6482 (mp0)
REVERT: A 1021 LYS cc_start: 0.8710 (mppt) cc_final: 0.8342 (mmtm)
REVERT: A 1087 MET cc_start: 0.8092 (mtt) cc_final: 0.7793 (mtp)
REVERT: A 1220 ARG cc_start: 0.7856 (ptm160) cc_final: 0.7290 (ptm-80)
REVERT: A 1318 LEU cc_start: 0.7674 (mt) cc_final: 0.7421 (mp)
  outliers start: 37
  outliers final: 29
  residues processed: 222
  average time/residue: 0.3291
  time to fit residues: 106.3707
Evaluate side-chains
  214 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 184
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 GLN
Chi-restraints excluded: chain E residue  270 LYS
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain B residue  276 MET
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain A residue 1034 HIS
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1222 SER
Chi-restraints excluded: chain A residue 1321 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0770
   chunk 53 optimal weight:    4.9990
   chunk 117 optimal weight:    0.0970
   chunk 77 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.5536

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

Flipped N/Q/H residues before XYZ refinement:
D 279 ASN
** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 HIS
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1375 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 = 0.4186 r_free = 0.4186 target = 0.169394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.130515 restraints weight = 36581.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 3.20
r_work: 0.3523 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3525
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3525 r_free = 0.3525    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3525 r_free = 0.3525    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3525
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.4164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13482  Z= 0.113
  Angle     :  0.586  10.122  18254  Z= 0.290
  Chirality :  0.041   0.220   2118
  Planarity :  0.004   0.052   2323
  Dihedral  :  4.268  42.625   1812
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.07 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.04 (0.21), residues: 1660
  helix:  0.89 (0.17), residues: 899
  sheet:  0.12 (0.65), residues: 67
  loop : -1.10 (0.24), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.028   0.001   PHE A 163 
 TYR   0.021   0.001   TYR E 247 
 ARG   0.009   0.000   ARG C 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03364 (  614)
  hydrogen bonds       : angle       3.91496 ( 1765)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       1.64317 (    4)
  covalent geometry    : bond        0.00255 (13480)
  covalent geometry    : angle       0.58522 (18250)

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

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

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3320 Ramachandran restraints generated.
    1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 190
  time to evaluate  : 1.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  247 TYR cc_start: 0.4882 (t80) cc_final: 0.4404 (m-10)
REVERT: E  267 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.6286 (pt0)
REVERT: A   35 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7922 (mp)
REVERT: A   62 SER cc_start: 0.7579 (m) cc_final: 0.7361 (p)
REVERT: A   65 ASP cc_start: 0.8447 (m-30) cc_final: 0.7979 (p0)
REVERT: A  332 ASP cc_start: 0.8001 (t0) cc_final: 0.7765 (t0)
REVERT: A  593 THR cc_start: 0.7934 (m) cc_final: 0.7689 (t)
REVERT: A  804 SER cc_start: 0.8903 (t) cc_final: 0.8650 (m)
REVERT: A  805 ASP cc_start: 0.7631 (m-30) cc_final: 0.7427 (m-30)
REVERT: A  871 TYR cc_start: 0.7918 (t80) cc_final: 0.7339 (t80)
REVERT: A 1017 GLU cc_start: 0.6764 (mp0) cc_final: 0.6473 (mp0)
REVERT: A 1021 LYS cc_start: 0.8685 (mppt) cc_final: 0.8334 (mmtm)
REVERT: A 1087 MET cc_start: 0.8210 (mtt) cc_final: 0.7972 (mtp)
REVERT: A 1220 ARG cc_start: 0.7807 (ptm160) cc_final: 0.7233 (ptm-80)
REVERT: A 1229 TYR cc_start: 0.7690 (m-80) cc_final: 0.7345 (m-80)
REVERT: A 1318 LEU cc_start: 0.7705 (mt) cc_final: 0.7443 (mp)
REVERT: A 1370 ARG cc_start: 0.8399 (ptm160) cc_final: 0.8140 (ptm-80)
  outliers start: 33
  outliers final: 28
  residues processed: 212
  average time/residue: 0.3146
  time to fit residues: 98.4227
Evaluate side-chains
  210 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 180
  time to evaluate  : 2.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  293 VAL
Chi-restraints excluded: chain D residue  309 LEU
Chi-restraints excluded: chain C residue  243 SER
Chi-restraints excluded: chain C residue  249 LEU
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain E residue  266 ILE
Chi-restraints excluded: chain E residue  267 GLN
Chi-restraints excluded: chain E residue  270 LYS
Chi-restraints excluded: chain E residue  308 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  240 MET
Chi-restraints excluded: chain A residue  265 ASP
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  462 THR
Chi-restraints excluded: chain A residue  475 HIS
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  509 GLU
Chi-restraints excluded: chain A residue  647 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  902 ILE
Chi-restraints excluded: chain A residue  971 SER
Chi-restraints excluded: chain A residue 1002 THR
Chi-restraints excluded: chain A residue 1034 HIS
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1222 SER
Chi-restraints excluded: chain A residue 1321 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 166
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 104 optimal weight:    0.5980
   chunk 69 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0370
   chunk 132 optimal weight:    3.9990
   chunk 112 optimal weight:    0.5980
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
D 279 ASN
** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  11 HIS
** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.169589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.130213 restraints weight = 41804.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 3.43
r_work: 0.3512 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.4273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13482  Z= 0.113
  Angle     :  0.579   9.875  18254  Z= 0.288
  Chirality :  0.041   0.220   2118
  Planarity :  0.004   0.038   2323
  Dihedral  :  4.200  42.108   1812
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 15.41 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.16 (0.21), residues: 1660
  helix:  0.99 (0.17), residues: 899
  sheet:  0.11 (0.65), residues: 67
  loop : -1.03 (0.24), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.026   0.001   PHE A 163 
 TYR   0.020   0.001   TYR E 247 
 ARG   0.006   0.000   ARG C 263 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  614)
  hydrogen bonds       : angle       3.91757 ( 1765)
  SS BOND              : bond        0.00194 (    2)
  SS BOND              : angle       1.62947 (    4)
  covalent geometry    : bond        0.00254 (13480)
  covalent geometry    : angle       0.57829 (18250)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7602.37 seconds
wall clock time: 134 minutes 43.63 seconds (8083.63 seconds total)