Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 04:09:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/04_2023/5sy1_8315_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/04_2023/5sy1_8315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/04_2023/5sy1_8315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/04_2023/5sy1_8315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/04_2023/5sy1_8315_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/04_2023/5sy1_8315_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 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: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 70 5.16 5 C 7472 2.51 5 N 1886 2.21 5 O 2026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 486": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11462 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1154 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "A" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4545 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 24, 'TRANS': 557} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4545 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 24, 'TRANS': 557} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "D" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1154 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.52, per 1000 atoms: 0.57 Number of scatterers: 11462 At special positions: 0 Unit cell: (131.775, 81.575, 134.285, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 70 16.00 O 2026 8.00 N 1886 7.00 C 7472 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: 4.67 Conformation dependent library (CDL) restraints added in 1.7 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 2 sheets defined 63.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'C' and resid 7 through 18 removed outlier: 4.192A pdb=" N PHE C 13 " --> pdb=" O GLN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 39 removed outlier: 3.612A pdb=" N THR C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 removed outlier: 3.751A pdb=" N ASN C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 56 " --> pdb=" O MET C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 76 removed outlier: 3.963A pdb=" N MET C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 4.070A pdb=" N ARG C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 4.001A pdb=" N VAL C 109 " --> pdb=" O GLU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.705A pdb=" N ILE C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'A' and resid 32 through 60 removed outlier: 4.582A pdb=" N LEU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 45 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 106 removed outlier: 4.050A pdb=" N CYS A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 131 through 134 No H-bonds generated for 'chain 'A' and resid 131 through 134' Processing helix chain 'A' and resid 136 through 143 removed outlier: 3.549A pdb=" N CYS A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 169 removed outlier: 3.781A pdb=" N VAL A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.724A pdb=" N LEU A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix removed outlier: 3.637A pdb=" N LEU A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 196 " --> pdb=" O CYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.695A pdb=" N GLY A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLN A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.520A pdb=" N VAL A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Proline residue: A 238 - end of helix Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.782A pdb=" N ALA A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 296 removed outlier: 3.657A pdb=" N SER A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.861A pdb=" N HIS A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE A 303 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 318 removed outlier: 3.702A pdb=" N LEU A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 375 removed outlier: 4.564A pdb=" N CYS A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 368 " --> pdb=" O MET A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 385 No H-bonds generated for 'chain 'A' and resid 382 through 385' Processing helix chain 'A' and resid 393 through 399 removed outlier: 3.657A pdb=" N VAL A 397 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS A 398 " --> pdb=" O PRO A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 429 removed outlier: 3.513A pdb=" N LEU A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 428 " --> pdb=" O CYS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 454 through 471 removed outlier: 3.889A pdb=" N LEU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 459 " --> pdb=" O TRP A 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.676A pdb=" N TYR A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 524 removed outlier: 3.828A pdb=" N MET A 502 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.796A pdb=" N GLU A 536 " --> pdb=" O ARG A 533 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ALA A 537 " --> pdb=" O ASN A 534 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 538 " --> pdb=" O VAL A 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 533 through 538' Processing helix chain 'A' and resid 540 through 553 removed outlier: 3.542A pdb=" N ILE A 551 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 removed outlier: 3.957A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 618 removed outlier: 3.530A pdb=" N TRP A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A 618 " --> pdb=" O TYR A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 627 removed outlier: 4.137A pdb=" N GLY A 624 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 60 removed outlier: 4.583A pdb=" N LEU B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 45 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 106 removed outlier: 4.049A pdb=" N CYS B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 131 through 134 No H-bonds generated for 'chain 'B' and resid 131 through 134' Processing helix chain 'B' and resid 136 through 143 removed outlier: 3.549A pdb=" N CYS B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THR B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 169 removed outlier: 3.781A pdb=" N VAL B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.724A pdb=" N LEU B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Proline residue: B 188 - end of helix removed outlier: 3.638A pdb=" N LEU B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.695A pdb=" N GLY B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLN B 209 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.520A pdb=" N VAL B 229 " --> pdb=" O TYR B 225 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYS B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Proline residue: B 238 - end of helix Processing helix chain 'B' and resid 253 through 261 removed outlier: 3.782A pdb=" N ALA B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 296 removed outlier: 3.658A pdb=" N SER B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.861A pdb=" N HIS B 302 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE B 303 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 318 removed outlier: 3.702A pdb=" N LEU B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 375 removed outlier: 4.563A pdb=" N CYS B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 354 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 367 " --> pdb=" O SER B 363 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 368 " --> pdb=" O MET B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 385 No H-bonds generated for 'chain 'B' and resid 382 through 385' Processing helix chain 'B' and resid 393 through 399 removed outlier: 3.657A pdb=" N VAL B 397 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 429 removed outlier: 3.513A pdb=" N LEU B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 428 " --> pdb=" O CYS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 454 through 471 removed outlier: 3.889A pdb=" N LEU B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 459 " --> pdb=" O TRP B 455 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.675A pdb=" N TYR B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 524 removed outlier: 3.828A pdb=" N MET B 502 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 506 " --> pdb=" O MET B 502 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 518 " --> pdb=" O ILE B 514 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 523 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLY B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.796A pdb=" N GLU B 536 " --> pdb=" O ARG B 533 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA B 537 " --> pdb=" O ASN B 534 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 538 " --> pdb=" O VAL B 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 533 through 538' Processing helix chain 'B' and resid 540 through 553 removed outlier: 3.542A pdb=" N ILE B 551 " --> pdb=" O HIS B 547 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.957A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 618 removed outlier: 3.530A pdb=" N TRP B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN B 618 " --> pdb=" O TYR B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 removed outlier: 4.136A pdb=" N GLY B 624 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 18 removed outlier: 4.192A pdb=" N PHE D 13 " --> pdb=" O GLN D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 39 removed outlier: 3.612A pdb=" N THR D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.752A pdb=" N ASN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 removed outlier: 3.964A pdb=" N MET D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET D 73 " --> pdb=" O PHE D 69 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 removed outlier: 4.070A pdb=" N ARG D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 112 removed outlier: 4.000A pdb=" N VAL D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 removed outlier: 3.704A pdb=" N ILE D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 147 Processing sheet with id= A, first strand: chain 'A' and resid 474 through 476 Processing sheet with id= B, first strand: chain 'B' and resid 474 through 476 481 hydrogen bonds defined for protein. 1395 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: 2.73 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3558 1.34 - 1.46: 2688 1.46 - 1.58: 5350 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 11708 Sorted by residual: bond pdb=" C TRP B 452 " pdb=" N PRO B 453 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.55e+00 bond pdb=" C TRP A 452 " pdb=" N PRO A 453 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.44e+00 bond pdb=" C THR B 264 " pdb=" N PRO B 265 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.34e-02 5.57e+03 4.90e+00 bond pdb=" C THR A 264 " pdb=" N PRO A 265 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.34e-02 5.57e+03 4.63e+00 bond pdb=" CB THR A 403 " pdb=" CG2 THR A 403 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.00e+00 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.46: 230 105.46 - 112.59: 6083 112.59 - 119.71: 4201 119.71 - 126.84: 5257 126.84 - 133.97: 139 Bond angle restraints: 15910 Sorted by residual: angle pdb=" N HIS A 109 " pdb=" CA HIS A 109 " pdb=" C HIS A 109 " ideal model delta sigma weight residual 109.81 119.53 -9.72 2.21e+00 2.05e-01 1.93e+01 angle pdb=" N HIS B 109 " pdb=" CA HIS B 109 " pdb=" C HIS B 109 " ideal model delta sigma weight residual 109.81 119.52 -9.71 2.21e+00 2.05e-01 1.93e+01 angle pdb=" N THR B 264 " pdb=" CA THR B 264 " pdb=" C THR B 264 " ideal model delta sigma weight residual 109.81 119.36 -9.55 2.21e+00 2.05e-01 1.87e+01 angle pdb=" N THR A 264 " pdb=" CA THR A 264 " pdb=" C THR A 264 " ideal model delta sigma weight residual 109.81 119.30 -9.49 2.21e+00 2.05e-01 1.84e+01 angle pdb=" C ASN B 119 " pdb=" N LYS B 120 " pdb=" CA LYS B 120 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.76e+01 ... (remaining 15905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.36: 6498 14.36 - 28.73: 345 28.73 - 43.09: 75 43.09 - 57.45: 16 57.45 - 71.82: 2 Dihedral angle restraints: 6936 sinusoidal: 2684 harmonic: 4252 Sorted by residual: dihedral pdb=" CA HIS B 109 " pdb=" C HIS B 109 " pdb=" N PRO B 110 " pdb=" CA PRO B 110 " ideal model delta harmonic sigma weight residual -180.00 -125.21 -54.79 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA HIS A 109 " pdb=" C HIS A 109 " pdb=" N PRO A 110 " pdb=" CA PRO A 110 " ideal model delta harmonic sigma weight residual 180.00 -125.25 -54.75 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CA THR B 264 " pdb=" C THR B 264 " pdb=" N PRO B 265 " pdb=" CA PRO B 265 " ideal model delta harmonic sigma weight residual -180.00 -138.07 -41.93 0 5.00e+00 4.00e-02 7.03e+01 ... (remaining 6933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1352 0.056 - 0.112: 443 0.112 - 0.168: 63 0.168 - 0.223: 8 0.223 - 0.279: 6 Chirality restraints: 1872 Sorted by residual: chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C13 CLR B 701 " pdb=" C12 CLR B 701 " pdb=" C14 CLR B 701 " pdb=" C17 CLR B 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA CYS B 171 " pdb=" N CYS B 171 " pdb=" C CYS B 171 " pdb=" CB CYS B 171 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1869 not shown) Planarity restraints: 1976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 237 " 0.052 5.00e-02 4.00e+02 7.74e-02 9.59e+00 pdb=" N PRO A 238 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 238 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 238 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 237 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO B 238 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 238 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 238 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 532 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" CG ASN A 532 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 532 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 532 " -0.015 2.00e-02 2.50e+03 ... (remaining 1973 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 10 2.20 - 2.87: 4229 2.87 - 3.55: 15783 3.55 - 4.22: 25907 4.22 - 4.90: 41723 Nonbonded interactions: 87652 Sorted by model distance: nonbonded pdb=" OD1 ASP C 57 " pdb=" OD1 ASP C 59 " model vdw 1.524 3.040 nonbonded pdb=" OD1 ASP D 57 " pdb=" OD1 ASP D 59 " model vdw 1.525 3.040 nonbonded pdb=" OD2 ASP D 21 " pdb=" OD1 ASP D 25 " model vdw 1.782 3.040 nonbonded pdb=" OD2 ASP C 21 " pdb=" OD1 ASP C 25 " model vdw 1.782 3.040 nonbonded pdb=" OD2 ASP C 23 " pdb=" OE2 GLU C 32 " model vdw 1.845 3.040 ... (remaining 87647 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.010 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 31.740 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 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 : 0.008 0.074 11708 Z= 0.516 Angle : 1.022 9.721 15910 Z= 0.540 Chirality : 0.055 0.279 1872 Planarity : 0.008 0.077 1976 Dihedral : 10.050 71.817 4188 Min Nonbonded Distance : 1.524 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.12 % Favored : 92.74 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.29 % 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: -5.23 (0.16), residues: 1446 helix: -3.96 (0.08), residues: 936 sheet: -2.76 (1.03), residues: 20 loop : -1.90 (0.28), residues: 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 396 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 397 average time/residue: 0.2696 time to fit residues: 144.5477 Evaluate side-chains 199 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.377 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN C 108 HIS ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 466 HIS A 500 ASN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 356 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN B 500 ASN B 519 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11708 Z= 0.192 Angle : 0.699 8.357 15910 Z= 0.363 Chirality : 0.042 0.194 1872 Planarity : 0.006 0.081 1976 Dihedral : 6.193 44.139 1580 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 2.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.20), residues: 1446 helix: -1.84 (0.14), residues: 954 sheet: -1.64 (1.22), residues: 20 loop : -1.75 (0.30), residues: 472 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 265 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 287 average time/residue: 0.2191 time to fit residues: 90.9249 Evaluate side-chains 219 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 203 time to evaluate : 1.402 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.1248 time to fit residues: 5.2772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 89 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 4 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 ASN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 11708 Z= 0.229 Angle : 0.673 7.984 15910 Z= 0.346 Chirality : 0.042 0.195 1872 Planarity : 0.006 0.079 1976 Dihedral : 5.897 41.844 1580 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.21), residues: 1446 helix: -0.89 (0.15), residues: 970 sheet: -1.69 (1.18), residues: 20 loop : -1.56 (0.31), residues: 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 213 time to evaluate : 1.430 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 20 residues processed: 238 average time/residue: 0.2256 time to fit residues: 78.3146 Evaluate side-chains 206 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1082 time to fit residues: 6.0783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.1980 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11708 Z= 0.228 Angle : 0.654 8.836 15910 Z= 0.334 Chirality : 0.041 0.191 1872 Planarity : 0.005 0.075 1976 Dihedral : 5.693 39.908 1580 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.22), residues: 1446 helix: -0.29 (0.16), residues: 968 sheet: -1.61 (1.24), residues: 20 loop : -1.55 (0.31), residues: 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 1.428 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 207 average time/residue: 0.2308 time to fit residues: 69.0815 Evaluate side-chains 180 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 173 time to evaluate : 1.354 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1073 time to fit residues: 3.3042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 0.0050 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 96 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS C 136 GLN A 109 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN D 9 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 11708 Z= 0.163 Angle : 0.612 8.469 15910 Z= 0.310 Chirality : 0.039 0.202 1872 Planarity : 0.005 0.073 1976 Dihedral : 5.425 40.613 1580 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.14 % 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: -0.72 (0.22), residues: 1446 helix: 0.07 (0.16), residues: 976 sheet: -1.44 (1.23), residues: 20 loop : -1.47 (0.32), residues: 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 208 time to evaluate : 1.385 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 214 average time/residue: 0.2332 time to fit residues: 72.2567 Evaluate side-chains 186 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 179 time to evaluate : 1.401 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1182 time to fit residues: 3.4031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 HIS ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 11708 Z= 0.167 Angle : 0.624 8.321 15910 Z= 0.315 Chirality : 0.040 0.193 1872 Planarity : 0.005 0.070 1976 Dihedral : 5.250 39.926 1580 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.14 % 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: -0.38 (0.23), residues: 1446 helix: 0.32 (0.16), residues: 980 sheet: -1.25 (1.25), residues: 20 loop : -1.31 (0.33), residues: 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.417 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 208 average time/residue: 0.2394 time to fit residues: 71.4194 Evaluate side-chains 183 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 175 time to evaluate : 1.409 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1109 time to fit residues: 3.5063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 HIS ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 11708 Z= 0.262 Angle : 0.673 9.054 15910 Z= 0.342 Chirality : 0.042 0.186 1872 Planarity : 0.005 0.074 1976 Dihedral : 5.450 40.166 1580 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.23), residues: 1446 helix: 0.27 (0.16), residues: 994 sheet: -1.11 (1.24), residues: 20 loop : -1.35 (0.33), residues: 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 1.393 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 191 average time/residue: 0.2208 time to fit residues: 62.2681 Evaluate side-chains 176 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.307 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1075 time to fit residues: 3.7681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 8.9990 chunk 82 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11708 Z= 0.199 Angle : 0.651 7.911 15910 Z= 0.329 Chirality : 0.041 0.187 1872 Planarity : 0.005 0.071 1976 Dihedral : 5.301 39.709 1580 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.14 % 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: -0.24 (0.23), residues: 1446 helix: 0.44 (0.16), residues: 990 sheet: -1.04 (1.29), residues: 20 loop : -1.35 (0.33), residues: 436 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 1.398 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 194 average time/residue: 0.2285 time to fit residues: 64.3549 Evaluate side-chains 181 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 174 time to evaluate : 1.329 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1062 time to fit residues: 3.1747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 HIS ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 11708 Z= 0.181 Angle : 0.657 10.559 15910 Z= 0.328 Chirality : 0.041 0.187 1872 Planarity : 0.005 0.071 1976 Dihedral : 5.234 39.625 1580 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.77 % Twisted General : 0.14 % 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: -0.18 (0.23), residues: 1446 helix: 0.48 (0.17), residues: 990 sheet: -1.02 (1.28), residues: 20 loop : -1.30 (0.33), residues: 436 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 190 time to evaluate : 1.448 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 194 average time/residue: 0.2391 time to fit residues: 67.6472 Evaluate side-chains 185 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.516 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1076 time to fit residues: 2.8355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 132 optimal weight: 0.0060 chunk 114 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 9 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 11708 Z= 0.214 Angle : 0.683 11.339 15910 Z= 0.342 Chirality : 0.042 0.194 1872 Planarity : 0.005 0.072 1976 Dihedral : 5.236 38.797 1580 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.14 % 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: -0.15 (0.23), residues: 1446 helix: 0.52 (0.17), residues: 986 sheet: -1.11 (1.27), residues: 20 loop : -1.33 (0.33), residues: 440 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 1.622 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 189 average time/residue: 0.2252 time to fit residues: 62.9748 Evaluate side-chains 173 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1055 time to fit residues: 2.3327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100891 restraints weight = 23526.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101701 restraints weight = 14735.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102170 restraints weight = 11086.105| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 11708 Z= 0.168 Angle : 0.675 11.999 15910 Z= 0.334 Chirality : 0.041 0.199 1872 Planarity : 0.005 0.069 1976 Dihedral : 5.105 38.955 1580 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.14 % 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 (0.23), residues: 1446 helix: 0.62 (0.17), residues: 992 sheet: -0.96 (1.34), residues: 20 loop : -1.23 (0.34), residues: 434 =============================================================================== Job complete usr+sys time: 2229.30 seconds wall clock time: 41 minutes 28.52 seconds (2488.52 seconds total)