Starting phenix.real_space_refine on Fri Feb 6 15:45:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tqg_56149/02_2026/9tqg_56149.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tqg_56149/02_2026/9tqg_56149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9tqg_56149/02_2026/9tqg_56149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tqg_56149/02_2026/9tqg_56149.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9tqg_56149/02_2026/9tqg_56149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tqg_56149/02_2026/9tqg_56149.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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 121 5.16 5 C 16287 2.51 5 N 4493 2.21 5 O 4777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25678 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4106 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "B" Number of atoms: 4106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4106 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "C" Number of atoms: 4106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4106 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "D" Number of atoms: 4106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4106 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "E" Number of atoms: 4081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4081 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 25, 'TRANS': 504} Chain breaks: 1 Chain: "F" Number of atoms: 4106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4106 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "L" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1022 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.50, per 1000 atoms: 0.25 Number of scatterers: 25678 At special positions: 0 Unit cell: (123, 159, 156, 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 121 16.00 O 4777 8.00 N 4493 7.00 C 16287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 22 sheets defined 50.7% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 12 through 37 removed outlier: 3.564A pdb=" N LEU A 25 " --> pdb=" O ASN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 55 through 64 Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.002A pdb=" N THR A 116 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.943A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.618A pdb=" N ALA A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 251 through 265 removed outlier: 3.585A pdb=" N ASN A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.833A pdb=" N THR A 290 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.679A pdb=" N ILE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 310 No H-bonds generated for 'chain 'A' and resid 309 through 310' Processing helix chain 'A' and resid 311 through 315 removed outlier: 3.506A pdb=" N SER A 314 " --> pdb=" O VAL A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 367 removed outlier: 3.537A pdb=" N ALA A 353 " --> pdb=" O PHE A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 389 through 404 removed outlier: 3.655A pdb=" N LYS A 396 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 4.208A pdb=" N TYR A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 446 through 465 removed outlier: 4.026A pdb=" N ASN A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 488 Processing helix chain 'A' and resid 490 through 497 removed outlier: 3.649A pdb=" N ALA A 496 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 497 " --> pdb=" O TYR A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'B' and resid 12 through 38 removed outlier: 3.655A pdb=" N LEU B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.599A pdb=" N ARG B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.685A pdb=" N ALA B 89 " --> pdb=" O ILE B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.646A pdb=" N THR B 116 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 removed outlier: 3.670A pdb=" N LYS B 123 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 156 removed outlier: 5.874A pdb=" N ASP B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.775A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.783A pdb=" N ALA B 193 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 224 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 234 through 241 removed outlier: 3.532A pdb=" N HIS B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 265 removed outlier: 3.649A pdb=" N ASN B 265 " --> pdb=" O VAL B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.657A pdb=" N ASP B 288 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 292 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.921A pdb=" N ARG B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 6.462A pdb=" N GLY B 313 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 314 " --> pdb=" O VAL B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 367 removed outlier: 3.652A pdb=" N ALA B 353 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 354 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 388 Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.505A pdb=" N HIS B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 424 removed outlier: 3.566A pdb=" N ALA B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.583A pdb=" N ALA B 430 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 464 removed outlier: 3.738A pdb=" N VAL B 453 " --> pdb=" O GLN B 449 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 488 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 508 through 521 removed outlier: 3.610A pdb=" N LEU B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.689A pdb=" N LEU C 25 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.583A pdb=" N GLN C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.688A pdb=" N LEU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.590A pdb=" N THR C 116 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.895A pdb=" N LYS C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 156 removed outlier: 5.651A pdb=" N ASP C 154 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 156 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.926A pdb=" N LEU C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 192 Processing helix chain 'C' and resid 193 through 199 removed outlier: 4.215A pdb=" N ALA C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 223 Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 251 through 264 removed outlier: 3.636A pdb=" N SER C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.868A pdb=" N ASP C 288 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 308 removed outlier: 3.511A pdb=" N ILE C 307 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 315 removed outlier: 3.795A pdb=" N SER C 314 " --> pdb=" O VAL C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 366 Processing helix chain 'C' and resid 382 through 388 Processing helix chain 'C' and resid 389 through 404 Processing helix chain 'C' and resid 418 through 423 removed outlier: 3.633A pdb=" N TYR C 422 " --> pdb=" O GLY C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 removed outlier: 3.790A pdb=" N ALA C 430 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 465 removed outlier: 3.886A pdb=" N GLN C 465 " --> pdb=" O LYS C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 488 Processing helix chain 'C' and resid 490 through 497 removed outlier: 3.504A pdb=" N ARG C 497 " --> pdb=" O TYR C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 507 No H-bonds generated for 'chain 'C' and resid 505 through 507' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'D' and resid 12 through 37 removed outlier: 3.682A pdb=" N ASN D 21 " --> pdb=" O ASN D 17 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 51 removed outlier: 3.807A pdb=" N GLN D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 Processing helix chain 'D' and resid 86 through 89 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 118 through 136 Processing helix chain 'D' and resid 149 through 156 removed outlier: 5.876A pdb=" N ASP D 154 " --> pdb=" O PRO D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.668A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 192 Processing helix chain 'D' and resid 193 through 199 removed outlier: 3.648A pdb=" N ALA D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 222 removed outlier: 3.963A pdb=" N ALA D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 234 Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 251 through 264 Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.502A pdb=" N ASP D 288 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.577A pdb=" N ILE D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 315 removed outlier: 6.326A pdb=" N GLY D 313 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 367 Processing helix chain 'D' and resid 382 through 389 Processing helix chain 'D' and resid 390 through 404 removed outlier: 3.730A pdb=" N LYS D 396 " --> pdb=" O LYS D 392 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET D 397 " --> pdb=" O HIS D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 424 removed outlier: 4.073A pdb=" N TYR D 422 " --> pdb=" O GLY D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 430 removed outlier: 3.781A pdb=" N ALA D 430 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 465 removed outlier: 3.591A pdb=" N GLN D 465 " --> pdb=" O LYS D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 489 removed outlier: 3.720A pdb=" N GLU D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN D 476 " --> pdb=" O GLU D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 497 removed outlier: 3.628A pdb=" N ARG D 497 " --> pdb=" O TYR D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'E' and resid 12 through 37 removed outlier: 4.252A pdb=" N ASN E 21 " --> pdb=" O ASN E 17 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 51 removed outlier: 3.714A pdb=" N GLN E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 63 Processing helix chain 'E' and resid 86 through 91 removed outlier: 4.157A pdb=" N ALA E 89 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 removed outlier: 3.841A pdb=" N GLY E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 136 Processing helix chain 'E' and resid 152 through 156 Processing helix chain 'E' and resid 164 through 174 removed outlier: 4.155A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN E 170 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 199 removed outlier: 3.673A pdb=" N ALA E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA E 199 " --> pdb=" O VAL E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 223 removed outlier: 3.611A pdb=" N VAL E 219 " --> pdb=" O GLY E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 234 Processing helix chain 'E' and resid 234 through 239 Processing helix chain 'E' and resid 251 through 264 removed outlier: 3.668A pdb=" N ALA E 255 " --> pdb=" O ASN E 251 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 292 removed outlier: 3.767A pdb=" N ASP E 288 " --> pdb=" O ASP E 285 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE E 292 " --> pdb=" O LEU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 308 Processing helix chain 'E' and resid 309 through 310 No H-bonds generated for 'chain 'E' and resid 309 through 310' Processing helix chain 'E' and resid 311 through 315 Processing helix chain 'E' and resid 349 through 367 removed outlier: 3.590A pdb=" N ALA E 353 " --> pdb=" O PHE E 349 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 362 " --> pdb=" O HIS E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 389 Processing helix chain 'E' and resid 390 through 403 Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 426 through 430 Processing helix chain 'E' and resid 446 through 464 Processing helix chain 'E' and resid 470 through 488 Processing helix chain 'E' and resid 490 through 497 removed outlier: 3.944A pdb=" N ARG E 497 " --> pdb=" O TYR E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 removed outlier: 3.550A pdb=" N LEU E 521 " --> pdb=" O LEU E 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 removed outlier: 3.916A pdb=" N LEU F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.643A pdb=" N GLN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 64 removed outlier: 3.538A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 89 removed outlier: 3.507A pdb=" N ALA F 89 " --> pdb=" O ILE F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 86 through 89' Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 118 through 136 removed outlier: 3.679A pdb=" N LYS F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 156 removed outlier: 5.715A pdb=" N ASP F 154 " --> pdb=" O PRO F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 175 removed outlier: 4.292A pdb=" N PHE F 167 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 3.594A pdb=" N ALA F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 224 removed outlier: 3.521A pdb=" N LYS F 220 " --> pdb=" O PRO F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 removed outlier: 3.559A pdb=" N GLY F 233 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.507A pdb=" N ARG F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 265 removed outlier: 3.626A pdb=" N SER F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN F 265 " --> pdb=" O VAL F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 292 removed outlier: 3.548A pdb=" N LEU F 289 " --> pdb=" O SER F 286 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR F 290 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 308 Processing helix chain 'F' and resid 309 through 310 No H-bonds generated for 'chain 'F' and resid 309 through 310' Processing helix chain 'F' and resid 311 through 315 removed outlier: 3.689A pdb=" N GLU F 315 " --> pdb=" O ASP F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 365 removed outlier: 3.511A pdb=" N HIS F 358 " --> pdb=" O GLN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 389 Processing helix chain 'F' and resid 390 through 404 removed outlier: 3.669A pdb=" N ALA F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS F 396 " --> pdb=" O LYS F 392 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET F 397 " --> pdb=" O HIS F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 424 removed outlier: 3.664A pdb=" N ALA F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET F 424 " --> pdb=" O GLY F 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 419 through 424' Processing helix chain 'F' and resid 426 through 430 removed outlier: 3.559A pdb=" N ALA F 430 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 464 removed outlier: 4.857A pdb=" N GLN F 456 " --> pdb=" O ASN F 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 490 Processing helix chain 'F' and resid 490 through 496 Processing helix chain 'F' and resid 505 through 507 No H-bonds generated for 'chain 'F' and resid 505 through 507' Processing helix chain 'F' and resid 508 through 520 Processing helix chain 'L' and resid 476 through 494 Processing helix chain 'L' and resid 497 through 503 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 removed outlier: 8.639A pdb=" N ILE A 140 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LEU A 142 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 106 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 201 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 319 removed outlier: 4.566A pdb=" N CYS A 329 " --> pdb=" O PHE A 319 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL A 371 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY A 340 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU A 373 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 342 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 370 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE A 411 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE A 372 " --> pdb=" O ILE A 411 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS A 408 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 8.697A pdb=" N TRP A 435 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR A 410 " --> pdb=" O TRP A 435 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 415 through 417 removed outlier: 6.207A pdb=" N SER A 416 " --> pdb=" O SER A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 73 removed outlier: 4.666A pdb=" N THR B 93 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N CYS B 139 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N VAL B 183 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR B 141 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU B 201 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 182 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 203 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N SER B 202 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ALA B 249 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET B 204 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 317 through 318 removed outlier: 4.062A pdb=" N PHE B 433 " --> pdb=" O LYS B 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 416 through 417 removed outlier: 6.058A pdb=" N SER B 416 " --> pdb=" O SER B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 70 through 72 removed outlier: 8.617A pdb=" N ILE C 140 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL C 104 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU C 142 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL C 106 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS C 139 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL C 183 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR C 141 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 201 " --> pdb=" O GLN C 180 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 205 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER C 202 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA C 249 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N MET C 204 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 187 through 188 Processing sheet with id=AA9, first strand: chain 'C' and resid 317 through 318 removed outlier: 3.537A pdb=" N PHE C 331 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 330 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N VAL C 371 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY C 340 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU C 373 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE C 342 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN C 375 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASN C 344 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 409 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN C 374 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE C 376 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY C 415 " --> pdb=" O ILE C 376 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS C 408 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N TRP C 435 " --> pdb=" O LYS C 408 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N THR C 410 " --> pdb=" O TRP C 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 317 through 318 removed outlier: 3.537A pdb=" N PHE C 331 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 330 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N VAL C 371 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY C 340 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU C 373 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE C 342 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN C 375 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASN C 344 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 409 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN C 374 " --> pdb=" O ILE C 411 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE C 376 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY C 415 " --> pdb=" O ILE C 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 71 through 73 removed outlier: 4.660A pdb=" N THR D 93 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 201 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 205 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 318 removed outlier: 8.244A pdb=" N VAL D 371 " --> pdb=" O PRO D 338 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY D 340 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU D 373 " --> pdb=" O GLY D 340 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE D 342 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE D 433 " --> pdb=" O LYS D 408 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 502 " --> pdb=" O LEU D 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 415 through 417 removed outlier: 6.299A pdb=" N SER D 416 " --> pdb=" O SER D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 71 through 72 removed outlier: 3.542A pdb=" N CYS E 103 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N CYS E 139 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL E 183 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR E 141 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER E 202 " --> pdb=" O HIS E 247 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA E 249 " --> pdb=" O SER E 202 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N MET E 204 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 187 through 189 removed outlier: 6.111A pdb=" N CYS E 188 " --> pdb=" O PHE E 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 317 through 319 removed outlier: 4.578A pdb=" N CYS E 329 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASN E 375 " --> pdb=" O ASN E 344 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 370 " --> pdb=" O PHE E 409 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE E 411 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE E 372 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL E 413 " --> pdb=" O PHE E 372 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN E 374 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY E 415 " --> pdb=" O GLN E 374 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS E 408 " --> pdb=" O PHE E 433 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N TRP E 435 " --> pdb=" O LYS E 408 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR E 410 " --> pdb=" O TRP E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 317 through 319 removed outlier: 4.578A pdb=" N CYS E 329 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASN E 375 " --> pdb=" O ASN E 344 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 370 " --> pdb=" O PHE E 409 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE E 411 " --> pdb=" O LEU E 370 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE E 372 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL E 413 " --> pdb=" O PHE E 372 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLN E 374 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY E 415 " --> pdb=" O GLN E 374 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARG E 441 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLY E 414 " --> pdb=" O ARG E 441 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N SER E 443 " --> pdb=" O GLY E 414 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER E 416 " --> pdb=" O SER E 443 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 71 through 73 removed outlier: 4.639A pdb=" N THR F 93 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N CYS F 139 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL F 183 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR F 141 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 201 " --> pdb=" O GLN F 180 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER F 202 " --> pdb=" O HIS F 247 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA F 249 " --> pdb=" O SER F 202 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET F 204 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 187 through 188 Processing sheet with id=AC2, first strand: chain 'F' and resid 317 through 318 removed outlier: 8.403A pdb=" N VAL F 371 " --> pdb=" O PRO F 338 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY F 340 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU F 373 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE F 342 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU F 370 " --> pdb=" O PHE F 409 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ILE F 411 " --> pdb=" O LEU F 370 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE F 372 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE F 433 " --> pdb=" O LYS F 408 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 415 through 416 Processing sheet with id=AC4, first strand: chain 'L' and resid 514 through 519 removed outlier: 3.559A pdb=" N ILE L 525 " --> pdb=" O TYR L 518 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE L 541 " --> pdb=" O LYS L 544 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG L 569 " --> pdb=" O TYR L 580 " (cutoff:3.500A) 1223 hydrogen bonds defined for protein. 3354 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: 5.07 Time building geometry restraints manager: 2.93 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: 5440 1.33 - 1.45: 5941 1.45 - 1.58: 14645 1.58 - 1.70: 0 1.70 - 1.82: 194 Bond restraints: 26220 Sorted by residual: bond pdb=" C VAL C 195 " pdb=" N PRO C 196 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.39e+00 bond pdb=" C LEU F 150 " pdb=" N PRO F 151 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.19e-02 7.06e+03 2.33e+00 bond pdb=" C LEU C 150 " pdb=" N PRO C 151 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.19e-02 7.06e+03 2.14e+00 bond pdb=" C ASN B 490 " pdb=" N PRO B 491 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.61e+00 bond pdb=" CA ALA C 430 " pdb=" CB ALA C 430 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.16e+00 ... (remaining 26215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 35227 2.33 - 4.65: 268 4.65 - 6.98: 21 6.98 - 9.31: 1 9.31 - 11.64: 1 Bond angle restraints: 35518 Sorted by residual: angle pdb=" N LEU E 232 " pdb=" CA LEU E 232 " pdb=" C LEU E 232 " ideal model delta sigma weight residual 114.62 109.74 4.88 1.14e+00 7.69e-01 1.83e+01 angle pdb=" N ILE D 390 " pdb=" CA ILE D 390 " pdb=" C ILE D 390 " ideal model delta sigma weight residual 112.96 108.99 3.97 1.00e+00 1.00e+00 1.57e+01 angle pdb=" N GLN C 75 " pdb=" CA GLN C 75 " pdb=" C GLN C 75 " ideal model delta sigma weight residual 110.97 115.09 -4.12 1.09e+00 8.42e-01 1.43e+01 angle pdb=" C GLY E 389 " pdb=" N ILE E 390 " pdb=" CA ILE E 390 " ideal model delta sigma weight residual 121.97 128.44 -6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA ARG E 165 " pdb=" CB ARG E 165 " pdb=" CG ARG E 165 " ideal model delta sigma weight residual 114.10 121.26 -7.16 2.00e+00 2.50e-01 1.28e+01 ... (remaining 35513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13969 17.97 - 35.94: 1330 35.94 - 53.91: 308 53.91 - 71.88: 85 71.88 - 89.85: 49 Dihedral angle restraints: 15741 sinusoidal: 6241 harmonic: 9500 Sorted by residual: dihedral pdb=" CA PHE A 157 " pdb=" C PHE A 157 " pdb=" N ALA A 158 " pdb=" CA ALA A 158 " ideal model delta harmonic sigma weight residual -180.00 -155.18 -24.82 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PHE E 157 " pdb=" C PHE E 157 " pdb=" N ALA E 158 " pdb=" CA ALA E 158 " ideal model delta harmonic sigma weight residual -180.00 -155.71 -24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA PHE C 157 " pdb=" C PHE C 157 " pdb=" N ALA C 158 " pdb=" CA ALA C 158 " ideal model delta harmonic sigma weight residual -180.00 -158.03 -21.97 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 15738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2819 0.041 - 0.082: 798 0.082 - 0.122: 286 0.122 - 0.163: 26 0.163 - 0.204: 1 Chirality restraints: 3930 Sorted by residual: chirality pdb=" CB ILE E 92 " pdb=" CA ILE E 92 " pdb=" CG1 ILE E 92 " pdb=" CG2 ILE E 92 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE E 411 " pdb=" N ILE E 411 " pdb=" C ILE E 411 " pdb=" CB ILE E 411 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA ILE L 541 " pdb=" N ILE L 541 " pdb=" C ILE L 541 " pdb=" CB ILE L 541 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 3927 not shown) Planarity restraints: 4655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 195 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.90e+00 pdb=" N PRO E 196 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 118 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO C 119 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 119 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 119 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 490 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO E 491 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 491 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 491 " 0.025 5.00e-02 4.00e+02 ... (remaining 4652 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 13046 3.01 - 3.48: 25030 3.48 - 3.95: 40104 3.95 - 4.43: 47204 4.43 - 4.90: 77491 Nonbonded interactions: 202875 Sorted by model distance: nonbonded pdb=" N ASP B 41 " pdb=" OD1 ASP B 41 " model vdw 2.533 3.120 nonbonded pdb=" N ASP F 41 " pdb=" OD1 ASP F 41 " model vdw 2.534 3.120 nonbonded pdb=" O THR C 326 " pdb=" OG1 THR C 326 " model vdw 2.581 3.040 nonbonded pdb=" N VAL E 244 " pdb=" N SER E 245 " model vdw 2.604 2.560 nonbonded pdb=" N SER F 443 " pdb=" O SER F 443 " model vdw 2.610 2.496 ... (remaining 202870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 223 or resid 227 through 535)) selection = (chain 'B' and (resid 3 through 223 or resid 227 through 535)) selection = (chain 'C' and (resid 3 through 223 or resid 227 through 535)) selection = (chain 'D' and (resid 3 through 223 or resid 227 through 535)) selection = (chain 'E' and resid 3 through 535) selection = (chain 'F' and (resid 3 through 223 or resid 227 through 535)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 26.580 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: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 25.430 Find NCS groups from input model: 0.730 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 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 : 0.002 0.029 26220 Z= 0.122 Angle : 0.563 11.636 35518 Z= 0.335 Chirality : 0.043 0.204 3930 Planarity : 0.004 0.049 4655 Dihedral : 16.011 89.851 9669 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 1.42 % Allowed : 14.09 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3305 helix: 0.51 (0.14), residues: 1438 sheet: 1.55 (0.24), residues: 455 loop : -1.05 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 441 TYR 0.027 0.001 TYR E 168 PHE 0.029 0.001 PHE E 149 TRP 0.015 0.001 TRP B 469 HIS 0.003 0.001 HIS E 162 Details of bonding type rmsd covalent geometry : bond 0.00225 (26220) covalent geometry : angle 0.56283 (35518) hydrogen bonds : bond 0.20236 ( 1195) hydrogen bonds : angle 6.66858 ( 3354) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7285 (pttm) cc_final: 0.6973 (pttp) REVERT: A 380 MET cc_start: 0.3727 (pmm) cc_final: 0.2079 (tpt) REVERT: A 452 ASN cc_start: 0.5102 (m-40) cc_final: 0.4480 (p0) REVERT: B 8 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7412 (pt) REVERT: B 212 PHE cc_start: 0.2577 (OUTLIER) cc_final: 0.0848 (p90) REVERT: C 155 GLN cc_start: 0.4221 (OUTLIER) cc_final: 0.3703 (tp40) REVERT: C 206 LYS cc_start: 0.6561 (tttt) cc_final: 0.5623 (pttt) REVERT: C 223 THR cc_start: 0.4815 (m) cc_final: 0.4257 (p) REVERT: C 445 MET cc_start: 0.2749 (mmt) cc_final: 0.2468 (mmp) REVERT: C 481 MET cc_start: 0.0682 (OUTLIER) cc_final: -0.0187 (mtm) REVERT: C 527 ASP cc_start: 0.7222 (p0) cc_final: 0.6920 (p0) REVERT: D 3 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7412 (mmmt) REVERT: D 30 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6794 (mtt90) REVERT: D 31 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.6074 (mm-30) REVERT: D 299 LYS cc_start: 0.7553 (mmmm) cc_final: 0.7308 (tptm) REVERT: D 526 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8033 (mt-10) REVERT: E 185 MET cc_start: 0.6312 (mpt) cc_final: 0.3703 (mtp) REVERT: E 260 ARG cc_start: 0.6106 (mtp-110) cc_final: 0.3724 (mtt180) REVERT: E 441 ARG cc_start: 0.4910 (mmt-90) cc_final: 0.3831 (mtp180) REVERT: E 445 MET cc_start: 0.3331 (ttp) cc_final: 0.3070 (ttp) REVERT: E 460 GLU cc_start: 0.2668 (OUTLIER) cc_final: 0.2082 (mt-10) REVERT: E 526 GLU cc_start: 0.6446 (mm-30) cc_final: 0.6052 (mt-10) REVERT: E 529 ARG cc_start: 0.7525 (mtp85) cc_final: 0.6404 (mpt-90) REVERT: F 165 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7604 (mmt-90) REVERT: F 357 SER cc_start: 0.6659 (m) cc_final: 0.5962 (p) REVERT: F 380 MET cc_start: 0.2506 (tpt) cc_final: -0.0204 (ptt) REVERT: F 445 MET cc_start: 0.5308 (ptp) cc_final: 0.4886 (mtm) REVERT: F 526 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6253 (mt-10) REVERT: L 546 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.5742 (pp-130) outliers start: 38 outliers final: 20 residues processed: 245 average time/residue: 0.6366 time to fit residues: 182.0770 Evaluate side-chains 241 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 527 ASP Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 495 SER Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain F residue 165 ARG Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain L residue 546 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 170 GLN C 75 GLN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 ASN D 484 GLN E 19 GLN F 101 ASN F 125 HIS F 480 GLN L 476 ASN L 501 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.224953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.192018 restraints weight = 34324.438| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.31 r_work: 0.4055 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26220 Z= 0.137 Angle : 0.542 7.568 35518 Z= 0.295 Chirality : 0.045 0.153 3930 Planarity : 0.005 0.048 4655 Dihedral : 6.324 77.957 3700 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 2.94 % Allowed : 13.79 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3305 helix: 0.75 (0.14), residues: 1457 sheet: 1.78 (0.26), residues: 377 loop : -1.19 (0.15), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.017 0.002 TYR L 549 PHE 0.017 0.002 PHE C 316 TRP 0.010 0.001 TRP B 469 HIS 0.004 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00303 (26220) covalent geometry : angle 0.54227 (35518) hydrogen bonds : bond 0.05302 ( 1195) hydrogen bonds : angle 5.02961 ( 3354) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 221 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.6195 (OUTLIER) cc_final: 0.5788 (mmp) REVERT: A 206 LYS cc_start: 0.7211 (pttm) cc_final: 0.6914 (pttp) REVERT: A 393 HIS cc_start: 0.7236 (m90) cc_final: 0.6746 (m90) REVERT: B 212 PHE cc_start: 0.2621 (OUTLIER) cc_final: 0.0880 (p90) REVERT: B 251 ASN cc_start: 0.6927 (p0) cc_final: 0.6499 (t0) REVERT: C 155 GLN cc_start: 0.4951 (OUTLIER) cc_final: 0.4284 (tp40) REVERT: C 223 THR cc_start: 0.4724 (m) cc_final: 0.4138 (p) REVERT: C 445 MET cc_start: 0.2741 (mmt) cc_final: 0.2477 (mmt) REVERT: C 481 MET cc_start: 0.0754 (OUTLIER) cc_final: -0.0143 (mtm) REVERT: C 527 ASP cc_start: 0.7353 (p0) cc_final: 0.7031 (p0) REVERT: D 3 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7414 (mmmt) REVERT: D 30 ARG cc_start: 0.7442 (mtp85) cc_final: 0.6776 (mtt90) REVERT: D 31 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.6001 (mm-30) REVERT: D 194 TYR cc_start: 0.7843 (m-80) cc_final: 0.7573 (m-80) REVERT: D 204 MET cc_start: 0.7424 (tpp) cc_final: 0.7217 (tpp) REVERT: D 299 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7283 (tptm) REVERT: E 14 GLU cc_start: 0.5445 (pt0) cc_final: 0.4836 (pm20) REVERT: E 185 MET cc_start: 0.6237 (mpt) cc_final: 0.5880 (mmt) REVERT: E 260 ARG cc_start: 0.6255 (mtp-110) cc_final: 0.4045 (mtt180) REVERT: E 441 ARG cc_start: 0.5003 (mmt-90) cc_final: 0.3902 (mtp180) REVERT: E 445 MET cc_start: 0.3246 (ttp) cc_final: 0.2979 (ttp) REVERT: E 460 GLU cc_start: 0.2007 (OUTLIER) cc_final: 0.1686 (mt-10) REVERT: E 526 GLU cc_start: 0.6525 (mm-30) cc_final: 0.6092 (mt-10) REVERT: E 529 ARG cc_start: 0.7545 (mtp85) cc_final: 0.6447 (mtt180) REVERT: F 165 ARG cc_start: 0.7979 (mmt-90) cc_final: 0.7709 (mmt-90) REVERT: F 357 SER cc_start: 0.6628 (m) cc_final: 0.5912 (p) REVERT: F 376 ILE cc_start: 0.2865 (OUTLIER) cc_final: 0.2594 (tp) REVERT: F 380 MET cc_start: 0.2293 (tpt) cc_final: -0.0387 (ptt) REVERT: F 445 MET cc_start: 0.5353 (ptp) cc_final: 0.4878 (mtm) outliers start: 79 outliers final: 29 residues processed: 273 average time/residue: 0.6068 time to fit residues: 194.8641 Evaluate side-chains 247 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 410 THR Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 425 CYS Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain L residue 525 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 286 optimal weight: 30.0000 chunk 87 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 306 optimal weight: 0.8980 chunk 260 optimal weight: 0.9980 chunk 323 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 293 optimal weight: 0.9980 chunk 110 optimal weight: 10.0000 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN F 135 ASN L 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.222140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.189196 restraints weight = 34394.703| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.34 r_work: 0.4021 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 26220 Z= 0.177 Angle : 0.601 10.403 35518 Z= 0.325 Chirality : 0.047 0.160 3930 Planarity : 0.005 0.053 4655 Dihedral : 6.128 76.081 3673 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.30 % Favored : 95.67 % Rotamer: Outliers : 3.88 % Allowed : 14.54 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3305 helix: 0.57 (0.14), residues: 1452 sheet: 1.62 (0.26), residues: 377 loop : -1.34 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 427 TYR 0.020 0.002 TYR F 337 PHE 0.023 0.002 PHE E 323 TRP 0.012 0.002 TRP B 469 HIS 0.009 0.001 HIS L 513 Details of bonding type rmsd covalent geometry : bond 0.00413 (26220) covalent geometry : angle 0.60058 (35518) hydrogen bonds : bond 0.05583 ( 1195) hydrogen bonds : angle 4.97831 ( 3354) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 213 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.6225 (OUTLIER) cc_final: 0.5913 (mmp) REVERT: A 206 LYS cc_start: 0.7243 (pttm) cc_final: 0.7025 (pttp) REVERT: B 204 MET cc_start: 0.2301 (mtp) cc_final: 0.1933 (mtt) REVERT: B 212 PHE cc_start: 0.2747 (OUTLIER) cc_final: 0.0977 (p90) REVERT: B 251 ASN cc_start: 0.6848 (p0) cc_final: 0.6510 (t0) REVERT: B 508 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6463 (m-30) REVERT: C 223 THR cc_start: 0.4579 (m) cc_final: 0.4008 (p) REVERT: C 411 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.5825 (pt) REVERT: C 481 MET cc_start: 0.0565 (OUTLIER) cc_final: -0.0288 (mtm) REVERT: C 498 LEU cc_start: 0.5696 (OUTLIER) cc_final: 0.5055 (mm) REVERT: C 527 ASP cc_start: 0.7478 (p0) cc_final: 0.7149 (p0) REVERT: D 3 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7471 (mmmt) REVERT: D 30 ARG cc_start: 0.7483 (mtp85) cc_final: 0.6810 (mtt90) REVERT: D 31 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.6111 (mm-30) REVERT: D 194 TYR cc_start: 0.7854 (m-80) cc_final: 0.7623 (m-80) REVERT: D 299 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7235 (tptm) REVERT: E 14 GLU cc_start: 0.5518 (pt0) cc_final: 0.4839 (pm20) REVERT: E 185 MET cc_start: 0.6446 (mpt) cc_final: 0.6023 (mmt) REVERT: E 260 ARG cc_start: 0.6273 (mtp-110) cc_final: 0.3712 (mmt180) REVERT: E 309 ARG cc_start: 0.6336 (OUTLIER) cc_final: 0.5867 (mtt-85) REVERT: E 441 ARG cc_start: 0.5102 (mmt-90) cc_final: 0.3892 (mtp-110) REVERT: E 460 GLU cc_start: 0.2040 (OUTLIER) cc_final: 0.1729 (mt-10) REVERT: E 521 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5756 (tp) REVERT: E 526 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6126 (mt-10) REVERT: E 529 ARG cc_start: 0.7591 (mtp85) cc_final: 0.6407 (mtt180) REVERT: F 165 ARG cc_start: 0.8058 (mmt-90) cc_final: 0.7752 (mmt-90) REVERT: F 380 MET cc_start: 0.2114 (OUTLIER) cc_final: -0.0518 (ptt) REVERT: F 445 MET cc_start: 0.5205 (ptp) cc_final: 0.4801 (mtm) REVERT: F 526 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.5478 (mt-10) outliers start: 104 outliers final: 48 residues processed: 284 average time/residue: 0.6147 time to fit residues: 205.3777 Evaluate side-chains 267 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 206 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 425 CYS Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 481 MET Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain L residue 525 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 242 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 312 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 135 ASN E 452 ASN L 501 GLN L 513 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.224604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.191490 restraints weight = 33995.522| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 2.23 r_work: 0.4056 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26220 Z= 0.116 Angle : 0.521 8.974 35518 Z= 0.280 Chirality : 0.044 0.150 3930 Planarity : 0.005 0.053 4655 Dihedral : 5.819 76.941 3670 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.51 % Favored : 96.46 % Rotamer: Outliers : 3.24 % Allowed : 15.92 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3305 helix: 0.84 (0.14), residues: 1456 sheet: 1.70 (0.26), residues: 371 loop : -1.26 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 427 TYR 0.015 0.001 TYR A 248 PHE 0.018 0.001 PHE D 319 TRP 0.011 0.001 TRP B 469 HIS 0.009 0.001 HIS L 513 Details of bonding type rmsd covalent geometry : bond 0.00254 (26220) covalent geometry : angle 0.52101 (35518) hydrogen bonds : bond 0.04343 ( 1195) hydrogen bonds : angle 4.65017 ( 3354) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 220 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 HIS cc_start: 0.7316 (m90) cc_final: 0.6826 (m90) REVERT: B 58 GLU cc_start: 0.6941 (mp0) cc_final: 0.6665 (mp0) REVERT: B 204 MET cc_start: 0.2356 (mtp) cc_final: 0.1972 (mtt) REVERT: B 212 PHE cc_start: 0.2722 (OUTLIER) cc_final: 0.0995 (p90) REVERT: B 251 ASN cc_start: 0.6899 (p0) cc_final: 0.6540 (t0) REVERT: C 206 LYS cc_start: 0.6706 (tttt) cc_final: 0.5631 (pttt) REVERT: C 223 THR cc_start: 0.4384 (m) cc_final: 0.3851 (p) REVERT: C 481 MET cc_start: 0.0558 (OUTLIER) cc_final: -0.0307 (mtm) REVERT: C 527 ASP cc_start: 0.7476 (p0) cc_final: 0.7193 (p0) REVERT: D 3 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7457 (mmmt) REVERT: D 30 ARG cc_start: 0.7460 (mtp85) cc_final: 0.6727 (mtt90) REVERT: D 31 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6062 (mm-30) REVERT: D 194 TYR cc_start: 0.7832 (m-80) cc_final: 0.7562 (m-80) REVERT: D 299 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7096 (tptm) REVERT: E 185 MET cc_start: 0.6439 (mpt) cc_final: 0.6052 (mmt) REVERT: E 260 ARG cc_start: 0.6266 (mtp-110) cc_final: 0.4057 (mmt180) REVERT: E 441 ARG cc_start: 0.4998 (mmt-90) cc_final: 0.3795 (mtp180) REVERT: E 460 GLU cc_start: 0.1797 (OUTLIER) cc_final: 0.1518 (mt-10) REVERT: E 521 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5740 (tp) REVERT: E 529 ARG cc_start: 0.7698 (mtp85) cc_final: 0.6431 (mtt180) REVERT: F 165 ARG cc_start: 0.8134 (mmt-90) cc_final: 0.7838 (mmt-90) REVERT: F 357 SER cc_start: 0.6743 (m) cc_final: 0.6060 (p) REVERT: F 380 MET cc_start: 0.2076 (tpt) cc_final: -0.0501 (ptt) outliers start: 87 outliers final: 43 residues processed: 284 average time/residue: 0.6155 time to fit residues: 205.3578 Evaluate side-chains 254 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 205 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 481 MET Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain F residue 410 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 65 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 303 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 318 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 354 GLN F 365 GLN L 501 GLN L 513 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.222608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.189859 restraints weight = 34176.581| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.39 r_work: 0.4026 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 26220 Z= 0.156 Angle : 0.576 11.343 35518 Z= 0.308 Chirality : 0.046 0.259 3930 Planarity : 0.005 0.057 4655 Dihedral : 5.993 76.837 3670 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 3.84 % Allowed : 16.70 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3305 helix: 0.69 (0.14), residues: 1457 sheet: 1.72 (0.26), residues: 368 loop : -1.37 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.018 0.002 TYR A 429 PHE 0.023 0.002 PHE D 477 TRP 0.011 0.001 TRP B 469 HIS 0.009 0.001 HIS L 513 Details of bonding type rmsd covalent geometry : bond 0.00363 (26220) covalent geometry : angle 0.57631 (35518) hydrogen bonds : bond 0.04943 ( 1195) hydrogen bonds : angle 4.73601 ( 3354) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 214 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 380 MET cc_start: 0.4448 (pmm) cc_final: 0.2049 (tpt) REVERT: B 8 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7284 (pt) REVERT: B 58 GLU cc_start: 0.6856 (mp0) cc_final: 0.6585 (mp0) REVERT: B 204 MET cc_start: 0.2480 (mtp) cc_final: 0.2079 (mtt) REVERT: B 212 PHE cc_start: 0.2778 (OUTLIER) cc_final: 0.1007 (p90) REVERT: B 251 ASN cc_start: 0.6866 (p0) cc_final: 0.6580 (t0) REVERT: B 508 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6417 (m-30) REVERT: C 141 TYR cc_start: 0.7114 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: C 206 LYS cc_start: 0.6644 (tttt) cc_final: 0.5642 (pttt) REVERT: C 223 THR cc_start: 0.4592 (m) cc_final: 0.4049 (p) REVERT: C 411 ILE cc_start: 0.6284 (OUTLIER) cc_final: 0.5681 (pt) REVERT: C 481 MET cc_start: 0.0597 (OUTLIER) cc_final: -0.0252 (mtm) REVERT: C 498 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5059 (mm) REVERT: C 527 ASP cc_start: 0.7420 (p0) cc_final: 0.7093 (p0) REVERT: D 3 LYS cc_start: 0.8185 (ttmm) cc_final: 0.7473 (mmmt) REVERT: D 30 ARG cc_start: 0.7434 (mtp85) cc_final: 0.6752 (mtt90) REVERT: D 31 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6028 (mm-30) REVERT: D 299 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.7137 (tptm) REVERT: E 185 MET cc_start: 0.6649 (mpt) cc_final: 0.6127 (mmt) REVERT: E 260 ARG cc_start: 0.6177 (mtp-110) cc_final: 0.3640 (mmt180) REVERT: E 309 ARG cc_start: 0.6268 (OUTLIER) cc_final: 0.5841 (mtt-85) REVERT: E 441 ARG cc_start: 0.5042 (mmt-90) cc_final: 0.3816 (mtp180) REVERT: E 460 GLU cc_start: 0.2014 (OUTLIER) cc_final: 0.1694 (mt-10) REVERT: E 521 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5703 (tp) REVERT: E 529 ARG cc_start: 0.7593 (mtp85) cc_final: 0.6425 (mtt180) REVERT: F 165 ARG cc_start: 0.8041 (mmt-90) cc_final: 0.7727 (mmt-90) REVERT: F 357 SER cc_start: 0.6630 (m) cc_final: 0.5902 (p) REVERT: F 380 MET cc_start: 0.2079 (OUTLIER) cc_final: -0.0504 (ptt) REVERT: F 526 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5366 (mt-10) outliers start: 103 outliers final: 59 residues processed: 288 average time/residue: 0.6127 time to fit residues: 207.8736 Evaluate side-chains 282 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 209 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 409 PHE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain E residue 7 GLN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 425 CYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 481 MET Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain L residue 525 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 254 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 chunk 28 optimal weight: 0.1980 chunk 141 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 252 optimal weight: 7.9990 chunk 307 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 HIS C 439 ASN F 365 GLN L 501 GLN L 513 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.223230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.190022 restraints weight = 34327.669| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.42 r_work: 0.4034 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26220 Z= 0.137 Angle : 0.549 10.727 35518 Z= 0.294 Chirality : 0.045 0.198 3930 Planarity : 0.005 0.058 4655 Dihedral : 5.938 77.236 3670 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 4.06 % Allowed : 17.11 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3305 helix: 0.78 (0.14), residues: 1457 sheet: 1.73 (0.26), residues: 368 loop : -1.35 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 304 TYR 0.016 0.001 TYR A 429 PHE 0.018 0.002 PHE D 319 TRP 0.010 0.001 TRP B 469 HIS 0.009 0.001 HIS L 513 Details of bonding type rmsd covalent geometry : bond 0.00312 (26220) covalent geometry : angle 0.54850 (35518) hydrogen bonds : bond 0.04585 ( 1195) hydrogen bonds : angle 4.62999 ( 3354) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 211 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 HIS cc_start: 0.7323 (m90) cc_final: 0.6821 (m90) REVERT: B 8 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7282 (pt) REVERT: B 58 GLU cc_start: 0.6864 (mp0) cc_final: 0.6599 (mp0) REVERT: B 155 GLN cc_start: 0.5981 (OUTLIER) cc_final: 0.5035 (mt0) REVERT: B 204 MET cc_start: 0.2472 (mtp) cc_final: 0.2135 (mtt) REVERT: B 212 PHE cc_start: 0.2791 (OUTLIER) cc_final: 0.1037 (p90) REVERT: B 251 ASN cc_start: 0.6884 (p0) cc_final: 0.6576 (t0) REVERT: B 508 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6396 (m-30) REVERT: C 141 TYR cc_start: 0.7090 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: C 160 LYS cc_start: 0.4818 (OUTLIER) cc_final: 0.4448 (tptp) REVERT: C 206 LYS cc_start: 0.6660 (tttt) cc_final: 0.5643 (pttt) REVERT: C 223 THR cc_start: 0.4448 (OUTLIER) cc_final: 0.3936 (p) REVERT: C 411 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5650 (pt) REVERT: C 481 MET cc_start: 0.0823 (OUTLIER) cc_final: -0.0154 (mtm) REVERT: C 498 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5054 (mm) REVERT: C 527 ASP cc_start: 0.7414 (p0) cc_final: 0.7119 (p0) REVERT: D 3 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7468 (mmmt) REVERT: D 30 ARG cc_start: 0.7413 (mtp85) cc_final: 0.6718 (mtt90) REVERT: D 31 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.5951 (mm-30) REVERT: D 299 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.7154 (tptm) REVERT: E 185 MET cc_start: 0.6594 (mpt) cc_final: 0.6182 (mmt) REVERT: E 260 ARG cc_start: 0.6160 (mtp-110) cc_final: 0.3965 (mmt180) REVERT: E 292 ILE cc_start: 0.6707 (mm) cc_final: 0.6413 (tp) REVERT: E 309 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5855 (mtt-85) REVERT: E 441 ARG cc_start: 0.4994 (mmt-90) cc_final: 0.3747 (mtp180) REVERT: E 460 GLU cc_start: 0.2068 (OUTLIER) cc_final: 0.1713 (mt-10) REVERT: E 529 ARG cc_start: 0.7551 (mtp85) cc_final: 0.6394 (mtt180) REVERT: F 165 ARG cc_start: 0.8027 (mmt-90) cc_final: 0.7715 (mmt-90) REVERT: F 357 SER cc_start: 0.6603 (m) cc_final: 0.5896 (p) REVERT: F 380 MET cc_start: 0.1993 (OUTLIER) cc_final: -0.0516 (ptt) REVERT: F 445 MET cc_start: 0.4673 (mtm) cc_final: 0.4244 (mtm) REVERT: F 526 GLU cc_start: 0.5697 (OUTLIER) cc_final: 0.5380 (mt-10) outliers start: 109 outliers final: 58 residues processed: 294 average time/residue: 0.5934 time to fit residues: 205.1221 Evaluate side-chains 280 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 206 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 425 CYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 481 MET Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain L residue 515 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 227 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 197 optimal weight: 0.0070 chunk 155 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 HIS ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 GLN L 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.222823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.189759 restraints weight = 34060.620| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.35 r_work: 0.4032 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26220 Z= 0.145 Angle : 0.561 10.699 35518 Z= 0.300 Chirality : 0.045 0.197 3930 Planarity : 0.005 0.061 4655 Dihedral : 5.906 77.602 3668 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 4.25 % Allowed : 17.29 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3305 helix: 0.75 (0.14), residues: 1457 sheet: 1.69 (0.26), residues: 368 loop : -1.40 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.017 0.002 TYR E 168 PHE 0.023 0.002 PHE D 477 TRP 0.015 0.001 TRP D 469 HIS 0.008 0.001 HIS L 513 Details of bonding type rmsd covalent geometry : bond 0.00335 (26220) covalent geometry : angle 0.56055 (35518) hydrogen bonds : bond 0.04693 ( 1195) hydrogen bonds : angle 4.63706 ( 3354) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 213 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 HIS cc_start: 0.7334 (m90) cc_final: 0.6798 (m90) REVERT: B 8 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7272 (pt) REVERT: B 58 GLU cc_start: 0.6846 (mp0) cc_final: 0.6547 (mp0) REVERT: B 204 MET cc_start: 0.2403 (mtp) cc_final: 0.2063 (mtt) REVERT: B 212 PHE cc_start: 0.2755 (OUTLIER) cc_final: 0.0998 (p90) REVERT: B 251 ASN cc_start: 0.6844 (p0) cc_final: 0.6585 (t0) REVERT: B 508 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6415 (m-30) REVERT: C 141 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6652 (m-80) REVERT: C 155 GLN cc_start: 0.5058 (tp40) cc_final: 0.4448 (tp40) REVERT: C 160 LYS cc_start: 0.4766 (OUTLIER) cc_final: 0.4486 (tptp) REVERT: C 206 LYS cc_start: 0.6562 (tttt) cc_final: 0.5622 (pttt) REVERT: C 223 THR cc_start: 0.4583 (OUTLIER) cc_final: 0.4059 (p) REVERT: C 411 ILE cc_start: 0.6254 (OUTLIER) cc_final: 0.5659 (pt) REVERT: C 445 MET cc_start: 0.2013 (mmp) cc_final: -0.1054 (mtp) REVERT: C 481 MET cc_start: 0.0612 (OUTLIER) cc_final: -0.0254 (mtm) REVERT: C 498 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5087 (mm) REVERT: C 527 ASP cc_start: 0.7412 (p0) cc_final: 0.7088 (p0) REVERT: D 3 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7467 (mmmt) REVERT: D 30 ARG cc_start: 0.7387 (mtp85) cc_final: 0.6711 (mtt90) REVERT: D 31 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.6018 (mm-30) REVERT: D 299 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7113 (tptm) REVERT: E 139 CYS cc_start: 0.6359 (OUTLIER) cc_final: 0.5290 (p) REVERT: E 185 MET cc_start: 0.6612 (mpt) cc_final: 0.6216 (mmt) REVERT: E 260 ARG cc_start: 0.6148 (mtp-110) cc_final: 0.3644 (mmt180) REVERT: E 292 ILE cc_start: 0.6693 (mm) cc_final: 0.6374 (tp) REVERT: E 309 ARG cc_start: 0.6210 (OUTLIER) cc_final: 0.5759 (mtt-85) REVERT: E 441 ARG cc_start: 0.4987 (mmt-90) cc_final: 0.3729 (mtp180) REVERT: E 460 GLU cc_start: 0.1966 (OUTLIER) cc_final: 0.1626 (mt-10) REVERT: E 529 ARG cc_start: 0.7570 (mtp85) cc_final: 0.6376 (mtt180) REVERT: F 165 ARG cc_start: 0.8025 (mmt-90) cc_final: 0.7686 (mmt-90) REVERT: F 231 GLU cc_start: 0.4711 (OUTLIER) cc_final: 0.3835 (mm-30) REVERT: F 357 SER cc_start: 0.6600 (m) cc_final: 0.5855 (p) REVERT: F 380 MET cc_start: 0.2090 (OUTLIER) cc_final: -0.0489 (ptt) REVERT: F 445 MET cc_start: 0.4610 (mtm) cc_final: 0.4221 (mtm) REVERT: L 546 MET cc_start: 0.5426 (OUTLIER) cc_final: 0.5175 (pp-130) REVERT: L 552 TYR cc_start: 0.6159 (OUTLIER) cc_final: 0.5555 (m-80) outliers start: 114 outliers final: 62 residues processed: 294 average time/residue: 0.6126 time to fit residues: 211.5062 Evaluate side-chains 294 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 214 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 141 TYR Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain D residue 490 ASN Chi-restraints excluded: chain E residue 7 GLN Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 425 CYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 546 MET Chi-restraints excluded: chain L residue 552 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 214 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 184 optimal weight: 0.0170 chunk 286 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 289 optimal weight: 9.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 153 GLN F 365 GLN L 501 GLN L 513 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.224997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.192221 restraints weight = 34186.561| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.47 r_work: 0.4057 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26220 Z= 0.108 Angle : 0.509 10.421 35518 Z= 0.271 Chirality : 0.044 0.200 3930 Planarity : 0.004 0.060 4655 Dihedral : 5.669 79.052 3668 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.36 % Favored : 96.58 % Rotamer: Outliers : 3.39 % Allowed : 18.34 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3305 helix: 1.00 (0.14), residues: 1457 sheet: 1.49 (0.25), residues: 412 loop : -1.23 (0.15), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.017 0.001 TYR A 248 PHE 0.019 0.001 PHE D 319 TRP 0.012 0.001 TRP D 469 HIS 0.007 0.001 HIS L 513 Details of bonding type rmsd covalent geometry : bond 0.00233 (26220) covalent geometry : angle 0.50898 (35518) hydrogen bonds : bond 0.03900 ( 1195) hydrogen bonds : angle 4.43512 ( 3354) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 217 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 HIS cc_start: 0.7322 (m90) cc_final: 0.6930 (m90) REVERT: B 8 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7273 (pt) REVERT: B 58 GLU cc_start: 0.6732 (mp0) cc_final: 0.6462 (mp0) REVERT: B 185 MET cc_start: 0.3716 (OUTLIER) cc_final: 0.3465 (ptp) REVERT: B 204 MET cc_start: 0.2482 (mtp) cc_final: 0.2129 (mtt) REVERT: B 251 ASN cc_start: 0.6835 (p0) cc_final: 0.6611 (t0) REVERT: B 449 GLN cc_start: 0.3172 (tt0) cc_final: 0.1685 (mp10) REVERT: C 155 GLN cc_start: 0.4994 (OUTLIER) cc_final: 0.4355 (tp40) REVERT: C 160 LYS cc_start: 0.4777 (OUTLIER) cc_final: 0.4425 (tptp) REVERT: C 206 LYS cc_start: 0.6570 (tttt) cc_final: 0.5625 (pttt) REVERT: C 223 THR cc_start: 0.4478 (OUTLIER) cc_final: 0.3960 (p) REVERT: C 381 VAL cc_start: 0.1748 (OUTLIER) cc_final: 0.1522 (p) REVERT: C 411 ILE cc_start: 0.6104 (OUTLIER) cc_final: 0.5541 (pt) REVERT: C 445 MET cc_start: 0.1976 (mmp) cc_final: -0.1025 (mtp) REVERT: C 481 MET cc_start: 0.0792 (OUTLIER) cc_final: -0.0161 (mtm) REVERT: C 527 ASP cc_start: 0.7224 (p0) cc_final: 0.6960 (p0) REVERT: D 3 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7447 (mmmt) REVERT: D 30 ARG cc_start: 0.7361 (mtp85) cc_final: 0.6647 (mtt90) REVERT: D 31 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5839 (mm-30) REVERT: D 299 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7125 (tptm) REVERT: E 139 CYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5327 (p) REVERT: E 185 MET cc_start: 0.6716 (mpt) cc_final: 0.6321 (mmt) REVERT: E 260 ARG cc_start: 0.6133 (mtp-110) cc_final: 0.3725 (mtt180) REVERT: E 292 ILE cc_start: 0.6625 (mm) cc_final: 0.6360 (tp) REVERT: E 397 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6930 (tpt) REVERT: E 441 ARG cc_start: 0.4890 (mmt-90) cc_final: 0.3635 (mtp180) REVERT: E 460 GLU cc_start: 0.2119 (OUTLIER) cc_final: 0.1736 (mt-10) REVERT: E 529 ARG cc_start: 0.7588 (mtp85) cc_final: 0.6400 (mtt180) REVERT: F 165 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7665 (mmt-90) REVERT: F 231 GLU cc_start: 0.4668 (OUTLIER) cc_final: 0.3747 (mm-30) REVERT: F 357 SER cc_start: 0.6600 (m) cc_final: 0.5898 (p) REVERT: F 380 MET cc_start: 0.2235 (OUTLIER) cc_final: -0.0386 (ptt) REVERT: F 445 MET cc_start: 0.4605 (mtm) cc_final: 0.4227 (mtm) REVERT: L 546 MET cc_start: 0.5440 (OUTLIER) cc_final: 0.5190 (pp-130) REVERT: L 552 TYR cc_start: 0.6091 (OUTLIER) cc_final: 0.5517 (m-80) outliers start: 91 outliers final: 47 residues processed: 286 average time/residue: 0.6047 time to fit residues: 202.7276 Evaluate side-chains 276 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 397 MET Chi-restraints excluded: chain E residue 425 CYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 365 GLN Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain L residue 546 MET Chi-restraints excluded: chain L residue 552 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 9 optimal weight: 7.9990 chunk 239 optimal weight: 0.0970 chunk 279 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 304 optimal weight: 0.6980 chunk 309 optimal weight: 0.2980 chunk 199 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 247 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 108 ASN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 ASN F 172 GLN L 501 GLN L 513 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.228986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.198630 restraints weight = 35070.988| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 2.15 r_work: 0.4160 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4073 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26220 Z= 0.097 Angle : 0.499 13.545 35518 Z= 0.264 Chirality : 0.043 0.190 3930 Planarity : 0.004 0.058 4655 Dihedral : 5.390 79.715 3663 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.55 % Rotamer: Outliers : 2.20 % Allowed : 19.64 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 3305 helix: 1.15 (0.14), residues: 1463 sheet: 1.47 (0.25), residues: 420 loop : -1.15 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 441 TYR 0.016 0.001 TYR A 248 PHE 0.027 0.001 PHE C 316 TRP 0.013 0.001 TRP D 469 HIS 0.008 0.001 HIS L 513 Details of bonding type rmsd covalent geometry : bond 0.00203 (26220) covalent geometry : angle 0.49874 (35518) hydrogen bonds : bond 0.03548 ( 1195) hydrogen bonds : angle 4.31723 ( 3354) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 HIS cc_start: 0.7364 (m90) cc_final: 0.6983 (m90) REVERT: B 8 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7250 (pt) REVERT: B 185 MET cc_start: 0.3752 (OUTLIER) cc_final: 0.3434 (ptp) REVERT: B 204 MET cc_start: 0.2557 (mtp) cc_final: 0.2193 (mtt) REVERT: B 251 ASN cc_start: 0.6837 (p0) cc_final: 0.6621 (t0) REVERT: B 449 GLN cc_start: 0.3166 (tt0) cc_final: 0.1662 (mp10) REVERT: C 155 GLN cc_start: 0.4822 (OUTLIER) cc_final: 0.4154 (tp40) REVERT: C 206 LYS cc_start: 0.6627 (tttt) cc_final: 0.5616 (pttt) REVERT: C 223 THR cc_start: 0.4527 (OUTLIER) cc_final: 0.4003 (p) REVERT: C 381 VAL cc_start: 0.1835 (OUTLIER) cc_final: 0.1602 (p) REVERT: C 397 MET cc_start: 0.5231 (ttt) cc_final: 0.3782 (tpt) REVERT: C 411 ILE cc_start: 0.6183 (OUTLIER) cc_final: 0.5583 (pt) REVERT: C 445 MET cc_start: 0.1836 (mmp) cc_final: -0.1087 (mtp) REVERT: C 481 MET cc_start: 0.0806 (OUTLIER) cc_final: -0.0240 (mtm) REVERT: C 527 ASP cc_start: 0.7255 (p0) cc_final: 0.6997 (p0) REVERT: D 3 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7482 (mmmt) REVERT: D 30 ARG cc_start: 0.7342 (mtp85) cc_final: 0.6599 (mtt90) REVERT: D 31 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5886 (mm-30) REVERT: D 299 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6915 (tptt) REVERT: E 260 ARG cc_start: 0.6239 (mtp-110) cc_final: 0.3795 (mtt180) REVERT: E 292 ILE cc_start: 0.6552 (mm) cc_final: 0.6290 (tp) REVERT: E 441 ARG cc_start: 0.4875 (mmt-90) cc_final: 0.3631 (mtp180) REVERT: E 460 GLU cc_start: 0.2062 (OUTLIER) cc_final: 0.1717 (mt-10) REVERT: E 529 ARG cc_start: 0.7721 (mtp85) cc_final: 0.6325 (mpp80) REVERT: F 165 ARG cc_start: 0.8042 (mmt-90) cc_final: 0.7714 (mmt-90) REVERT: F 357 SER cc_start: 0.6604 (m) cc_final: 0.5896 (p) REVERT: F 380 MET cc_start: 0.2174 (OUTLIER) cc_final: -0.0381 (ptt) REVERT: F 445 MET cc_start: 0.4484 (mtm) cc_final: 0.4113 (mtm) REVERT: L 546 MET cc_start: 0.5316 (OUTLIER) cc_final: 0.5069 (pp-130) REVERT: L 552 TYR cc_start: 0.6100 (OUTLIER) cc_final: 0.5528 (m-80) outliers start: 59 outliers final: 38 residues processed: 250 average time/residue: 0.5499 time to fit residues: 162.2029 Evaluate side-chains 254 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain L residue 546 MET Chi-restraints excluded: chain L residue 552 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 266 optimal weight: 10.0000 chunk 323 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 178 optimal weight: 0.4980 chunk 162 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN F 365 GLN L 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.226363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.194459 restraints weight = 35225.048| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 2.04 r_work: 0.4138 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4054 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26220 Z= 0.139 Angle : 0.551 7.981 35518 Z= 0.294 Chirality : 0.045 0.171 3930 Planarity : 0.005 0.060 4655 Dihedral : 5.546 79.032 3662 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 2.53 % Allowed : 19.53 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.14), residues: 3305 helix: 0.99 (0.14), residues: 1456 sheet: 1.75 (0.27), residues: 374 loop : -1.25 (0.15), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 268 TYR 0.017 0.001 TYR A 429 PHE 0.030 0.002 PHE B 15 TRP 0.011 0.001 TRP C 499 HIS 0.008 0.001 HIS L 513 Details of bonding type rmsd covalent geometry : bond 0.00319 (26220) covalent geometry : angle 0.55065 (35518) hydrogen bonds : bond 0.04392 ( 1195) hydrogen bonds : angle 4.47643 ( 3354) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6610 Ramachandran restraints generated. 3305 Oldfield, 0 Emsley, 3305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 204 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 HIS cc_start: 0.7487 (m90) cc_final: 0.7008 (m90) REVERT: B 8 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7289 (pt) REVERT: B 58 GLU cc_start: 0.6916 (mp0) cc_final: 0.6636 (mp0) REVERT: B 204 MET cc_start: 0.2619 (mtp) cc_final: 0.2270 (mtt) REVERT: B 212 PHE cc_start: 0.2758 (OUTLIER) cc_final: 0.1005 (p90) REVERT: B 251 ASN cc_start: 0.6924 (p0) cc_final: 0.6695 (t0) REVERT: B 449 GLN cc_start: 0.3303 (tt0) cc_final: 0.1776 (mp10) REVERT: C 155 GLN cc_start: 0.5103 (OUTLIER) cc_final: 0.4407 (tp40) REVERT: C 160 LYS cc_start: 0.4671 (OUTLIER) cc_final: 0.4362 (tptp) REVERT: C 206 LYS cc_start: 0.6613 (tttt) cc_final: 0.5627 (pttt) REVERT: C 223 THR cc_start: 0.4652 (OUTLIER) cc_final: 0.4111 (p) REVERT: C 381 VAL cc_start: 0.1834 (OUTLIER) cc_final: 0.1583 (p) REVERT: C 397 MET cc_start: 0.5205 (ttt) cc_final: 0.3812 (tpt) REVERT: C 411 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.5736 (pt) REVERT: C 445 MET cc_start: 0.1993 (mmp) cc_final: -0.1016 (mtp) REVERT: C 481 MET cc_start: 0.1031 (OUTLIER) cc_final: -0.0164 (mtm) REVERT: C 527 ASP cc_start: 0.7342 (p0) cc_final: 0.7040 (p0) REVERT: D 3 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7504 (mmmt) REVERT: D 30 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6700 (mtt90) REVERT: D 31 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5993 (mm-30) REVERT: D 299 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6946 (tptm) REVERT: E 260 ARG cc_start: 0.6341 (mtp-110) cc_final: 0.3792 (mmt180) REVERT: E 292 ILE cc_start: 0.6599 (mm) cc_final: 0.6292 (tp) REVERT: E 441 ARG cc_start: 0.5007 (mmt-90) cc_final: 0.3752 (mtp180) REVERT: E 460 GLU cc_start: 0.2229 (OUTLIER) cc_final: 0.1804 (mt-10) REVERT: E 529 ARG cc_start: 0.7698 (mtp85) cc_final: 0.6431 (mtt180) REVERT: F 165 ARG cc_start: 0.8069 (mmt-90) cc_final: 0.7729 (mmt-90) REVERT: F 207 ASN cc_start: 0.7133 (t0) cc_final: 0.6060 (m-40) REVERT: F 357 SER cc_start: 0.6642 (m) cc_final: 0.5910 (p) REVERT: F 380 MET cc_start: 0.2196 (OUTLIER) cc_final: -0.0371 (ptt) REVERT: F 445 MET cc_start: 0.4563 (mtm) cc_final: 0.4197 (mtm) REVERT: L 552 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5569 (m-80) outliers start: 68 outliers final: 45 residues processed: 256 average time/residue: 0.5775 time to fit residues: 173.7633 Evaluate side-chains 264 residues out of total 2683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 MET Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 22 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 480 GLN Chi-restraints excluded: chain C residue 481 MET Chi-restraints excluded: chain C residue 509 THR Chi-restraints excluded: chain D residue 31 GLU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 487 THR Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 239 CYS Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 460 GLU Chi-restraints excluded: chain E residue 518 SER Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 374 GLN Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 MET Chi-restraints excluded: chain L residue 552 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 131 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 199 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 174 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 365 GLN L 501 GLN L 513 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.225303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.192997 restraints weight = 35204.385| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 2.07 r_work: 0.4129 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4045 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26220 Z= 0.157 Angle : 0.585 14.179 35518 Z= 0.312 Chirality : 0.046 0.167 3930 Planarity : 0.005 0.062 4655 Dihedral : 5.715 78.349 3662 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 2.91 % Allowed : 19.27 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3305 helix: 0.91 (0.14), residues: 1417 sheet: 1.74 (0.27), residues: 367 loop : -1.30 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 268 TYR 0.019 0.002 TYR E 168 PHE 0.026 0.002 PHE D 477 TRP 0.013 0.002 TRP C 499 HIS 0.009 0.001 HIS L 513 Details of bonding type rmsd covalent geometry : bond 0.00366 (26220) covalent geometry : angle 0.58515 (35518) hydrogen bonds : bond 0.04826 ( 1195) hydrogen bonds : angle 4.61192 ( 3354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9630.84 seconds wall clock time: 164 minutes 41.11 seconds (9881.11 seconds total)