Starting phenix.real_space_refine on Sun Jul 5 00:06:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y5a_33614/07_2026/7y5a_33614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y5a_33614/07_2026/7y5a_33614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y5a_33614/07_2026/7y5a_33614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y5a_33614/07_2026/7y5a_33614.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y5a_33614/07_2026/7y5a_33614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y5a_33614/07_2026/7y5a_33614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y5a_33614/07_2026/7y5a_33614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y5a_33614/07_2026/7y5a_33614.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 5 5.21 5 S 74 5.16 5 C 15085 2.51 5 N 4198 2.21 5 O 4600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23975 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3766 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 22, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3713 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 20, 'TRANS': 472} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3643 Classifications: {'peptide': 489} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 20, 'TRANS': 468} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3495 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3486 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ASP:plan': 11, 'GLU:plan': 5, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "F" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3525 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 440} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2195 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.35, per 1000 atoms: 0.18 Number of scatterers: 23975 At special positions: 0 Unit cell: (129.8, 156.2, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 13 15.00 Mg 5 11.99 O 4600 8.00 N 4198 7.00 C 15085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 897.0 milliseconds 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5754 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 24 sheets defined 46.3% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 4.159A pdb=" N LYS A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.988A pdb=" N PHE A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 107 " --> pdb=" O ASP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 179 through 189 Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.211A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 3.536A pdb=" N ILE A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 262 removed outlier: 3.627A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Proline residue: A 250 - end of helix removed outlier: 4.104A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.878A pdb=" N LEU A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 removed outlier: 3.739A pdb=" N THR A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.599A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 392 through 408 removed outlier: 4.224A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.558A pdb=" N LEU A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 454 through 457 Processing helix chain 'A' and resid 464 through 478 removed outlier: 3.569A pdb=" N GLU A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.871A pdb=" N ASP A 484 " --> pdb=" O SER A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.795A pdb=" N LYS A 509 " --> pdb=" O ASN A 505 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.930A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.521A pdb=" N VAL B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 195 removed outlier: 3.758A pdb=" N THR B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 248 through 262 removed outlier: 3.770A pdb=" N HIS B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.891A pdb=" N LEU B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 297 Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 383 through 403 removed outlier: 3.887A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.694A pdb=" N ALA B 407 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 414 through 432 removed outlier: 4.569A pdb=" N LYS B 432 " --> pdb=" O VAL B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 460 through 479 removed outlier: 3.849A pdb=" N GLN B 465 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.535A pdb=" N ASP B 484 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 511 removed outlier: 3.987A pdb=" N LYS B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.539A pdb=" N ASP C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA C 158 " --> pdb=" O LYS C 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 158' Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.953A pdb=" N GLY C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 242 through 262 removed outlier: 3.984A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) Proline residue: C 250 - end of helix removed outlier: 4.128A pdb=" N ILE C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 293 through 297 removed outlier: 4.148A pdb=" N ALA C 296 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 311 Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.731A pdb=" N THR C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.597A pdb=" N ALA C 390 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.832A pdb=" N ASP C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 431 removed outlier: 3.551A pdb=" N LEU C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 454 removed outlier: 3.839A pdb=" N GLY C 454 " --> pdb=" O LEU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 478 removed outlier: 3.560A pdb=" N PHE C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU C 472 " --> pdb=" O GLU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 490 removed outlier: 3.838A pdb=" N ASP C 484 " --> pdb=" O SER C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 506 Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.521A pdb=" N PHE C 511 " --> pdb=" O LYS C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 147 Processing helix chain 'D' and resid 165 through 178 removed outlier: 3.647A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 223 through 228 removed outlier: 3.889A pdb=" N ARG D 227 " --> pdb=" O PRO D 223 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET D 228 " --> pdb=" O PRO D 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 223 through 228' Processing helix chain 'D' and resid 229 through 245 Processing helix chain 'D' and resid 256 through 270 removed outlier: 3.993A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU D 265 " --> pdb=" O GLN D 261 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL D 266 " --> pdb=" O ALA D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 295 removed outlier: 3.972A pdb=" N GLU D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.850A pdb=" N ASP D 313 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 326 removed outlier: 3.976A pdb=" N ALA D 321 " --> pdb=" O ASP D 317 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR D 322 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 347 through 351 removed outlier: 4.152A pdb=" N SER D 351 " --> pdb=" O PRO D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 390 removed outlier: 3.712A pdb=" N TYR D 366 " --> pdb=" O GLY D 362 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE D 388 " --> pdb=" O ASP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 394 removed outlier: 3.515A pdb=" N LEU D 394 " --> pdb=" O ILE D 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 395 through 412 Processing helix chain 'D' and resid 419 through 424 removed outlier: 3.504A pdb=" N THR D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 445 Processing helix chain 'D' and resid 446 through 450 removed outlier: 4.195A pdb=" N HIS D 449 " --> pdb=" O GLU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.521A pdb=" N PHE D 456 " --> pdb=" O GLN D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 470 Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.627A pdb=" N ASP E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU E 146 " --> pdb=" O LYS E 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 141 through 146' Processing helix chain 'E' and resid 165 through 180 removed outlier: 3.532A pdb=" N LEU E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 208 Processing helix chain 'E' and resid 225 through 246 removed outlier: 3.763A pdb=" N ARG E 229 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN E 245 " --> pdb=" O PHE E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 271 removed outlier: 4.093A pdb=" N THR E 260 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 294 removed outlier: 3.558A pdb=" N GLU E 286 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE E 294 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 324 Processing helix chain 'E' and resid 357 through 387 removed outlier: 7.664A pdb=" N ASP E 363 " --> pdb=" O ALA E 359 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N GLU E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N HIS E 365 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR E 366 " --> pdb=" O GLY E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 394 Processing helix chain 'E' and resid 395 through 412 Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.576A pdb=" N THR E 435 " --> pdb=" O PRO E 431 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 444 " --> pdb=" O ASP E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 450 Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.950A pdb=" N PHE E 455 " --> pdb=" O PRO E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'F' and resid 141 through 147 Processing helix chain 'F' and resid 165 through 179 removed outlier: 4.160A pdb=" N ARG F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 removed outlier: 3.852A pdb=" N GLY F 197 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP F 206 " --> pdb=" O VAL F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 228 removed outlier: 3.723A pdb=" N MET F 228 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 244 Processing helix chain 'F' and resid 255 through 271 removed outlier: 3.856A pdb=" N PHE F 259 " --> pdb=" O ASN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 292 removed outlier: 3.534A pdb=" N GLU F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 314 Processing helix chain 'F' and resid 317 through 324 removed outlier: 3.936A pdb=" N THR F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 334 through 341 Processing helix chain 'F' and resid 347 through 351 removed outlier: 3.640A pdb=" N SER F 351 " --> pdb=" O PRO F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 389 removed outlier: 3.901A pdb=" N TYR F 366 " --> pdb=" O GLY F 362 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL F 368 " --> pdb=" O GLU F 364 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 412 Processing helix chain 'F' and resid 418 through 422 removed outlier: 4.321A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 445 Processing helix chain 'F' and resid 451 through 455 removed outlier: 3.551A pdb=" N ALA F 454 " --> pdb=" O PRO F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 470 removed outlier: 3.872A pdb=" N GLU F 469 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 61 removed outlier: 3.838A pdb=" N ALA G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Proline residue: G 45 - end of helix removed outlier: 4.392A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 69 Processing helix chain 'G' and resid 91 through 111 removed outlier: 3.836A pdb=" N VAL G 96 " --> pdb=" O TYR G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 130 removed outlier: 3.738A pdb=" N LEU G 124 " --> pdb=" O GLY G 120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE G 129 " --> pdb=" O GLY G 125 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG G 130 " --> pdb=" O TYR G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.695A pdb=" N ALA G 150 " --> pdb=" O THR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 302 removed outlier: 4.005A pdb=" N LEU G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Proline residue: G 237 - end of helix removed outlier: 4.581A pdb=" N ASP G 272 " --> pdb=" O ASP G 268 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU G 273 " --> pdb=" O ASN G 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.598A pdb=" N THR A 33 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 45 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N HIS A 43 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 37 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 67 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 66 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU A 54 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 55 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.518A pdb=" N ALA A 236 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 325 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE A 271 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.619A pdb=" N LEU A 355 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 540 removed outlier: 6.435A pdb=" N VAL A 538 " --> pdb=" O GLU G 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 37 removed outlier: 3.810A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 43 " --> pdb=" O ASP B 36 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 67 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 101 removed outlier: 3.666A pdb=" N ARG B 130 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 331 removed outlier: 8.524A pdb=" N ILE B 330 " --> pdb=" O GLN B 168 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE B 170 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 31 through 37 removed outlier: 3.693A pdb=" N THR C 33 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N HIS C 43 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA C 37 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN C 68 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 77 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA C 66 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 66 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU C 54 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C 55 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 99 through 102 Processing sheet with id=AB3, first strand: chain 'C' and resid 109 through 111 removed outlier: 6.373A pdb=" N ARG C 109 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA C 236 " --> pdb=" O ARG C 109 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL C 111 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 207 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR C 325 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 271 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE C 170 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 16 removed outlier: 6.832A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 88 through 89 removed outlier: 3.810A pdb=" N VAL D 88 " --> pdb=" O TRP D 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP D 118 " --> pdb=" O VAL D 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 98 through 99 removed outlier: 3.816A pdb=" N PHE D 217 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N SER D 185 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N VAL D 216 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE D 187 " --> pdb=" O VAL D 216 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N GLY D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY D 189 " --> pdb=" O GLY D 218 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 254 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL D 190 " --> pdb=" O ASP D 254 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE D 156 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.697A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LEU E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU E 39 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU E 78 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL E 79 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY E 10 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.898A pdb=" N GLU E 116 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.667A pdb=" N PHE E 99 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN E 219 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY E 191 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL E 249 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 303 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 307 " --> pdb=" O ILE E 253 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99 removed outlier: 6.667A pdb=" N PHE E 99 " --> pdb=" O PHE E 217 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLN E 219 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY E 191 " --> pdb=" O GLY E 218 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL E 249 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR E 303 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA E 307 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E 159 " --> pdb=" O THR E 331 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 136 through 137 removed outlier: 4.101A pdb=" N TYR E 150 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 15 removed outlier: 6.974A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU F 61 " --> pdb=" O HIS F 56 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N HIS F 56 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG F 63 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS F 47 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N GLU F 39 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU F 78 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL F 79 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 10 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 87 through 89 Processing sheet with id=AC5, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.571A pdb=" N PHE F 99 " --> pdb=" O PHE F 217 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLN F 219 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA F 214 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE F 187 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL F 216 " --> pdb=" O PHE F 187 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE F 156 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL F 308 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU F 158 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA F 329 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA F 157 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR F 331 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER F 352 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 136 through 138 removed outlier: 10.624A pdb=" N GLU G 136 " --> pdb=" O PRO G 114 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU G 116 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N TRP G 138 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL G 118 " --> pdb=" O TRP G 138 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 12.314A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) 1096 hydrogen bonds defined for protein. 3135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8159 1.34 - 1.46: 4843 1.46 - 1.58: 11226 1.58 - 1.70: 19 1.70 - 1.81: 130 Bond restraints: 24377 Sorted by residual: bond pdb=" CA HIS D 326 " pdb=" C HIS D 326 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.20e-02 6.94e+03 1.83e+00 bond pdb=" N SER D 119 " pdb=" CA SER D 119 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.55e+00 bond pdb=" CA SER C 437 " pdb=" CB SER C 437 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.22e+00 bond pdb=" C PHE F 343 " pdb=" N PRO F 344 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.16e+00 bond pdb=" CA VAL D 277 " pdb=" C VAL D 277 " ideal model delta sigma weight residual 1.523 1.536 -0.013 1.27e-02 6.20e+03 1.12e+00 ... (remaining 24372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 32514 1.94 - 3.88: 477 3.88 - 5.82: 70 5.82 - 7.77: 10 7.77 - 9.71: 4 Bond angle restraints: 33075 Sorted by residual: angle pdb=" N TRP D 118 " pdb=" CA TRP D 118 " pdb=" C TRP D 118 " ideal model delta sigma weight residual 108.34 114.95 -6.61 1.31e+00 5.83e-01 2.55e+01 angle pdb=" C PHE C 340 " pdb=" N ILE C 341 " pdb=" CA ILE C 341 " ideal model delta sigma weight residual 120.33 123.34 -3.01 8.00e-01 1.56e+00 1.41e+01 angle pdb=" N ILE D 120 " pdb=" CA ILE D 120 " pdb=" C ILE D 120 " ideal model delta sigma weight residual 113.53 110.13 3.40 9.80e-01 1.04e+00 1.20e+01 angle pdb=" CB MET E 67 " pdb=" CG MET E 67 " pdb=" SD MET E 67 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C PHE A 340 " pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta sigma weight residual 120.33 122.92 -2.59 8.00e-01 1.56e+00 1.05e+01 ... (remaining 33070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 13231 17.84 - 35.69: 1136 35.69 - 53.53: 214 53.53 - 71.37: 45 71.37 - 89.22: 32 Dihedral angle restraints: 14658 sinusoidal: 5697 harmonic: 8961 Sorted by residual: dihedral pdb=" CA ARG E 258 " pdb=" C ARG E 258 " pdb=" N PHE E 259 " pdb=" CA PHE E 259 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLY D 263 " pdb=" C GLY D 263 " pdb=" N SER D 264 " pdb=" CA SER D 264 " ideal model delta harmonic sigma weight residual 180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ILE B 383 " pdb=" C ILE B 383 " pdb=" N LYS B 384 " pdb=" CA LYS B 384 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 14655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2579 0.034 - 0.067: 840 0.067 - 0.101: 284 0.101 - 0.135: 124 0.135 - 0.168: 4 Chirality restraints: 3831 Sorted by residual: chirality pdb=" CA TRP D 118 " pdb=" N TRP D 118 " pdb=" C TRP D 118 " pdb=" CB TRP D 118 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CB VAL B 102 " pdb=" CA VAL B 102 " pdb=" CG1 VAL B 102 " pdb=" CG2 VAL B 102 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CG LEU D 146 " pdb=" CB LEU D 146 " pdb=" CD1 LEU D 146 " pdb=" CD2 LEU D 146 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 3828 not shown) Planarity restraints: 4320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 310 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.20e+00 pdb=" N PRO E 311 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO E 311 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 311 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 430 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.33e+00 pdb=" N PRO D 431 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 431 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 431 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 430 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO E 431 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 431 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 431 " 0.025 5.00e-02 4.00e+02 ... (remaining 4317 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 208 2.57 - 3.15: 19995 3.15 - 3.73: 37296 3.73 - 4.32: 46952 4.32 - 4.90: 78930 Nonbonded interactions: 183381 Sorted by model distance: nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.986 2.170 nonbonded pdb=" O1A ATP B 600 " pdb="MG MG B 601 " model vdw 2.014 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.026 2.170 nonbonded pdb=" O1G ATP B 600 " pdb="MG MG B 601 " model vdw 2.059 2.170 nonbonded pdb=" O3B ADP F 600 " pdb="MG MG F 601 " model vdw 2.074 2.170 ... (remaining 183376 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 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 44 or (resid 45 and (name N or name CA or name C or name \ O or name CB )) or resid 46 through 132 or (resid 133 and (name N or name CA or \ name C or name O or name CB )) or resid 134 through 355 or (resid 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 or (resid 358 and (n \ ame N or name CA or name C or name O or name CB )) or resid 359 through 400 or ( \ resid 401 through 402 and (name N or name CA or name C or name O or name CB )) o \ r resid 403 through 410 or resid 414 through 416 or (resid 417 through 419 and ( \ name N or name CA or name C or name O or name CB )) or resid 420 through 461 or \ (resid 462 through 463 and (name N or name CA or name C or name O or name CB )) \ or resid 464 through 467 or (resid 468 and (name N or name CA or name C or name \ O or name CB )) or resid 469 or (resid 470 and (name N or name CA or name C or n \ ame O or name CB )) or resid 471 through 475 or (resid 476 through 477 and (name \ N or name CA or name C or name O or name CB )) or resid 478 through 494 or (res \ id 495 through 499 and (name N or name CA or name C or name O or name CB )) or r \ esid 500 through 505 or (resid 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 through 515 or resid 537 through 538 or resid 540 or re \ sid 600 through 601)) selection = (chain 'B' and ((resid 29 and (name N or name CA or name C or name O or name CB \ )) or resid 30 through 44 or (resid 45 and (name N or name CA or name C or name \ O or name CB )) or resid 46 through 132 or (resid 133 and (name N or name CA or \ name C or name O or name CB )) or resid 134 through 190 or (resid 191 through 19 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 193 through \ 316 or (resid 317 and (name N or name CA or name C or name O or name CB )) or re \ sid 318 through 355 or (resid 356 and (name N or name CA or name C or name O or \ name CB )) or resid 357 or (resid 358 and (name N or name CA or name C or name O \ or name CB )) or resid 359 through 401 or (resid 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 410 or resid 414 through 416 \ or (resid 417 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 through 467 or (resid 468 and (name N or name C \ A or name C or name O or name CB )) or resid 469 through 475 or (resid 476 throu \ gh 477 and (name N or name CA or name C or name O or name CB )) or resid 478 thr \ ough 493 or (resid 494 through 499 and (name N or name CA or name C or name O or \ name CB )) or resid 500 through 505 or (resid 506 and (name N or name CA or nam \ e C or name O or name CB )) or resid 507 through 514 or (resid 515 and (name N o \ r name CA or name C or name O or name CB )) or resid 518 through 601)) selection = (chain 'C' and (resid 29 through 190 or (resid 191 through 192 and (name N or na \ me CA or name C or name O or name CB )) or resid 193 through 316 or (resid 317 a \ nd (name N or name CA or name C or name O or name CB )) or resid 318 through 400 \ or (resid 401 through 402 and (name N or name CA or name C or name O or name CB \ )) or resid 403 through 456 or (resid 457 and (name N or name CA or name C or n \ ame O or name CB )) or resid 458 through 469 or (resid 470 and (name N or name C \ A or name C or name O or name CB )) or resid 471 through 493 or (resid 494 throu \ gh 499 and (name N or name CA or name C or name O or name CB )) or resid 500 thr \ ough 515 or resid 518 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 or (resid 107 through 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 198 or (resid 199 and (name N or name CA or name C or name O or name \ CB )) or resid 200 through 202 or (resid 203 and (name N or name CA or name C o \ r name O or name CB )) or resid 204 through 205 or (resid 206 through 207 and (n \ ame N or name CA or name C or name O or name CB )) or resid 208 through 285 or ( \ resid 286 and (name N or name CA or name C or name O or name CB )) or resid 287 \ through 362 or (resid 363 through 364 and (name N or name CA or name C or name O \ or name CB )) or resid 365 through 369 or (resid 370 through 371 and (name N or \ name CA or name C or name O or name CB )) or resid 372 through 380 or (resid 38 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 382 through \ 391 or (resid 392 through 393 and (name N or name CA or name C or name O or name \ CB )) or resid 394 through 402 or (resid 403 and (name N or name CA or name C o \ r name O or name CB )) or resid 404 through 424 or (resid 425 and (name N or nam \ e CA or name C or name O or name CB )) or resid 426 through 471)) selection = (chain 'E' and (resid 8 through 104 or (resid 105 and (name N or name CA or name \ C or name O or name CB )) or resid 106 through 137 or (resid 138 and (name N or \ name CA or name C or name O or name CB )) or resid 139 through 220 or (resid 22 \ 1 through 222 and (name N or name CA or name C or name O or name CB )) or resid \ 223 through 285 or (resid 286 and (name N or name CA or name C or name O or name \ CB )) or resid 287 through 288 or (resid 289 and (name N or name CA or name C o \ r name O or name CB )) or resid 290 through 291 or (resid 292 and (name N or nam \ e CA or name C or name O or name CB )) or resid 293 through 370 or (resid 371 an \ d (name N or name CA or name C or name O or name CB )) or resid 372 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 461 or (resid 462 through 463 and (name N or name CA or \ name C or name O or name CB )) or resid 464 through 465 or (resid 466 and (name \ N or name CA or name C or name O or name CB )) or resid 467 through 471)) selection = (chain 'F' and (resid 8 through 103 or (resid 104 through 105 and (name N or nam \ e CA or name C or name O or name CB )) or resid 106 through 107 or (resid 108 an \ d (name N or name CA or name C or name O or name CB )) or resid 109 through 113 \ or (resid 114 and (name N or name CA or name C or name O or name CB )) or resid \ 115 through 134 or (resid 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 198 or (resid 199 and (name N or nam \ e CA or name C or name O or name CB )) or resid 200 through 202 or (resid 203 an \ d (name N or name CA or name C or name O or name CB )) or resid 204 through 205 \ or (resid 206 through 207 and (name N or name CA or name C or name O or name CB \ )) or resid 208 through 220 or (resid 221 through 222 and (name N or name CA or \ name C or name O or name CB )) or resid 223 through 291 or (resid 292 and (name \ N or name CA or name C or name O or name CB )) or resid 293 through 369 or (resi \ d 370 through 371 and (name N or name CA or name C or name O or name CB )) or re \ sid 372 through 380 or (resid 381 and (name N or name CA or name C or name O or \ name CB )) or resid 382 through 383 or (resid 384 and (name N or name CA or name \ C or name O or name CB )) or resid 385 through 391 or (resid 392 through 393 an \ d (name N or name CA or name C or name O or name CB )) or resid 394 through 395 \ or (resid 396 through 398 and (name N or name CA or name C or name O or name CB \ )) or resid 399 through 402 or (resid 403 and (name N or name CA or name C or na \ me O or name CB )) or resid 404 through 432 or (resid 433 and (name N or name CA \ or name C or name O or name CB )) or resid 434 through 461 or (resid 462 throug \ h 463 and (name N or name CA or name C or name O or name CB )) or resid 464 thro \ ugh 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) o \ r resid 467 through 471)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.100 Set scattering table: 0.040 Process input model: 19.000 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24377 Z= 0.129 Angle : 0.595 9.708 33075 Z= 0.322 Chirality : 0.041 0.168 3831 Planarity : 0.004 0.062 4320 Dihedral : 14.472 89.218 8904 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.04 % Allowed : 0.20 % Favored : 99.76 % 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: 0.45 (0.15), residues: 3142 helix: 1.55 (0.15), residues: 1218 sheet: 0.71 (0.25), residues: 401 loop : -0.86 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 229 TYR 0.010 0.001 TYR C 231 PHE 0.017 0.001 PHE D 439 TRP 0.012 0.001 TRP G 138 HIS 0.004 0.001 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (24377) covalent geometry : angle 0.59537 / 0.32 (33075) hydrogen bonds : bond 0.16164 / 10.60 ( 1088) hydrogen bonds : angle 6.21091 / 4.40 ( 3135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: C 261 MET cc_start: 0.7827 (mmm) cc_final: 0.7372 (tpt) REVERT: D 255 ASN cc_start: 0.8213 (t0) cc_final: 0.7732 (t0) REVERT: D 273 MET cc_start: 0.8918 (mmm) cc_final: 0.8643 (mtt) REVERT: D 309 TYR cc_start: 0.8124 (t80) cc_final: 0.7908 (t80) REVERT: D 323 THR cc_start: 0.8902 (p) cc_final: 0.8691 (p) REVERT: E 343 PHE cc_start: 0.8609 (t80) cc_final: 0.8347 (t80) REVERT: F 365 HIS cc_start: 0.7228 (m90) cc_final: 0.6822 (m170) REVERT: G 53 MET cc_start: 0.8716 (ppp) cc_final: 0.8493 (ppp) outliers start: 1 outliers final: 0 residues processed: 120 average time/residue: 0.1325 time to fit residues: 27.3799 Evaluate side-chains 100 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.050115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.041130 restraints weight = 141097.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.042299 restraints weight = 74580.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.043115 restraints weight = 48189.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.043690 restraints weight = 35229.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.044060 restraints weight = 27804.371| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24377 Z= 0.179 Angle : 0.573 7.583 33075 Z= 0.299 Chirality : 0.042 0.149 3831 Planarity : 0.004 0.048 4320 Dihedral : 4.909 78.029 3427 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.24 % Allowed : 6.49 % Favored : 93.26 % 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: 0.46 (0.15), residues: 3142 helix: 1.62 (0.15), residues: 1249 sheet: 0.56 (0.24), residues: 427 loop : -0.95 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 258 TYR 0.018 0.001 TYR E 366 PHE 0.013 0.001 PHE D 259 TRP 0.019 0.001 TRP D 118 HIS 0.004 0.001 HIS C 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (24377) covalent geometry : angle 0.57311 / 0.30 (33075) hydrogen bonds : bond 0.05507 / 3.71 ( 1088) hydrogen bonds : angle 4.86243 / 3.48 ( 3135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 300 ASP cc_start: 0.7240 (t0) cc_final: 0.7014 (t0) REVERT: D 255 ASN cc_start: 0.7943 (t160) cc_final: 0.7552 (t0) REVERT: D 309 TYR cc_start: 0.8201 (t80) cc_final: 0.7974 (t80) REVERT: E 343 PHE cc_start: 0.8567 (t80) cc_final: 0.8251 (t80) REVERT: G 53 MET cc_start: 0.8743 (ppp) cc_final: 0.8465 (ppp) REVERT: G 206 MET cc_start: 0.6886 (ppp) cc_final: 0.6610 (ppp) REVERT: G 288 GLN cc_start: 0.9004 (tp40) cc_final: 0.8506 (tp-100) outliers start: 6 outliers final: 4 residues processed: 109 average time/residue: 0.1362 time to fit residues: 25.4294 Evaluate side-chains 103 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain F residue 305 MET Chi-restraints excluded: chain G residue 292 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 110 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 302 optimal weight: 20.0000 chunk 241 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 284 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN A 382 GLN B 43 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.048660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.039657 restraints weight = 142533.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.040806 restraints weight = 75842.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.041603 restraints weight = 49258.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042163 restraints weight = 36118.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.042525 restraints weight = 28634.847| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 24377 Z= 0.238 Angle : 0.623 7.895 33075 Z= 0.326 Chirality : 0.043 0.185 3831 Planarity : 0.004 0.053 4320 Dihedral : 5.229 78.873 3427 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.77 % Allowed : 11.62 % Favored : 87.62 % 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: 0.29 (0.15), residues: 3142 helix: 1.45 (0.15), residues: 1248 sheet: 0.54 (0.24), residues: 427 loop : -1.04 (0.16), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 229 TYR 0.018 0.001 TYR C 231 PHE 0.018 0.002 PHE B 340 TRP 0.034 0.002 TRP D 118 HIS 0.008 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (24377) covalent geometry : angle 0.62287 / 0.33 (33075) hydrogen bonds : bond 0.06105 / 4.09 ( 1088) hydrogen bonds : angle 4.82507 / 3.44 ( 3135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.832 Fit side-chains REVERT: A 300 ASP cc_start: 0.7532 (t0) cc_final: 0.7282 (t0) REVERT: C 324 MET cc_start: 0.8221 (mmm) cc_final: 0.7418 (tpp) REVERT: D 255 ASN cc_start: 0.8026 (t160) cc_final: 0.7574 (t0) REVERT: D 287 MET cc_start: 0.8788 (ttp) cc_final: 0.8553 (ttm) REVERT: D 309 TYR cc_start: 0.8370 (t80) cc_final: 0.8156 (t80) REVERT: E 255 ASN cc_start: 0.6621 (t0) cc_final: 0.5956 (t0) REVERT: G 53 MET cc_start: 0.8695 (ppp) cc_final: 0.8422 (ppp) REVERT: G 288 GLN cc_start: 0.8961 (tp40) cc_final: 0.8518 (tp-100) REVERT: G 292 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7946 (pt0) outliers start: 19 outliers final: 11 residues processed: 120 average time/residue: 0.1321 time to fit residues: 27.0992 Evaluate side-chains 110 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain G residue 292 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 117 optimal weight: 0.0570 chunk 313 optimal weight: 2.9990 chunk 78 optimal weight: 0.2980 chunk 82 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 229 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 272 optimal weight: 0.9990 overall best weight: 1.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN A 382 GLN C 121 GLN D 326 HIS E 171 GLN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.041372 restraints weight = 139911.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.042558 restraints weight = 74181.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043386 restraints weight = 47968.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.043960 restraints weight = 35001.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.044346 restraints weight = 27659.274| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.002 0.024 24377 Z= 0.107 Angle : 0.521 8.029 33075 Z= 0.267 Chirality : 0.041 0.140 3831 Planarity : 0.004 0.061 4320 Dihedral : 4.924 88.048 3427 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.41 % Allowed : 13.47 % Favored : 85.11 % 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: 0.55 (0.15), residues: 3142 helix: 1.74 (0.15), residues: 1252 sheet: 0.69 (0.24), residues: 410 loop : -0.97 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 406 TYR 0.022 0.001 TYR E 366 PHE 0.011 0.001 PHE D 439 TRP 0.022 0.001 TRP D 118 HIS 0.004 0.001 HIS E 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (24377) covalent geometry : angle 0.52112 / 0.27 (33075) hydrogen bonds : bond 0.04453 / 3.00 ( 1088) hydrogen bonds : angle 4.34076 / 3.10 ( 3135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 0.676 Fit side-chains REVERT: A 300 ASP cc_start: 0.7318 (t0) cc_final: 0.6961 (t0) REVERT: B 431 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8902 (mm) REVERT: C 324 MET cc_start: 0.8238 (mmm) cc_final: 0.7255 (tpp) REVERT: D 255 ASN cc_start: 0.7945 (t160) cc_final: 0.7482 (t0) REVERT: D 309 TYR cc_start: 0.8243 (t80) cc_final: 0.7981 (t80) REVERT: E 171 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8254 (pt0) REVERT: E 255 ASN cc_start: 0.6786 (t0) cc_final: 0.6004 (t0) REVERT: E 412 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8977 (mm) REVERT: F 32 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.9009 (tt) REVERT: F 416 MET cc_start: 0.9359 (mmm) cc_final: 0.9154 (tpp) REVERT: G 53 MET cc_start: 0.8673 (ppp) cc_final: 0.8413 (ppp) REVERT: G 206 MET cc_start: 0.6910 (ppp) cc_final: 0.6657 (ppp) REVERT: G 288 GLN cc_start: 0.9016 (tp40) cc_final: 0.8758 (tp-100) REVERT: G 291 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8731 (pt0) REVERT: G 295 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8660 (tm-30) outliers start: 35 outliers final: 16 residues processed: 134 average time/residue: 0.1248 time to fit residues: 28.9398 Evaluate side-chains 122 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 205 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 177 optimal weight: 0.3980 chunk 277 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN D 326 HIS E 171 GLN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.050266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.041239 restraints weight = 139102.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042415 restraints weight = 74069.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043238 restraints weight = 47976.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043780 restraints weight = 34995.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044213 restraints weight = 27827.017| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24377 Z= 0.119 Angle : 0.517 7.793 33075 Z= 0.265 Chirality : 0.041 0.140 3831 Planarity : 0.004 0.057 4320 Dihedral : 4.830 88.317 3427 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.53 % Allowed : 14.64 % Favored : 83.82 % 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: 0.60 (0.15), residues: 3142 helix: 1.80 (0.15), residues: 1248 sheet: 0.72 (0.24), residues: 410 loop : -0.94 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 176 TYR 0.011 0.001 TYR C 231 PHE 0.010 0.001 PHE B 449 TRP 0.020 0.001 TRP D 118 HIS 0.004 0.001 HIS E 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (24377) covalent geometry : angle 0.51733 / 0.26 (33075) hydrogen bonds : bond 0.04448 / 2.99 ( 1088) hydrogen bonds : angle 4.27584 / 3.05 ( 3135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 0.972 Fit side-chains REVERT: A 300 ASP cc_start: 0.7412 (t0) cc_final: 0.6983 (t0) REVERT: B 431 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8870 (mm) REVERT: C 261 MET cc_start: 0.7788 (tpt) cc_final: 0.7398 (tpt) REVERT: D 255 ASN cc_start: 0.7876 (t160) cc_final: 0.7457 (t0) REVERT: D 309 TYR cc_start: 0.8221 (t80) cc_final: 0.7942 (t80) REVERT: E 171 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8636 (pt0) REVERT: E 255 ASN cc_start: 0.6840 (t0) cc_final: 0.6011 (t0) REVERT: E 265 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8616 (tp30) REVERT: E 412 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8951 (mm) REVERT: F 416 MET cc_start: 0.9360 (mmm) cc_final: 0.9140 (tpp) REVERT: G 53 MET cc_start: 0.8704 (ppp) cc_final: 0.8475 (ppp) REVERT: G 162 MET cc_start: 0.9134 (mmm) cc_final: 0.8933 (mmm) REVERT: G 206 MET cc_start: 0.6936 (ppp) cc_final: 0.6613 (ppp) REVERT: G 288 GLN cc_start: 0.9233 (tp40) cc_final: 0.9001 (tp40) outliers start: 38 outliers final: 22 residues processed: 138 average time/residue: 0.1437 time to fit residues: 33.9440 Evaluate side-chains 126 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 263 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 102 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 243 optimal weight: 6.9990 chunk 246 optimal weight: 0.3980 chunk 303 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN C 168 GLN D 326 HIS E 171 GLN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.050483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.041462 restraints weight = 138862.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.042652 restraints weight = 73559.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.043460 restraints weight = 47513.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.044037 restraints weight = 34720.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044454 restraints weight = 27437.224| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24377 Z= 0.109 Angle : 0.518 8.435 33075 Z= 0.263 Chirality : 0.041 0.138 3831 Planarity : 0.003 0.054 4320 Dihedral : 4.765 89.412 3427 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.77 % Allowed : 15.05 % Favored : 83.18 % 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: 0.64 (0.15), residues: 3142 helix: 1.83 (0.15), residues: 1249 sheet: 0.83 (0.24), residues: 410 loop : -0.95 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 176 TYR 0.010 0.001 TYR C 231 PHE 0.011 0.001 PHE B 449 TRP 0.019 0.001 TRP D 118 HIS 0.005 0.001 HIS E 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (24377) covalent geometry : angle 0.51769 / 0.26 (33075) hydrogen bonds : bond 0.04270 / 2.86 ( 1088) hydrogen bonds : angle 4.19530 / 2.99 ( 3135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 105 time to evaluate : 0.936 Fit side-chains REVERT: A 300 ASP cc_start: 0.7481 (t0) cc_final: 0.7073 (t0) REVERT: B 431 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8874 (mm) REVERT: C 324 MET cc_start: 0.8212 (mmm) cc_final: 0.7442 (tpp) REVERT: D 255 ASN cc_start: 0.7892 (t160) cc_final: 0.7456 (t0) REVERT: D 309 TYR cc_start: 0.8202 (t80) cc_final: 0.7927 (t80) REVERT: E 171 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8679 (pp30) REVERT: E 255 ASN cc_start: 0.6977 (t0) cc_final: 0.6234 (t0) REVERT: E 265 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8621 (tp30) REVERT: E 343 PHE cc_start: 0.8685 (t80) cc_final: 0.8449 (t80) REVERT: E 412 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8921 (mm) REVERT: G 53 MET cc_start: 0.8733 (ppp) cc_final: 0.8510 (ppp) REVERT: G 162 MET cc_start: 0.9189 (mmm) cc_final: 0.8923 (mmm) REVERT: G 206 MET cc_start: 0.6948 (ppp) cc_final: 0.6632 (ppp) REVERT: G 288 GLN cc_start: 0.9237 (tp40) cc_final: 0.9009 (tp40) outliers start: 44 outliers final: 26 residues processed: 145 average time/residue: 0.1433 time to fit residues: 35.9500 Evaluate side-chains 132 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 177 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 220 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 GLN ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN E 171 GLN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.049089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.040058 restraints weight = 140924.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041233 restraints weight = 75451.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.042037 restraints weight = 48950.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.042567 restraints weight = 35760.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.042979 restraints weight = 28596.517| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24377 Z= 0.193 Angle : 0.582 11.235 33075 Z= 0.300 Chirality : 0.042 0.172 3831 Planarity : 0.004 0.053 4320 Dihedral : 4.975 89.298 3427 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.10 % Allowed : 15.41 % Favored : 82.49 % 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: 0.50 (0.15), residues: 3142 helix: 1.72 (0.15), residues: 1244 sheet: 0.74 (0.24), residues: 429 loop : -1.06 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 229 TYR 0.015 0.001 TYR C 231 PHE 0.015 0.001 PHE B 340 TRP 0.027 0.001 TRP D 118 HIS 0.005 0.001 HIS A 455 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (24377) covalent geometry : angle 0.58187 / 0.30 (33075) hydrogen bonds : bond 0.05263 / 3.52 ( 1088) hydrogen bonds : angle 4.42839 / 3.16 ( 3135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 101 time to evaluate : 0.843 Fit side-chains REVERT: A 300 ASP cc_start: 0.7584 (t0) cc_final: 0.7244 (t0) REVERT: B 431 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8888 (mm) REVERT: C 324 MET cc_start: 0.8414 (mmm) cc_final: 0.7397 (tpp) REVERT: D 255 ASN cc_start: 0.7921 (t160) cc_final: 0.7488 (t0) REVERT: D 309 TYR cc_start: 0.8273 (t80) cc_final: 0.8029 (t80) REVERT: E 171 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8563 (pp30) REVERT: E 255 ASN cc_start: 0.7087 (t0) cc_final: 0.6372 (t0) REVERT: E 265 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8542 (tp30) REVERT: E 416 MET cc_start: 0.7448 (mpp) cc_final: 0.6982 (mtt) REVERT: G 53 MET cc_start: 0.8735 (ppp) cc_final: 0.8518 (ppp) REVERT: G 162 MET cc_start: 0.9259 (mmm) cc_final: 0.9019 (mmm) REVERT: G 206 MET cc_start: 0.7111 (ppp) cc_final: 0.6784 (ppp) REVERT: G 288 GLN cc_start: 0.9213 (tp40) cc_final: 0.8968 (tp40) outliers start: 52 outliers final: 40 residues processed: 145 average time/residue: 0.1398 time to fit residues: 34.9310 Evaluate side-chains 142 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 210 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 150 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 303 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN B 68 ASN ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.047889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.038929 restraints weight = 142347.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.040053 restraints weight = 76439.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.040825 restraints weight = 49839.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.041363 restraints weight = 36793.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.041719 restraints weight = 29344.722| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 24377 Z= 0.277 Angle : 0.664 11.864 33075 Z= 0.346 Chirality : 0.044 0.196 3831 Planarity : 0.004 0.052 4320 Dihedral : 5.351 85.631 3427 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.34 % Allowed : 15.89 % Favored : 81.77 % 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: 0.18 (0.15), residues: 3142 helix: 1.36 (0.15), residues: 1250 sheet: 0.58 (0.24), residues: 439 loop : -1.16 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 229 TYR 0.020 0.002 TYR C 231 PHE 0.019 0.002 PHE E 439 TRP 0.035 0.002 TRP D 118 HIS 0.007 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.28 (24377) covalent geometry : angle 0.66410 / 0.35 (33075) hydrogen bonds : bond 0.06240 / 4.18 ( 1088) hydrogen bonds : angle 4.74244 / 3.38 ( 3135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 95 time to evaluate : 0.935 Fit side-chains REVERT: A 300 ASP cc_start: 0.7811 (t0) cc_final: 0.7577 (t0) REVERT: B 431 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 324 MET cc_start: 0.8589 (mmm) cc_final: 0.7733 (tpp) REVERT: D 255 ASN cc_start: 0.8000 (t160) cc_final: 0.7547 (t0) REVERT: D 273 MET cc_start: 0.9033 (mmm) cc_final: 0.8813 (mtt) REVERT: E 171 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8540 (pp30) REVERT: E 255 ASN cc_start: 0.7355 (t0) cc_final: 0.6805 (t0) REVERT: E 416 MET cc_start: 0.7500 (mpp) cc_final: 0.7106 (mtt) REVERT: G 162 MET cc_start: 0.9300 (mmm) cc_final: 0.9050 (mmm) REVERT: G 206 MET cc_start: 0.7317 (ppp) cc_final: 0.6950 (ppp) REVERT: G 291 GLN cc_start: 0.9183 (tp40) cc_final: 0.8820 (pt0) REVERT: G 295 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8666 (tm-30) outliers start: 58 outliers final: 43 residues processed: 145 average time/residue: 0.1386 time to fit residues: 35.1323 Evaluate side-chains 140 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 95 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 343 PHE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 22 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 210 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 15 optimal weight: 3.9990 chunk 300 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 286 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 292 optimal weight: 10.0000 chunk 155 optimal weight: 0.0870 chunk 254 optimal weight: 4.9990 chunk 271 optimal weight: 0.8980 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS E 171 GLN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.049728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.040653 restraints weight = 140663.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.041843 restraints weight = 75037.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.042672 restraints weight = 48575.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.043245 restraints weight = 35438.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.043647 restraints weight = 27992.619| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24377 Z= 0.114 Angle : 0.547 10.322 33075 Z= 0.278 Chirality : 0.041 0.151 3831 Planarity : 0.004 0.050 4320 Dihedral : 4.973 80.626 3427 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.86 % Allowed : 16.66 % Favored : 81.48 % 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: 0.44 (0.15), residues: 3142 helix: 1.62 (0.15), residues: 1267 sheet: 0.68 (0.25), residues: 413 loop : -1.05 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 365 TYR 0.012 0.001 TYR C 231 PHE 0.016 0.001 PHE E 439 TRP 0.023 0.001 TRP D 118 HIS 0.005 0.001 HIS E 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (24377) covalent geometry : angle 0.54687 / 0.28 (33075) hydrogen bonds : bond 0.04681 / 3.14 ( 1088) hydrogen bonds : angle 4.30008 / 3.05 ( 3135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 104 time to evaluate : 1.051 Fit side-chains REVERT: A 300 ASP cc_start: 0.7634 (t0) cc_final: 0.7311 (t0) REVERT: B 431 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8874 (mm) REVERT: C 261 MET cc_start: 0.8101 (tpt) cc_final: 0.7765 (tpt) REVERT: C 324 MET cc_start: 0.8422 (mmm) cc_final: 0.7827 (tpp) REVERT: D 255 ASN cc_start: 0.7819 (t160) cc_final: 0.7349 (t0) REVERT: D 273 MET cc_start: 0.9019 (mmm) cc_final: 0.8777 (mtt) REVERT: E 171 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8563 (pp30) REVERT: E 255 ASN cc_start: 0.7349 (t0) cc_final: 0.6827 (t0) REVERT: E 265 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8582 (tp30) REVERT: E 416 MET cc_start: 0.7423 (mpp) cc_final: 0.7036 (mtt) REVERT: F 343 PHE cc_start: 0.8554 (m-80) cc_final: 0.8081 (t80) REVERT: G 162 MET cc_start: 0.9306 (mmm) cc_final: 0.9031 (mmm) REVERT: G 206 MET cc_start: 0.7146 (ppp) cc_final: 0.6851 (ppp) REVERT: G 291 GLN cc_start: 0.9137 (tp40) cc_final: 0.8746 (pt0) REVERT: G 295 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8606 (tm-30) outliers start: 46 outliers final: 38 residues processed: 144 average time/residue: 0.1439 time to fit residues: 35.9409 Evaluate side-chains 142 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 210 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 270 optimal weight: 0.0970 chunk 268 optimal weight: 4.9990 chunk 310 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 267 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 251 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN D 326 HIS E 171 GLN ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 415 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.049072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.040067 restraints weight = 141945.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.041228 restraints weight = 75418.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.042011 restraints weight = 48952.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.042578 restraints weight = 36001.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.042954 restraints weight = 28478.624| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24377 Z= 0.177 Angle : 0.576 10.274 33075 Z= 0.297 Chirality : 0.042 0.156 3831 Planarity : 0.004 0.049 4320 Dihedral : 5.013 81.536 3427 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.94 % Allowed : 16.78 % Favored : 81.28 % 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: 0.36 (0.15), residues: 3142 helix: 1.54 (0.15), residues: 1273 sheet: 0.63 (0.25), residues: 419 loop : -1.09 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 229 TYR 0.014 0.001 TYR C 231 PHE 0.017 0.001 PHE D 343 TRP 0.026 0.001 TRP D 118 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (24377) covalent geometry : angle 0.57617 / 0.30 (33075) hydrogen bonds : bond 0.05099 / 3.42 ( 1088) hydrogen bonds : angle 4.39638 / 3.12 ( 3135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.945 Fit side-chains REVERT: A 300 ASP cc_start: 0.7699 (t0) cc_final: 0.7402 (t0) REVERT: B 431 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8887 (mm) REVERT: C 261 MET cc_start: 0.8100 (tpt) cc_final: 0.7722 (tpt) REVERT: C 324 MET cc_start: 0.8540 (mmm) cc_final: 0.7943 (tpp) REVERT: D 255 ASN cc_start: 0.7836 (t160) cc_final: 0.7349 (t0) REVERT: D 273 MET cc_start: 0.9010 (mmm) cc_final: 0.8781 (mtt) REVERT: E 255 ASN cc_start: 0.7351 (t0) cc_final: 0.6852 (t0) REVERT: E 265 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8646 (tp30) REVERT: E 416 MET cc_start: 0.7397 (mpp) cc_final: 0.7045 (mtt) REVERT: G 162 MET cc_start: 0.9320 (mmm) cc_final: 0.9051 (mmm) REVERT: G 206 MET cc_start: 0.7200 (ppp) cc_final: 0.6900 (ppp) REVERT: G 291 GLN cc_start: 0.9146 (tp40) cc_final: 0.8761 (pt0) outliers start: 48 outliers final: 41 residues processed: 143 average time/residue: 0.1373 time to fit residues: 34.5083 Evaluate side-chains 142 residues out of total 2561 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 479 HIS Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 217 PHE Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 338 PHE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 415 ASN Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 226 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain G residue 210 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 300 optimal weight: 20.0000 chunk 235 optimal weight: 2.9990 chunk 283 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 285 optimal weight: 0.0770 chunk 108 optimal weight: 5.9990 chunk 218 optimal weight: 0.9980 chunk 292 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 326 HIS ** E 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.048949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.039951 restraints weight = 141123.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.041101 restraints weight = 75310.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.041902 restraints weight = 48982.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042454 restraints weight = 35866.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.042848 restraints weight = 28488.277| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24377 Z= 0.185 Angle : 0.586 11.671 33075 Z= 0.302 Chirality : 0.042 0.161 3831 Planarity : 0.004 0.049 4320 Dihedral : 5.076 81.616 3427 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.10 % Allowed : 16.78 % Favored : 81.12 % 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: 0.38 (0.15), residues: 3142 helix: 1.58 (0.15), residues: 1261 sheet: 0.65 (0.24), residues: 425 loop : -1.09 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 229 TYR 0.015 0.001 TYR C 231 PHE 0.019 0.001 PHE D 343 TRP 0.027 0.001 TRP D 118 HIS 0.005 0.001 HIS E 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (24377) covalent geometry : angle 0.58588 / 0.30 (33075) hydrogen bonds : bond 0.05230 / 3.51 ( 1088) hydrogen bonds : angle 4.42363 / 3.14 ( 3135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3517.75 seconds wall clock time: 61 minutes 52.83 seconds (3712.83 seconds total)