Starting phenix.real_space_refine on Tue Dec 12 20:27:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjw_25934/12_2023/7tjw_25934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjw_25934/12_2023/7tjw_25934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjw_25934/12_2023/7tjw_25934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjw_25934/12_2023/7tjw_25934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjw_25934/12_2023/7tjw_25934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjw_25934/12_2023/7tjw_25934_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 15 5.49 5 Mg 5 5.21 5 S 29 5.16 5 C 14226 2.51 5 N 3996 2.21 5 O 4229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 257": "OE1" <-> "OE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 136": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 22500 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3505 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'PHE:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3430 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 454} Chain breaks: 1 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 224 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 21, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 133 Chain: "C" Number of atoms: 3648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3648 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 462} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3353 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 441} Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 18, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 112 Chain: "E" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3308 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 24, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 158 Chain: "F" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3430 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 19, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 96 Chain: "G" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1666 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 9, 'TRANS': 249} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 285 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 187 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: 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: "F" 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} Time building chain proxies: 12.00, per 1000 atoms: 0.53 Number of scatterers: 22500 At special positions: 0 Unit cell: (126.665, 126.665, 153.615, 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 29 16.00 P 15 15.00 Mg 5 11.99 O 4229 8.00 N 3996 7.00 C 14226 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 - 3.50 Amino acid : False - 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: 8.58 Conformation dependent library (CDL) restraints added in 4.8 seconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5626 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 23 sheets defined 43.8% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.776A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 261 Proline residue: A 249 - end of helix removed outlier: 3.807A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 300 through 310 removed outlier: 3.691A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 385 through 402 removed outlier: 4.086A pdb=" N ALA A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLY A 390 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER A 391 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 440 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 454 through 457 removed outlier: 4.058A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.585A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.851A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix removed outlier: 3.713A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.080A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS B 304 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG B 306 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 392 through 403 Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.895A pdb=" N LEU B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 422 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 460 through 476 removed outlier: 4.362A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 467 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 468 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 471 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.573A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 212 through 225 Processing helix chain 'C' and resid 227 through 230 Processing helix chain 'C' and resid 242 through 262 Proline residue: C 249 - end of helix removed outlier: 3.523A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 removed outlier: 3.508A pdb=" N ALA C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 310 removed outlier: 4.597A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 383 through 403 removed outlier: 3.921A pdb=" N GLN C 387 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 Processing helix chain 'C' and resid 414 through 430 removed outlier: 3.847A pdb=" N GLU C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 460 through 477 removed outlier: 4.505A pdb=" N GLY C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU C 465 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 487 removed outlier: 3.690A pdb=" N GLU C 484 " --> pdb=" O GLU C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 507 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 163 through 174 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 226 through 245 removed outlier: 4.631A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 272 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 283 through 296 removed outlier: 4.306A pdb=" N ALA D 286 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 288 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU D 294 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG D 295 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.046A pdb=" N THR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE D 326 " --> pdb=" O PRO D 322 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 365 through 391 removed outlier: 3.856A pdb=" N SER D 383 " --> pdb=" O GLN D 379 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 398 through 413 removed outlier: 5.258A pdb=" N THR D 403 " --> pdb=" O GLN D 399 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 412 " --> pdb=" O ARG D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 422 Processing helix chain 'D' and resid 434 through 446 Processing helix chain 'D' and resid 454 through 457 Processing helix chain 'D' and resid 463 through 473 removed outlier: 4.224A pdb=" N GLU D 471 " --> pdb=" O VAL D 467 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS D 472 " --> pdb=" O ALA D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 163 through 178 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 245 removed outlier: 4.782A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 271 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 283 through 293 removed outlier: 4.256A pdb=" N ALA E 286 " --> pdb=" O PRO E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 327 Processing helix chain 'E' and resid 337 through 341 Processing helix chain 'E' and resid 360 through 391 removed outlier: 7.707A pdb=" N GLN E 365 " --> pdb=" O ALA E 361 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N GLU E 366 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 383 " --> pdb=" O GLN E 379 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 414 removed outlier: 3.999A pdb=" N ARG E 412 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 446 removed outlier: 3.605A pdb=" N GLU E 446 " --> pdb=" O LYS E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 474 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 163 through 177 removed outlier: 4.891A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 Processing helix chain 'F' and resid 226 through 245 removed outlier: 3.602A pdb=" N ARG F 231 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR F 242 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 272 removed outlier: 3.797A pdb=" N ALA F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU F 271 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 285 through 296 removed outlier: 3.882A pdb=" N LEU F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.314A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 360 through 363 No H-bonds generated for 'chain 'F' and resid 360 through 363' Processing helix chain 'F' and resid 365 through 390 removed outlier: 5.102A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 398 through 414 removed outlier: 3.651A pdb=" N LYS F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 425 removed outlier: 4.976A pdb=" N VAL F 423 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR F 425 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 474 Processing helix chain 'G' and resid 3 through 55 removed outlier: 3.686A pdb=" N ILE G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 99 removed outlier: 3.570A pdb=" N HIS G 88 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER G 89 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN G 90 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU G 91 " --> pdb=" O HIS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 120 removed outlier: 4.629A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 133 through 135 No H-bonds generated for 'chain 'G' and resid 133 through 135' Processing helix chain 'G' and resid 140 through 152 removed outlier: 3.570A pdb=" N LYS G 149 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 185 through 190 removed outlier: 4.015A pdb=" N GLU G 189 " --> pdb=" O ALA G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 197 removed outlier: 4.294A pdb=" N GLY G 195 " --> pdb=" O PRO G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 274 removed outlier: 4.315A pdb=" N ASP G 208 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU G 211 " --> pdb=" O ASP G 208 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TYR G 212 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN G 216 " --> pdb=" O THR G 213 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR G 251 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL G 268 " --> pdb=" O ASN G 265 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.725A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU A 68 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 101 Processing sheet with id= C, first strand: chain 'A' and resid 350 through 353 removed outlier: 3.640A pdb=" N GLY A 171 " --> pdb=" O ILE A 329 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 231 through 236 removed outlier: 6.718A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU A 326 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY A 321 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 32 through 37 removed outlier: 6.519A pdb=" N ARG B 42 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL B 36 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 76 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ALA B 65 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.526A pdb=" N GLY B 127 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 351 through 353 removed outlier: 6.576A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 236 removed outlier: 6.667A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 321 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.454A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU C 68 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= K, first strand: chain 'C' and resid 350 through 354 removed outlier: 3.717A pdb=" N ASP C 172 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 231 through 236 removed outlier: 6.598A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 326 " --> pdb=" O TYR C 270 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 12 through 17 removed outlier: 6.834A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 331 through 334 removed outlier: 8.005A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLY D 157 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL D 310 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL D 251 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL D 307 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU D 253 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ALA D 309 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE D 255 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N TYR D 311 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE D 181 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE D 254 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL D 183 " --> pdb=" O PHE D 254 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP D 256 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR D 185 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.580A pdb=" N LYS E 75 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS E 40 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS E 24 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL E 13 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 306 through 309 removed outlier: 6.469A pdb=" N ALA E 331 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE E 156 " --> pdb=" O ALA E 331 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR E 333 " --> pdb=" O PHE E 156 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 215 through 219 removed outlier: 6.653A pdb=" N SER E 182 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL E 218 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE E 184 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU E 252 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N THR E 185 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE E 254 " --> pdb=" O THR E 185 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.564A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= V, first strand: chain 'F' and resid 331 through 335 removed outlier: 7.736A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 163 through 168 931 hydrogen bonds defined for protein. 2376 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: 7.44 Time building geometry restraints manager: 9.23 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: 7576 1.34 - 1.46: 4121 1.46 - 1.58: 11076 1.58 - 1.69: 21 1.69 - 1.81: 54 Bond restraints: 22848 Sorted by residual: bond pdb=" CB PRO E 8 " pdb=" CG PRO E 8 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.78e+00 bond pdb=" CB ASP C 38 " pdb=" CG ASP C 38 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.65e+00 bond pdb=" C SER G 191 " pdb=" N PRO G 192 " ideal model delta sigma weight residual 1.336 1.348 -0.012 1.20e-02 6.94e+03 1.05e+00 bond pdb=" CG PRO B 365 " pdb=" CD PRO B 365 " ideal model delta sigma weight residual 1.512 1.486 0.026 2.70e-02 1.37e+03 9.43e-01 bond pdb=" CA ILE B 363 " pdb=" CB ILE B 363 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 9.04e-01 ... (remaining 22843 not shown) Histogram of bond angle deviations from ideal: 98.85 - 106.99: 709 106.99 - 115.13: 14046 115.13 - 123.28: 15591 123.28 - 131.42: 750 131.42 - 139.56: 23 Bond angle restraints: 31119 Sorted by residual: angle pdb=" C ASP D 256 " pdb=" N ASN D 257 " pdb=" CA ASN D 257 " ideal model delta sigma weight residual 121.70 128.54 -6.84 1.80e+00 3.09e-01 1.44e+01 angle pdb=" C ASP F 256 " pdb=" N ASN F 257 " pdb=" CA ASN F 257 " ideal model delta sigma weight residual 121.70 128.44 -6.74 1.80e+00 3.09e-01 1.40e+01 angle pdb=" N VAL A 388 " pdb=" CA VAL A 388 " pdb=" C VAL A 388 " ideal model delta sigma weight residual 113.71 110.82 2.89 9.50e-01 1.11e+00 9.28e+00 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.18 -5.48 1.80e+00 3.09e-01 9.27e+00 angle pdb=" N GLY D 220 " pdb=" CA GLY D 220 " pdb=" C GLY D 220 " ideal model delta sigma weight residual 113.18 106.13 7.05 2.37e+00 1.78e-01 8.85e+00 ... (remaining 31114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12967 17.99 - 35.98: 623 35.98 - 53.97: 151 53.97 - 71.96: 50 71.96 - 89.95: 26 Dihedral angle restraints: 13817 sinusoidal: 5027 harmonic: 8790 Sorted by residual: dihedral pdb=" CA PHE E 219 " pdb=" C PHE E 219 " pdb=" N GLY E 220 " pdb=" CA GLY E 220 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA PHE F 219 " pdb=" C PHE F 219 " pdb=" N GLY F 220 " pdb=" CA GLY F 220 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN A 351 " pdb=" C GLN A 351 " pdb=" N ILE A 352 " pdb=" CA ILE A 352 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 13814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3263 0.065 - 0.129: 459 0.129 - 0.194: 23 0.194 - 0.258: 3 0.258 - 0.322: 12 Chirality restraints: 3760 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -3.00 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.94 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.99 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 3757 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 228 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ALA E 228 " 0.032 2.00e-02 2.50e+03 pdb=" O ALA E 228 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG E 229 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 248 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO C 249 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 249 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 249 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO E 276 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.024 5.00e-02 4.00e+02 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.46: 53 2.46 - 3.07: 16687 3.07 - 3.68: 33026 3.68 - 4.29: 49799 4.29 - 4.90: 81899 Nonbonded interactions: 181464 Sorted by model distance: nonbonded pdb=" O3G ATP C 600 " pdb="MG MG C 601 " model vdw 1.855 2.170 nonbonded pdb=" O1B ATP C 600 " pdb="MG MG C 601 " model vdw 1.914 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.963 2.170 nonbonded pdb=" O3G ATP B 600 " pdb="MG MG B 601 " model vdw 1.971 2.170 nonbonded pdb=" OG1 THR B 178 " pdb="MG MG B 601 " model vdw 2.031 2.170 ... (remaining 181459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 68 or (resid 69 and ( \ name N or name CA or name C or name O or name CB )) or resid 70 through 80 or (r \ esid 81 and (name N or name CA or name C or name O or name CB )) or resid 82 thr \ ough 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or \ resid 89 through 110 or (resid 111 through 112 and (name N or name CA or name C \ or name O or name CB )) or resid 113 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N \ or name CA or name C or name O or name CB )) or resid 121 through 133 or (resid \ 134 through 135 and (name N or name CA or name C or name O or name CB )) or resi \ d 136 through 155 or (resid 156 through 157 and (name N or name CA or name C or \ name O or name CB )) or resid 158 through 164 or (resid 165 and (name N or name \ CA or name C or name O or name CB )) or resid 166 or (resid 167 through 168 and \ (name N or name CA or name C or name O or name CB )) or resid 169 through 195 or \ (resid 196 through 197 and (name N or name CA or name C or name O or name CB )) \ or resid 198 through 239 or (resid 240 through 242 and (name N or name CA or na \ me C or name O or name CB )) or resid 243 through 317 or (resid 318 and (name N \ or name CA or name C or name O or name CB )) or resid 319 through 322 or (resid \ 323 and (name N or name CA or name C or name O or name CB )) or resid 324 throug \ h 329 or (resid 330 and (name N or name CA or name C or name O or name CB )) or \ resid 331 through 334 or (resid 335 and (name N or name CA or name C or name O o \ r name CB )) or resid 336 through 354 or (resid 355 through 357 and (name N or n \ ame CA or name C or name O or name CB )) or resid 358 through 392 or (resid 393 \ and (name N or name CA or name C or name O or name CB )) or resid 394 through 39 \ 7 or (resid 398 and (name N or name CA or name C or name O or name CB )) or resi \ d 399 through 405 or (resid 413 through 420 and (name N or name CA or name C or \ name O or name CB )) or resid 421 through 431 or (resid 432 and (name N or name \ CA or name C or name O or name CB )) or resid 433 or (resid 434 and (name N or n \ ame CA or name C or name O or name CB )) or resid 435 through 440 or (resid 441 \ through 442 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 3 through 461 or (resid 462 and (name N or name CA or name C or name O or name C \ B )) or resid 463 through 464 or (resid 465 through 467 and (name N or name CA o \ r name C or name O or name CB )) or resid 468 through 473 or (resid 474 through \ 475 and (name N or name CA or name C or name O or name CB )) or resid 476 throug \ h 481 or (resid 482 and (name N or name CA or name C or name O or name CB )) or \ resid 483 through 492 or (resid 493 through 497 and (name N or name CA or name C \ or name O or name CB )) or resid 498 through 509 or resid 600 through 601)) selection = (chain 'B' and (resid 28 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 61 or (resid 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 through 85 or (res \ id 86 and (name N or name CA or name C or name O or name CB )) or resid 87 throu \ gh 123 or (resid 124 through 126 and (name N or name CA or name C or name O or n \ ame CB )) or resid 127 through 167 or (resid 168 and (name N or name CA or name \ C or name O or name CB )) or resid 169 through 182 or (resid 183 and (name N or \ name CA or name C or name O or name CB )) or resid 184 through 188 or (resid 189 \ and (name N or name CA or name C or name O or name CB )) or resid 190 through 2 \ 75 or (resid 276 through 277 and (name N or name CA or name C or name O or name \ CB )) or resid 278 through 293 or (resid 294 through 295 and (name N or name CA \ or name C or name O or name CB )) or resid 296 through 307 or (resid 308 and (na \ me N or name CA or name C or name O or name CB )) or resid 309 through 334 or (r \ esid 335 and (name N or name CA or name C or name O or name CB )) or resid 336 t \ hrough 382 or (resid 383 through 384 and (name N or name CA or name C or name O \ or name CB )) or resid 385 through 386 or (resid 387 and (name N or name CA or n \ ame C or name O or name CB )) or resid 388 through 427 or (resid 428 and (name N \ or name CA or name C or name O or name CB )) or resid 429 through 465 or (resid \ 466 through 467 and (name N or name CA or name C or name O or name CB )) or res \ id 468 through 486 or (resid 487 through 488 and (name N or name CA or name C or \ name O or name CB )) or resid 489 or (resid 490 and (name N or name CA or name \ C or name O or name CB )) or resid 491 through 494 or (resid 495 through 497 and \ (name N or name CA or name C or name O or name CB )) or resid 498 through 509 o \ r resid 600 through 601)) selection = (chain 'C' and (resid 28 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 51 or (resid 52 through 53 and (na \ me N or name CA or name C or name O or name CB )) or resid 54 through 61 or (res \ id 62 and (name N or name CA or name C or name O or name CB )) or resid 63 throu \ gh 68 or (resid 69 and (name N or name CA or name C or name O or name CB )) or r \ esid 70 through 80 or (resid 81 and (name N or name CA or name C or name O or na \ me CB )) or resid 82 through 85 or (resid 86 and (name N or name CA or name C or \ name O or name CB )) or resid 87 or (resid 88 and (name N or name CA or name C \ or name O or name CB )) or resid 89 through 110 or (resid 111 through 112 and (n \ ame N or name CA or name C or name O or name CB )) or resid 113 through 117 or ( \ resid 118 and (name N or name CA or name C or name O or name CB )) or resid 119 \ or (resid 120 and (name N or name CA or name C or name O or name CB )) or resid \ 121 through 123 or (resid 124 through 126 and (name N or name CA or name C or na \ me O or name CB )) or resid 127 through 133 or (resid 134 through 135 and (name \ N or name CA or name C or name O or name CB )) or resid 136 through 155 or (resi \ d 156 through 157 and (name N or name CA or name C or name O or name CB )) or re \ sid 158 through 164 or (resid 165 and (name N or name CA or name C or name O or \ name CB )) or resid 166 or (resid 167 through 168 and (name N or name CA or name \ C or name O or name CB )) or resid 169 through 182 or (resid 183 and (name N or \ name CA or name C or name O or name CB )) or resid 184 through 188 or (resid 18 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 190 through \ 195 or (resid 196 through 197 and (name N or name CA or name C or name O or name \ CB )) or resid 198 through 239 or (resid 240 through 242 and (name N or name CA \ or name C or name O or name CB )) or resid 243 through 275 or (resid 276 throug \ h 277 and (name N or name CA or name C or name O or name CB )) or resid 278 thro \ ugh 293 or (resid 294 through 295 and (name N or name CA or name C or name O or \ name CB )) or resid 296 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 316 or (resid 317 through 318 an \ d (name N or name CA or name C or name O or name CB )) or resid 319 through 322 \ or (resid 323 and (name N or name CA or name C or name O or name CB )) or resid \ 324 through 354 or (resid 355 through 357 and (name N or name CA or name C or na \ me O or name CB )) or resid 358 through 382 or (resid 383 through 384 and (name \ N or name CA or name C or name O or name CB )) or resid 385 through 386 or (resi \ d 387 and (name N or name CA or name C or name O or name CB )) or resid 388 thro \ ugh 392 or (resid 393 and (name N or name CA or name C or name O or name CB )) o \ r resid 394 through 397 or (resid 398 and (name N or name CA or name C or name O \ or name CB )) or resid 399 through 400 or (resid 401 and (name N or name CA or \ name C or name O or name CB )) or resid 402 through 405 or (resid 413 through 42 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 421 through \ 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or re \ sid 425 through 427 or (resid 428 and (name N or name CA or name C or name O or \ name CB )) or resid 429 through 431 or (resid 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 or (resid 434 and (name N or name CA or \ name C or name O or name CB )) or resid 435 through 440 or (resid 441 through 44 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 443 through \ 458 or (resid 459 and (name N or name CA or name C or name O or name CB )) or re \ sid 460 through 461 or (resid 462 and (name N or name CA or name C or name O or \ name CB )) or resid 463 through 464 or (resid 465 through 467 and (name N or nam \ e CA or name C or name O or name CB )) or resid 468 through 473 or (resid 474 th \ rough 475 and (name N or name CA or name C or name O or name CB )) or resid 476 \ through 479 or (resid 480 and (name N or name CA or name C or name O or name CB \ )) or resid 481 or (resid 482 and (name N or name CA or name C or name O or name \ CB )) or resid 483 or (resid 484 and (name N or name CA or name C or name O or \ name CB )) or resid 485 through 486 or (resid 487 through 488 and (name N or nam \ e CA or name C or name O or name CB )) or resid 489 or (resid 490 and (name N or \ name CA or name C or name O or name CB )) or resid 491 through 492 or (resid 49 \ 3 through 497 and (name N or name CA or name C or name O or name CB )) or resid \ 498 through 499 or (resid 500 and (name N or name CA or name C or name O or name \ CB )) or resid 501 through 509 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 10 through 25 or (resid 26 through 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 or (resid 29 and (name N or nam \ e CA or name C or name O or name CB )) or resid 30 through 42 or (resid 43 and ( \ name N or name CA or name C or name O or name CB )) or resid 44 through 100 or ( \ resid 101 and (name N or name CA or name C or name O or name CB )) or resid 102 \ through 134 or (resid 135 and (name N or name CA or name C or name O or name CB \ )) or resid 136 through 138 or (resid 139 and (name N or name CA or name C or na \ me O or name CB )) or resid 140 through 162 or (resid 163 and (name N or name CA \ or name C or name O or name CB )) or resid 164 through 168 or (resid 169 and (n \ ame N or name CA or name C or name O or name CB )) or resid 170 through 188 or ( \ resid 189 and (name N or name CA or name C or name O or name CB )) or resid 190 \ through 192 or (resid 193 and (name N or name CA or name C or name O or name CB \ )) or resid 194 through 207 or (resid 208 through 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 or (resid 212 and (name N or name CA \ or name C or name O or name CB )) or resid 213 through 221 or (resid 222 and (n \ ame N or name CA or name C or name O or name CB )) or resid 223 through 252 or ( \ resid 253 and (name N or name CA or name C or name O or name CB )) or resid 254 \ through 255 or (resid 256 and (name N or name CA or name C or name O or name CB \ )) or resid 257 through 262 or (resid 263 through 264 and (name N or name CA or \ name C or name O or name CB )) or resid 265 through 266 or (resid 267 and (name \ N or name CA or name C or name O or name CB )) or resid 268 through 293 or (resi \ d 294 and (name N or name CA or name C or name O or name CB )) or resid 295 thro \ ugh 300 or (resid 301 and (name N or name CA or name C or name O or name CB )) o \ r resid 302 through 314 or (resid 315 and (name N or name CA or name C or name O \ or name CB )) or resid 316 through 336 or (resid 337 and (name N or name CA or \ name C or name O or name CB )) or resid 338 through 355 or (resid 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 through 365 or (resi \ d 366 and (name N or name CA or name C or name O or name CB )) or resid 367 thro \ ugh 385 or (resid 386 through 391 and (name N or name CA or name C or name O or \ name CB )) or (resid 392 through 402 and (name N or name CA or name C or name O \ or name CB )) or resid 403 through 404 or (resid 405 and (name N or name CA or n \ ame C or name O or name CB )) or resid 406 through 407 or (resid 408 through 409 \ and (name N or name CA or name C or name O or name CB )) or resid 410 through 4 \ 15 or (resid 416 and (name N or name CA or name C or name O or name CB )) or res \ id 417 through 429 or (resid 430 and (name N or name CA or name C or name O or n \ ame CB )) or resid 431 through 441 or (resid 442 through 443 and (name N or name \ CA or name C or name O or name CB )) or resid 444 through 451 or (resid 452 and \ (name N or name CA or name C or name O or name CB )) or resid 453 through 457 o \ r (resid 458 through 459 and (name N or name CA or name C or name O or name CB ) \ ) or resid 460 through 463 or (resid 464 through 465 and (name N or name CA or n \ ame C or name O or name CB )) or resid 466 through 471 or (resid 472 through 474 \ and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 55 or (resid 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 64 or (resid 65 and ( \ name N or name CA or name C or name O or name CB )) or resid 66 through 89 or (r \ esid 90 and (name N or name CA or name C or name O or name CB )) or resid 91 thr \ ough 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 through 112 or (resid 113 and (name N or name CA or name C or name O o \ r name CB )) or resid 114 through 162 or (resid 163 and (name N or name CA or na \ me C or name O or name CB )) or resid 164 through 184 or (resid 185 and (name N \ or name CA or name C or name O or name CB )) or resid 186 through 188 or (resid \ 189 and (name N or name CA or name C or name O or name CB )) or resid 190 throug \ h 192 or (resid 193 and (name N or name CA or name C or name O or name CB )) or \ resid 194 through 207 or (resid 208 through 210 and (name N or name CA or name C \ or name O or name CB )) or resid 211 through 221 or (resid 222 and (name N or n \ ame CA or name C or name O or name CB )) or resid 223 or (resid 224 and (name N \ or name CA or name C or name O or name CB )) or resid 225 through 244 or (resid \ 245 through 247 and (name N or name CA or name C or name O or name CB )) or resi \ d 248 through 252 or (resid 253 and (name N or name CA or name C or name O or na \ me CB )) or resid 254 through 255 or (resid 256 and (name N or name CA or name C \ or name O or name CB )) or resid 257 through 266 or (resid 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 through 299 or (resid 300 \ through 301 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 2 through 348 or (resid 349 and (name N or name CA or name C or name O or name C \ B )) or resid 350 or (resid 351 through 352 and (name N or name CA or name C or \ name O or name CB )) or resid 353 through 381 or (resid 382 and (name N or name \ CA or name C or name O or name CB )) or resid 383 or (resid 384 through 391 and \ (name N or name CA or name C or name O or name CB )) or (resid 392 through 402 a \ nd (name N or name CA or name C or name O or name CB )) or resid 403 through 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 through 464 or (resid 465 and (name N or name CA or name C or name O or nam \ e CB )) or resid 466 through 474)) selection = (chain 'F' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 or (resid 40 and (name N or name CA or nam \ e C or name O or name CB )) or resid 41 through 55 or (resid 56 and (name N or n \ ame CA or name C or name O or name CB )) or resid 57 through 64 or (resid 65 and \ (name N or name CA or name C or name O or name CB )) or resid 66 through 67 or \ (resid 68 and (name N or name CA or name C or name O or name CB )) or resid 69 t \ hrough 89 or (resid 90 and (name N or name CA or name C or name O or name CB )) \ or resid 91 through 96 or (resid 97 and (name N or name CA or name C or name O o \ r name CB )) or resid 98 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or resid 102 through 104 or (resid 105 and (name N o \ r name CA or name C or name O or name CB )) or resid 106 through 112 or (resid 1 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 114 through \ 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or r \ esid 133 through 134 or (resid 135 and (name N or name CA or name C or name O or \ name CB )) or resid 136 through 138 or (resid 139 and (name N or name CA or nam \ e C or name O or name CB )) or resid 140 through 141 or (resid 142 and (name N o \ r name CA or name C or name O or name CB )) or resid 143 through 177 or (resid 1 \ 78 and (name N or name CA or name C or name O or name CB )) or resid 179 through \ 184 or (resid 185 and (name N or name CA or name C or name O or name CB )) or r \ esid 186 through 211 or (resid 212 and (name N or name CA or name C or name O or \ name CB )) or resid 213 through 223 or (resid 224 and (name N or name CA or nam \ e C or name O or name CB )) or resid 225 through 244 or (resid 245 through 247 a \ nd (name N or name CA or name C or name O or name CB )) or resid 248 through 262 \ or (resid 263 through 264 and (name N or name CA or name C or name O or name CB \ )) or resid 265 through 299 or (resid 300 through 301 and (name N or name CA or \ name C or name O or name CB )) or resid 302 through 314 or (resid 315 and (name \ N or name CA or name C or name O or name CB )) or resid 316 through 336 or (res \ id 337 and (name N or name CA or name C or name O or name CB )) or resid 338 thr \ ough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 or (resid 351 through 352 and (name N or name CA or name C or name \ O or name CB )) or resid 353 through 355 or (resid 356 and (name N or name CA or \ name C or name O or name CB )) or resid 357 through 365 or (resid 366 and (name \ N or name CA or name C or name O or name CB )) or resid 367 through 381 or (res \ id 382 and (name N or name CA or name C or name O or name CB )) or resid 383 or \ (resid 384 through 391 and (name N or name CA or name C or name O or name CB )) \ or resid 392 or (resid 393 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 403 through 407 or (resid 408 through 409 and (name N o \ r name CA or name C or name O or name CB )) or resid 410 through 415 or (resid 4 \ 16 and (name N or name CA or name C or name O or name CB )) or resid 417 through \ 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) or r \ esid 431 through 434 or (resid 435 through 436 and (name N or name CA or name C \ or name O or name CB )) or resid 437 through 441 or (resid 442 through 443 and ( \ name N or name CA or name C or name O or name CB )) or resid 444 through 445 or \ (resid 446 and (name N or name CA or name C or name O or name CB )) or resid 447 \ or (resid 448 and (name N or name CA or name C or name O or name CB )) or resid \ 449 through 451 or (resid 452 and (name N or name CA or name C or name O or nam \ e CB )) or resid 453 through 457 or (resid 458 through 459 and (name N or name C \ A or name C or name O or name CB )) or resid 460 through 472 or (resid 473 throu \ gh 474 and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 4.970 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 61.100 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 0.083 22848 Z= 0.186 Angle : 0.639 7.762 31119 Z= 0.353 Chirality : 0.046 0.322 3760 Planarity : 0.004 0.043 4009 Dihedral : 13.065 89.950 8191 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.15), residues: 3077 helix: 0.44 (0.14), residues: 1212 sheet: 0.07 (0.23), residues: 481 loop : 0.05 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 258 HIS 0.008 0.001 HIS E 367 PHE 0.023 0.002 PHE A 506 TYR 0.022 0.002 TYR D 458 ARG 0.006 0.001 ARG F 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 961 time to evaluate : 2.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 961 average time/residue: 0.3507 time to fit residues: 515.1608 Evaluate side-chains 722 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 722 time to evaluate : 2.479 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS ** A 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 381 GLN A 454 HIS B 47 ASN B 193 ASN B 265 HIS B 343 ASN C 47 ASN C 276 GLN D 35 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 195 ASN F 118 HIS F 221 GLN F 399 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22848 Z= 0.278 Angle : 0.619 7.280 31119 Z= 0.327 Chirality : 0.045 0.261 3760 Planarity : 0.005 0.049 4009 Dihedral : 8.583 89.263 3488 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.53 % Allowed : 12.35 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 3077 helix: 0.62 (0.14), residues: 1242 sheet: 0.03 (0.22), residues: 498 loop : 0.18 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 258 HIS 0.006 0.001 HIS A 145 PHE 0.030 0.002 PHE C 395 TYR 0.024 0.002 TYR F 198 ARG 0.010 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 737 time to evaluate : 3.216 Fit side-chains revert: symmetry clash outliers start: 99 outliers final: 68 residues processed: 780 average time/residue: 0.3491 time to fit residues: 427.6459 Evaluate side-chains 738 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 670 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.2008 time to fit residues: 29.4248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 299 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 275 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN B 174 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 225 HIS ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 ASN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN F 365 GLN ** G 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 22848 Z= 0.432 Angle : 0.689 7.391 31119 Z= 0.359 Chirality : 0.047 0.287 3760 Planarity : 0.005 0.053 4009 Dihedral : 8.637 84.359 3488 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.29 % Allowed : 15.32 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3077 helix: 0.28 (0.14), residues: 1230 sheet: 0.03 (0.23), residues: 487 loop : -0.06 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 191 HIS 0.008 0.001 HIS A 145 PHE 0.028 0.002 PHE C 395 TYR 0.024 0.002 TYR F 198 ARG 0.007 0.001 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 703 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 46 residues processed: 730 average time/residue: 0.3366 time to fit residues: 390.6107 Evaluate side-chains 710 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 664 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.2096 time to fit residues: 21.5947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 0.8980 chunk 208 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 186 optimal weight: 0.0980 chunk 278 optimal weight: 4.9990 chunk 294 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 224 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** C 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN D 195 ASN G 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 22848 Z= 0.185 Angle : 0.559 7.410 31119 Z= 0.291 Chirality : 0.043 0.285 3760 Planarity : 0.004 0.049 4009 Dihedral : 7.689 75.978 3488 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.92 % Allowed : 17.33 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3077 helix: 0.67 (0.15), residues: 1231 sheet: 0.14 (0.23), residues: 491 loop : 0.17 (0.18), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 258 HIS 0.006 0.001 HIS A 145 PHE 0.024 0.001 PHE D 259 TYR 0.018 0.002 TYR F 198 ARG 0.013 0.001 ARG E 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 699 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 26 residues processed: 710 average time/residue: 0.3315 time to fit residues: 371.4149 Evaluate side-chains 684 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 658 time to evaluate : 2.561 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2093 time to fit residues: 13.7131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 0.0870 chunk 167 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 203 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 150 optimal weight: 0.0570 chunk 264 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN B 187 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN C 47 ASN C 276 GLN C 304 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN G 256 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22848 Z= 0.177 Angle : 0.539 7.734 31119 Z= 0.280 Chirality : 0.043 0.296 3760 Planarity : 0.004 0.044 4009 Dihedral : 7.093 73.732 3488 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.37 % Allowed : 20.35 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 3077 helix: 0.86 (0.15), residues: 1231 sheet: 0.31 (0.24), residues: 487 loop : 0.19 (0.18), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 258 HIS 0.004 0.001 HIS F 367 PHE 0.029 0.001 PHE D 259 TYR 0.019 0.001 TYR F 198 ARG 0.006 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 689 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 697 average time/residue: 0.3318 time to fit residues: 364.5559 Evaluate side-chains 672 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 652 time to evaluate : 2.670 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2416 time to fit residues: 12.1839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 0.0040 chunk 265 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 173 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 154 optimal weight: 0.1980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN F 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22848 Z= 0.159 Angle : 0.531 7.761 31119 Z= 0.274 Chirality : 0.042 0.310 3760 Planarity : 0.004 0.042 4009 Dihedral : 6.781 71.526 3488 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.37 % Allowed : 22.04 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3077 helix: 1.02 (0.15), residues: 1224 sheet: 0.40 (0.25), residues: 471 loop : 0.24 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 191 HIS 0.010 0.001 HIS A 145 PHE 0.030 0.001 PHE C 395 TYR 0.020 0.001 TYR E 242 ARG 0.007 0.000 ARG C 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 672 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 22 residues processed: 683 average time/residue: 0.3250 time to fit residues: 350.3951 Evaluate side-chains 662 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 640 time to evaluate : 2.345 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2003 time to fit residues: 11.7146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 164 optimal weight: 0.7980 chunk 293 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 GLN F 52 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 22848 Z= 0.416 Angle : 0.673 8.273 31119 Z= 0.348 Chirality : 0.047 0.315 3760 Planarity : 0.005 0.047 4009 Dihedral : 7.696 74.239 3488 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.93 % Allowed : 22.77 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3077 helix: 0.71 (0.15), residues: 1194 sheet: 0.22 (0.25), residues: 465 loop : -0.04 (0.17), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 258 HIS 0.007 0.001 HIS A 304 PHE 0.034 0.002 PHE D 259 TYR 0.023 0.002 TYR F 198 ARG 0.008 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 651 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 50 residues processed: 674 average time/residue: 0.3289 time to fit residues: 348.4456 Evaluate side-chains 676 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 626 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.2078 time to fit residues: 22.6403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 175 optimal weight: 0.0040 chunk 88 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 0.3980 chunk 186 optimal weight: 0.4980 chunk 200 optimal weight: 0.0370 chunk 145 optimal weight: 2.9990 chunk 27 optimal weight: 0.0270 chunk 231 optimal weight: 3.9990 overall best weight: 0.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 127 GLN D 173 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 22848 Z= 0.160 Angle : 0.574 9.198 31119 Z= 0.291 Chirality : 0.043 0.281 3760 Planarity : 0.004 0.045 4009 Dihedral : 6.735 67.675 3488 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.82 % Allowed : 23.23 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 3077 helix: 0.96 (0.15), residues: 1227 sheet: 0.35 (0.25), residues: 476 loop : 0.19 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 258 HIS 0.006 0.001 HIS E 367 PHE 0.029 0.001 PHE D 259 TYR 0.029 0.001 TYR D 147 ARG 0.006 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 677 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 685 average time/residue: 0.3328 time to fit residues: 359.1545 Evaluate side-chains 641 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 633 time to evaluate : 2.605 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2067 time to fit residues: 6.4566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 0.0870 chunk 281 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 247 optimal weight: 0.1980 chunk 259 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 ASN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 115 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 173 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22848 Z= 0.209 Angle : 0.592 10.285 31119 Z= 0.299 Chirality : 0.044 0.332 3760 Planarity : 0.004 0.044 4009 Dihedral : 6.814 69.633 3488 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.96 % Allowed : 25.79 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.16), residues: 3077 helix: 1.04 (0.15), residues: 1217 sheet: 0.33 (0.25), residues: 474 loop : 0.12 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 191 HIS 0.004 0.001 HIS E 367 PHE 0.033 0.001 PHE D 259 TYR 0.038 0.002 TYR D 147 ARG 0.006 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 642 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 14 residues processed: 648 average time/residue: 0.3514 time to fit residues: 358.7145 Evaluate side-chains 640 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 626 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2291 time to fit residues: 9.4296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 9.9990 chunk 289 optimal weight: 5.9990 chunk 176 optimal weight: 0.0770 chunk 137 optimal weight: 0.0000 chunk 201 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 279 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 186 optimal weight: 0.0970 chunk 148 optimal weight: 0.9980 overall best weight: 0.3740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 173 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22848 Z= 0.174 Angle : 0.584 10.559 31119 Z= 0.295 Chirality : 0.043 0.332 3760 Planarity : 0.004 0.053 4009 Dihedral : 6.593 68.881 3488 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.32 % Allowed : 26.34 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 3077 helix: 1.05 (0.15), residues: 1230 sheet: 0.43 (0.25), residues: 469 loop : 0.15 (0.18), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.004 0.001 HIS E 367 PHE 0.035 0.001 PHE D 326 TYR 0.027 0.001 TYR D 147 ARG 0.007 0.000 ARG G 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 638 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 642 average time/residue: 0.3262 time to fit residues: 329.7343 Evaluate side-chains 613 residues out of total 2513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 611 time to evaluate : 2.527 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2148 time to fit residues: 4.4973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 0.6980 chunk 257 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 242 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 174 GLN A 188 GLN ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN C 47 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 GLN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.137811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.118646 restraints weight = 35108.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.122007 restraints weight = 19102.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.124211 restraints weight = 11879.734| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 22848 Z= 0.241 Angle : 0.604 9.992 31119 Z= 0.306 Chirality : 0.044 0.317 3760 Planarity : 0.005 0.084 4009 Dihedral : 6.837 69.933 3488 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.55 % Allowed : 27.07 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 3077 helix: 1.11 (0.15), residues: 1212 sheet: 0.33 (0.25), residues: 479 loop : 0.15 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 191 HIS 0.011 0.001 HIS A 145 PHE 0.043 0.002 PHE D 326 TYR 0.030 0.002 TYR D 147 ARG 0.014 0.001 ARG E 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6328.20 seconds wall clock time: 114 minutes 13.28 seconds (6853.28 seconds total)