Starting phenix.real_space_refine on Thu Feb 15 06:55:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/02_2024/5sy1_8315_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/02_2024/5sy1_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_8315/02_2024/5sy1_8315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/02_2024/5sy1_8315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/02_2024/5sy1_8315_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5sy1_8315/02_2024/5sy1_8315_updated.pdb" } resolution = 3.9 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= 0.005 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.24, per 1000 atoms: 0.54 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: 4.57 Conformation dependent library (CDL) restraints added in 2.3 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: 2.30 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: 2.82 Time building geometry restraints manager: 4.66 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: 6593 14.36 - 28.73: 362 28.73 - 43.09: 75 43.09 - 57.45: 16 57.45 - 71.82: 2 Dihedral angle restraints: 7048 sinusoidal: 2796 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 7045 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: 0.540 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: 2.400 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.080 Find NCS groups from input model: 0.610 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.580 ------------------------------------------------------------------------------- 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 : 10.045 71.817 4300 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 % Allowed : 1.63 % Favored : 98.29 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 399 HIS 0.007 0.002 HIS B 609 PHE 0.038 0.004 PHE A 40 TYR 0.014 0.003 TYR B 94 ARG 0.010 0.001 ARG A 486 *********************** 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 : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 3 ASP cc_start: 0.7028 (m-30) cc_final: 0.6428 (t70) REVERT: C 4 GLN cc_start: 0.8855 (tt0) cc_final: 0.8605 (tt0) REVERT: C 8 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8197 (pm20) REVERT: C 15 GLU cc_start: 0.8639 (tp30) cc_final: 0.8371 (tp30) REVERT: C 38 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8168 (ptp-110) REVERT: C 52 MET cc_start: 0.8763 (mtp) cc_final: 0.8066 (ttp) REVERT: C 73 MET cc_start: 0.8033 (mmm) cc_final: 0.7756 (mmp) REVERT: C 77 MET cc_start: 0.7526 (mpt) cc_final: 0.6730 (mpp) REVERT: C 85 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7907 (tm-30) REVERT: C 93 PHE cc_start: 0.7242 (m-80) cc_final: 0.6484 (m-80) REVERT: C 101 ILE cc_start: 0.6517 (mt) cc_final: 0.6267 (mp) REVERT: C 124 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7943 (tp30) REVERT: C 125 MET cc_start: 0.7466 (mtt) cc_final: 0.6561 (mmm) REVERT: A 52 MET cc_start: 0.7390 (mtp) cc_final: 0.6923 (ttt) REVERT: A 104 MET cc_start: 0.8396 (ttp) cc_final: 0.8059 (tmm) REVERT: A 109 HIS cc_start: 0.7137 (p90) cc_final: 0.6588 (t70) REVERT: A 150 TYR cc_start: 0.8249 (m-80) cc_final: 0.8022 (m-80) REVERT: A 187 LEU cc_start: 0.8634 (mt) cc_final: 0.8409 (mt) REVERT: A 215 ASN cc_start: 0.6243 (p0) cc_final: 0.5617 (m-40) REVERT: A 220 LEU cc_start: 0.8833 (tp) cc_final: 0.8534 (mt) REVERT: A 249 LYS cc_start: 0.6213 (tttt) cc_final: 0.6004 (mtmt) REVERT: A 268 VAL cc_start: 0.8414 (t) cc_final: 0.7780 (p) REVERT: A 286 LEU cc_start: 0.6102 (tp) cc_final: 0.5902 (tp) REVERT: A 532 ASN cc_start: 0.8530 (t0) cc_final: 0.8102 (t0) REVERT: A 550 LYS cc_start: 0.7850 (ttmm) cc_final: 0.7459 (mmtp) REVERT: A 602 ASN cc_start: 0.7139 (t0) cc_final: 0.6652 (t0) REVERT: A 604 LYS cc_start: 0.8333 (tptt) cc_final: 0.8083 (mtpp) REVERT: B 53 LEU cc_start: 0.7843 (mt) cc_final: 0.7418 (tt) REVERT: B 109 HIS cc_start: 0.7039 (p90) cc_final: 0.6189 (t70) REVERT: B 125 ILE cc_start: 0.7715 (mt) cc_final: 0.7458 (pt) REVERT: B 130 TYR cc_start: 0.7500 (t80) cc_final: 0.7263 (t80) REVERT: B 181 TYR cc_start: 0.8668 (t80) cc_final: 0.8468 (t80) REVERT: B 186 SER cc_start: 0.7362 (m) cc_final: 0.7123 (p) REVERT: B 220 LEU cc_start: 0.8656 (tp) cc_final: 0.8371 (mt) REVERT: B 235 LYS cc_start: 0.7346 (tttt) cc_final: 0.6555 (tmtt) REVERT: B 268 VAL cc_start: 0.8198 (t) cc_final: 0.7456 (p) REVERT: B 326 ASP cc_start: 0.6283 (t0) cc_final: 0.5855 (t0) REVERT: D 4 GLN cc_start: 0.9047 (tt0) cc_final: 0.8237 (tm-30) REVERT: D 8 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8182 (pm20) REVERT: D 15 GLU cc_start: 0.8882 (tp30) cc_final: 0.8680 (tp30) REVERT: D 17 PHE cc_start: 0.8742 (t80) cc_final: 0.8515 (t80) REVERT: D 38 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8385 (ptp-110) REVERT: D 69 PHE cc_start: 0.6796 (t80) cc_final: 0.6557 (t80) REVERT: D 85 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7774 (tm-30) REVERT: D 93 PHE cc_start: 0.7375 (m-80) cc_final: 0.6851 (m-80) REVERT: D 95 LYS cc_start: 0.7247 (mttt) cc_final: 0.6959 (mtmt) REVERT: D 101 ILE cc_start: 0.7001 (mt) cc_final: 0.6519 (mp) REVERT: D 124 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7740 (tp30) REVERT: D 125 MET cc_start: 0.7875 (mtt) cc_final: 0.7095 (mmm) outliers start: 1 outliers final: 0 residues processed: 397 average time/residue: 0.2710 time to fit residues: 145.8097 Evaluate side-chains 225 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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: 0.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 0.0020 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN C 108 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 466 HIS A 500 ASN 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: 0.6211 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11708 Z= 0.184 Angle : 0.690 8.120 15910 Z= 0.358 Chirality : 0.042 0.201 1872 Planarity : 0.006 0.084 1976 Dihedral : 6.477 46.426 1692 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.87 % Allowed : 10.02 % Favored : 88.11 % 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: -2.97 (0.20), residues: 1446 helix: -1.88 (0.13), residues: 966 sheet: -1.62 (1.22), residues: 20 loop : -1.76 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 158 HIS 0.005 0.001 HIS D 108 PHE 0.023 0.001 PHE C 17 TYR 0.025 0.001 TYR B 178 ARG 0.003 0.000 ARG B 368 *********************** 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 307 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8887 (tt0) cc_final: 0.8077 (tm-30) REVERT: C 12 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8210 (mm-30) REVERT: C 15 GLU cc_start: 0.8673 (tp30) cc_final: 0.8394 (tt0) REVERT: C 38 ARG cc_start: 0.8258 (ttm110) cc_final: 0.8049 (ttm110) REVERT: C 85 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8100 (tm-30) REVERT: C 91 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7326 (mmt90) REVERT: C 93 PHE cc_start: 0.7309 (m-80) cc_final: 0.6709 (m-80) REVERT: C 124 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8049 (tp30) REVERT: C 125 MET cc_start: 0.7675 (mtt) cc_final: 0.6841 (mmm) REVERT: C 139 TYR cc_start: 0.7711 (t80) cc_final: 0.7436 (t80) REVERT: A 52 MET cc_start: 0.7343 (mtp) cc_final: 0.6887 (ttm) REVERT: A 109 HIS cc_start: 0.7221 (p90) cc_final: 0.6816 (m-70) REVERT: A 150 TYR cc_start: 0.8419 (m-80) cc_final: 0.8040 (m-80) REVERT: A 186 SER cc_start: 0.7123 (m) cc_final: 0.6791 (p) REVERT: A 200 TYR cc_start: 0.7362 (m-10) cc_final: 0.6517 (m-80) REVERT: A 215 ASN cc_start: 0.6251 (p0) cc_final: 0.5466 (m-40) REVERT: A 220 LEU cc_start: 0.8775 (tp) cc_final: 0.8444 (mt) REVERT: A 224 TYR cc_start: 0.7001 (t80) cc_final: 0.6774 (t80) REVERT: A 249 LYS cc_start: 0.6130 (tttt) cc_final: 0.5894 (mtmt) REVERT: A 268 VAL cc_start: 0.8021 (t) cc_final: 0.7510 (p) REVERT: A 532 ASN cc_start: 0.8385 (t0) cc_final: 0.8021 (t0) REVERT: A 550 LYS cc_start: 0.7971 (ttmm) cc_final: 0.7543 (mmtp) REVERT: A 602 ASN cc_start: 0.7008 (t0) cc_final: 0.6490 (t0) REVERT: B 53 LEU cc_start: 0.7704 (mt) cc_final: 0.7346 (tt) REVERT: B 109 HIS cc_start: 0.7190 (p90) cc_final: 0.6471 (m-70) REVERT: B 130 TYR cc_start: 0.7541 (t80) cc_final: 0.7294 (t80) REVERT: B 186 SER cc_start: 0.7173 (m) cc_final: 0.6848 (p) REVERT: B 235 LYS cc_start: 0.7283 (tttt) cc_final: 0.6504 (tmtt) REVERT: B 268 VAL cc_start: 0.7575 (t) cc_final: 0.7083 (p) REVERT: B 329 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: B 502 MET cc_start: 0.7899 (mmp) cc_final: 0.7627 (mmp) REVERT: B 610 TRP cc_start: 0.7274 (m-10) cc_final: 0.6871 (m-10) REVERT: D 4 GLN cc_start: 0.8941 (tt0) cc_final: 0.8190 (tm-30) REVERT: D 12 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8081 (mm-30) REVERT: D 15 GLU cc_start: 0.8914 (tp30) cc_final: 0.8659 (tt0) REVERT: D 38 ARG cc_start: 0.8392 (ttm110) cc_final: 0.8086 (ptp-110) REVERT: D 83 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7237 (mp0) REVERT: D 91 ARG cc_start: 0.8064 (mtt90) cc_final: 0.7437 (mtt-85) REVERT: D 101 ILE cc_start: 0.5538 (mt) cc_final: 0.5258 (mt) REVERT: D 124 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7953 (tm-30) REVERT: D 125 MET cc_start: 0.7744 (mtt) cc_final: 0.6775 (mmm) REVERT: D 139 TYR cc_start: 0.7675 (t80) cc_final: 0.7211 (t80) outliers start: 23 outliers final: 14 residues processed: 299 average time/residue: 0.2211 time to fit residues: 95.2658 Evaluate side-chains 230 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 215 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain D residue 53 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 108 optimal weight: 0.0470 chunk 89 optimal weight: 4.9990 chunk 36 optimal weight: 0.0670 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 112 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** D 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11708 Z= 0.160 Angle : 0.625 7.784 15910 Z= 0.319 Chirality : 0.040 0.190 1872 Planarity : 0.005 0.078 1976 Dihedral : 5.781 44.846 1692 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.93 % Allowed : 13.19 % Favored : 83.88 % 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: -1.71 (0.21), residues: 1446 helix: -0.76 (0.15), residues: 946 sheet: -1.40 (1.29), residues: 20 loop : -1.62 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 452 HIS 0.009 0.001 HIS D 108 PHE 0.028 0.001 PHE D 17 TYR 0.014 0.001 TYR A 180 ARG 0.003 0.000 ARG D 38 *********************** 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 286 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 250 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8745 (tt0) cc_final: 0.7960 (tm-30) REVERT: C 38 ARG cc_start: 0.8308 (ttm110) cc_final: 0.8051 (ptp-110) REVERT: C 72 MET cc_start: 0.8649 (mtp) cc_final: 0.8365 (mtp) REVERT: C 91 ARG cc_start: 0.7744 (mtt90) cc_final: 0.7318 (mmt90) REVERT: C 93 PHE cc_start: 0.7350 (m-80) cc_final: 0.6648 (m-80) REVERT: C 108 HIS cc_start: 0.7911 (t70) cc_final: 0.7442 (t70) REVERT: C 124 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8134 (tp30) REVERT: C 125 MET cc_start: 0.7732 (mtt) cc_final: 0.6942 (mmm) REVERT: A 52 MET cc_start: 0.7432 (mtp) cc_final: 0.7028 (ttm) REVERT: A 109 HIS cc_start: 0.7090 (p90) cc_final: 0.6756 (m-70) REVERT: A 215 ASN cc_start: 0.5928 (p0) cc_final: 0.5372 (m-40) REVERT: A 220 LEU cc_start: 0.8705 (tp) cc_final: 0.8329 (mt) REVERT: A 249 LYS cc_start: 0.5918 (tttt) cc_final: 0.5655 (mtmt) REVERT: A 268 VAL cc_start: 0.8001 (t) cc_final: 0.7560 (p) REVERT: A 532 ASN cc_start: 0.8189 (t0) cc_final: 0.7950 (t0) REVERT: A 550 LYS cc_start: 0.7864 (ttmm) cc_final: 0.7450 (mmtp) REVERT: B 109 HIS cc_start: 0.7238 (p90) cc_final: 0.6749 (m-70) REVERT: B 130 TYR cc_start: 0.7535 (t80) cc_final: 0.7275 (t80) REVERT: B 135 TYR cc_start: 0.8063 (m-80) cc_final: 0.7760 (m-80) REVERT: B 268 VAL cc_start: 0.7524 (t) cc_final: 0.7032 (p) REVERT: B 329 GLU cc_start: 0.8070 (tp30) cc_final: 0.7846 (mp0) REVERT: B 370 ASN cc_start: 0.7808 (m-40) cc_final: 0.7576 (m-40) REVERT: B 568 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8269 (mm) REVERT: D 4 GLN cc_start: 0.8929 (tt0) cc_final: 0.8211 (tm-30) REVERT: D 12 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7996 (mm-30) REVERT: D 15 GLU cc_start: 0.8892 (tp30) cc_final: 0.8635 (tt0) REVERT: D 37 MET cc_start: 0.8812 (mmt) cc_final: 0.8570 (mmt) REVERT: D 72 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8102 (mtp) REVERT: D 77 MET cc_start: 0.6837 (mpt) cc_final: 0.6521 (mpp) REVERT: D 83 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7245 (mp0) REVERT: D 91 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7446 (mtt-85) REVERT: D 124 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8004 (tm-30) REVERT: D 125 MET cc_start: 0.7811 (mtt) cc_final: 0.6638 (mmm) REVERT: D 139 TYR cc_start: 0.7548 (t80) cc_final: 0.7191 (t80) outliers start: 36 outliers final: 15 residues processed: 272 average time/residue: 0.2170 time to fit residues: 85.1087 Evaluate side-chains 218 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 0.0000 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- 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 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN B 199 GLN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11708 Z= 0.188 Angle : 0.621 7.854 15910 Z= 0.316 Chirality : 0.040 0.181 1872 Planarity : 0.005 0.076 1976 Dihedral : 5.626 44.603 1692 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.18 % Allowed : 14.09 % Favored : 82.74 % 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: -0.94 (0.22), residues: 1446 helix: -0.14 (0.16), residues: 954 sheet: -1.63 (1.19), residues: 20 loop : -1.37 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 452 HIS 0.009 0.001 HIS C 108 PHE 0.044 0.001 PHE B 40 TYR 0.016 0.001 TYR B 181 ARG 0.002 0.000 ARG D 38 *********************** 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 252 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 213 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8702 (tt0) cc_final: 0.8071 (tm-30) REVERT: C 12 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7930 (tp30) REVERT: C 15 GLU cc_start: 0.8476 (tt0) cc_final: 0.8112 (tp30) REVERT: C 38 ARG cc_start: 0.8322 (ttm110) cc_final: 0.8082 (ptp-110) REVERT: C 83 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7899 (mp0) REVERT: C 93 PHE cc_start: 0.7367 (m-80) cc_final: 0.6666 (m-80) REVERT: C 124 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8194 (tp30) REVERT: C 125 MET cc_start: 0.7698 (mtt) cc_final: 0.7393 (mtt) REVERT: A 52 MET cc_start: 0.7486 (mtp) cc_final: 0.7086 (ttm) REVERT: A 215 ASN cc_start: 0.5932 (p0) cc_final: 0.5419 (m-40) REVERT: A 220 LEU cc_start: 0.8685 (tp) cc_final: 0.8343 (mt) REVERT: A 249 LYS cc_start: 0.5910 (tttt) cc_final: 0.5631 (mtmt) REVERT: A 268 VAL cc_start: 0.7993 (t) cc_final: 0.7514 (p) REVERT: A 550 LYS cc_start: 0.7916 (ttmm) cc_final: 0.7526 (mmtp) REVERT: B 109 HIS cc_start: 0.7156 (p90) cc_final: 0.6740 (m-70) REVERT: B 135 TYR cc_start: 0.8119 (m-80) cc_final: 0.7865 (m-80) REVERT: B 268 VAL cc_start: 0.7766 (t) cc_final: 0.7249 (p) REVERT: B 287 TYR cc_start: 0.5746 (t80) cc_final: 0.5493 (t80) REVERT: B 329 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: B 568 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8261 (mm) REVERT: D 4 GLN cc_start: 0.8912 (tt0) cc_final: 0.8187 (tm-30) REVERT: D 12 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7987 (mm-30) REVERT: D 15 GLU cc_start: 0.8928 (tp30) cc_final: 0.8672 (tt0) REVERT: D 72 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8552 (mtp) REVERT: D 83 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7273 (mp0) REVERT: D 91 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7376 (mtt-85) REVERT: D 124 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8102 (tm-30) REVERT: D 125 MET cc_start: 0.7858 (mtt) cc_final: 0.6759 (mmm) REVERT: D 139 TYR cc_start: 0.7586 (t80) cc_final: 0.7208 (t80) outliers start: 39 outliers final: 21 residues processed: 234 average time/residue: 0.2253 time to fit residues: 75.5776 Evaluate side-chains 215 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 142 PHE 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: 5.9990 chunk 2 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** 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 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.4405 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= 0.194 Angle : 0.615 7.919 15910 Z= 0.312 Chirality : 0.040 0.185 1872 Planarity : 0.005 0.074 1976 Dihedral : 5.461 43.650 1692 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.26 % Allowed : 13.84 % Favored : 82.90 % 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: -0.54 (0.22), residues: 1446 helix: 0.22 (0.16), residues: 966 sheet: -1.39 (1.22), residues: 20 loop : -1.40 (0.32), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 452 HIS 0.007 0.001 HIS C 108 PHE 0.020 0.001 PHE B 427 TYR 0.011 0.001 TYR B 181 ARG 0.004 0.000 ARG A 255 *********************** 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 252 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 212 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8695 (tt0) cc_final: 0.8039 (tm-30) REVERT: C 12 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7908 (mm-30) REVERT: C 38 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7977 (ptp-110) REVERT: C 72 MET cc_start: 0.8643 (mtp) cc_final: 0.8386 (mtp) REVERT: C 83 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7866 (mp0) REVERT: C 93 PHE cc_start: 0.7340 (m-80) cc_final: 0.6681 (m-80) REVERT: C 124 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8264 (tm-30) REVERT: C 125 MET cc_start: 0.7707 (mtt) cc_final: 0.7199 (mtt) REVERT: C 139 TYR cc_start: 0.7409 (t80) cc_final: 0.7159 (t80) REVERT: A 52 MET cc_start: 0.7472 (mtp) cc_final: 0.7101 (ttm) REVERT: A 215 ASN cc_start: 0.5889 (p0) cc_final: 0.5432 (m-40) REVERT: A 220 LEU cc_start: 0.8663 (tp) cc_final: 0.8317 (mt) REVERT: A 268 VAL cc_start: 0.8019 (t) cc_final: 0.7539 (p) REVERT: A 550 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7539 (mmtp) REVERT: B 135 TYR cc_start: 0.8042 (m-80) cc_final: 0.7800 (m-80) REVERT: B 268 VAL cc_start: 0.7823 (t) cc_final: 0.7288 (p) REVERT: B 329 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: D 4 GLN cc_start: 0.8891 (tt0) cc_final: 0.8209 (tm-30) REVERT: D 15 GLU cc_start: 0.8940 (tp30) cc_final: 0.8710 (tt0) REVERT: D 83 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7265 (mp0) REVERT: D 124 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8123 (tm-30) REVERT: D 125 MET cc_start: 0.7939 (mtt) cc_final: 0.6809 (mmm) REVERT: D 139 TYR cc_start: 0.7468 (t80) cc_final: 0.7072 (t80) outliers start: 40 outliers final: 26 residues processed: 235 average time/residue: 0.2298 time to fit residues: 77.0971 Evaluate side-chains 210 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 142 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 136 GLN ** 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** A 532 ASN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11708 Z= 0.183 Angle : 0.607 8.658 15910 Z= 0.309 Chirality : 0.040 0.189 1872 Planarity : 0.005 0.072 1976 Dihedral : 5.306 43.602 1692 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.69 % Allowed : 14.50 % Favored : 82.82 % 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: -0.33 (0.23), residues: 1446 helix: 0.43 (0.16), residues: 978 sheet: -1.23 (1.25), residues: 20 loop : -1.50 (0.32), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 452 HIS 0.007 0.001 HIS C 108 PHE 0.022 0.001 PHE A 427 TYR 0.012 0.001 TYR A 180 ARG 0.004 0.000 ARG A 255 *********************** 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 236 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 203 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8754 (tt0) cc_final: 0.8044 (tm-30) REVERT: C 12 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7928 (mm-30) REVERT: C 38 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7977 (ptp-110) REVERT: C 83 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7806 (mp0) REVERT: C 93 PHE cc_start: 0.7498 (m-80) cc_final: 0.6848 (m-80) REVERT: C 124 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8259 (tm-30) REVERT: C 125 MET cc_start: 0.7698 (mtt) cc_final: 0.7187 (mtt) REVERT: C 139 TYR cc_start: 0.7454 (t80) cc_final: 0.7192 (t80) REVERT: A 52 MET cc_start: 0.7480 (mtp) cc_final: 0.7118 (ttm) REVERT: A 215 ASN cc_start: 0.5869 (p0) cc_final: 0.5452 (m-40) REVERT: A 220 LEU cc_start: 0.8645 (tp) cc_final: 0.8298 (mt) REVERT: A 268 VAL cc_start: 0.8027 (t) cc_final: 0.7535 (p) REVERT: A 550 LYS cc_start: 0.7847 (ttmm) cc_final: 0.7552 (mmtp) REVERT: B 135 TYR cc_start: 0.8024 (m-80) cc_final: 0.7796 (m-80) REVERT: B 268 VAL cc_start: 0.7831 (t) cc_final: 0.7301 (p) REVERT: B 287 TYR cc_start: 0.5715 (t80) cc_final: 0.5492 (t80) REVERT: B 329 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: B 486 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7335 (mtt-85) REVERT: D 4 GLN cc_start: 0.8915 (tt0) cc_final: 0.8304 (tm-30) REVERT: D 15 GLU cc_start: 0.8865 (tp30) cc_final: 0.8654 (tt0) REVERT: D 83 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7320 (mp0) REVERT: D 124 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8125 (tm-30) REVERT: D 125 MET cc_start: 0.7936 (mtt) cc_final: 0.6823 (mmm) REVERT: D 139 TYR cc_start: 0.7497 (t80) cc_final: 0.7017 (t80) outliers start: 33 outliers final: 29 residues processed: 222 average time/residue: 0.2363 time to fit residues: 75.1627 Evaluate side-chains 210 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 142 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 0.0010 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 85 optimal weight: 6.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 ASN ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11708 Z= 0.155 Angle : 0.614 9.470 15910 Z= 0.306 Chirality : 0.039 0.193 1872 Planarity : 0.005 0.071 1976 Dihedral : 5.175 42.902 1692 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.28 % Allowed : 14.90 % Favored : 82.82 % 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: 0.05 (0.23), residues: 1446 helix: 0.71 (0.17), residues: 972 sheet: -1.07 (1.27), residues: 20 loop : -1.29 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 452 HIS 0.008 0.000 HIS C 108 PHE 0.021 0.001 PHE A 427 TYR 0.010 0.001 TYR A 180 ARG 0.006 0.000 ARG A 255 *********************** 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 227 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8692 (tt0) cc_final: 0.7937 (tm-30) REVERT: C 12 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8062 (tp30) REVERT: C 38 ARG cc_start: 0.8252 (ttm110) cc_final: 0.8026 (ptp-110) REVERT: C 83 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7949 (mp0) REVERT: C 124 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8265 (tm-30) REVERT: C 125 MET cc_start: 0.7875 (mtt) cc_final: 0.7314 (mtt) REVERT: C 139 TYR cc_start: 0.7393 (t80) cc_final: 0.7137 (t80) REVERT: A 52 MET cc_start: 0.7453 (mtp) cc_final: 0.7061 (ttp) REVERT: A 220 LEU cc_start: 0.8566 (tp) cc_final: 0.8222 (mt) REVERT: A 268 VAL cc_start: 0.7992 (t) cc_final: 0.7496 (p) REVERT: A 550 LYS cc_start: 0.7840 (ttmm) cc_final: 0.7549 (mmtp) REVERT: B 135 TYR cc_start: 0.7912 (m-80) cc_final: 0.7700 (m-80) REVERT: B 268 VAL cc_start: 0.7991 (t) cc_final: 0.7466 (p) REVERT: B 329 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: B 486 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.7278 (mtt-85) REVERT: D 4 GLN cc_start: 0.8926 (tt0) cc_final: 0.8304 (tm-30) REVERT: D 83 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7420 (mp0) REVERT: D 124 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8148 (tm-30) REVERT: D 125 MET cc_start: 0.7914 (mtt) cc_final: 0.6836 (mmm) REVERT: D 139 TYR cc_start: 0.7392 (t80) cc_final: 0.6945 (t80) outliers start: 28 outliers final: 20 residues processed: 215 average time/residue: 0.2416 time to fit residues: 74.5106 Evaluate side-chains 205 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain D residue 64 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 5.9990 chunk 82 optimal weight: 0.0050 chunk 41 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 68 optimal weight: 0.0870 chunk 12 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 overall best weight: 0.8176 ------------------------------------------------------------------------------- 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** ** 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** A 519 ASN ** 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 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11708 Z= 0.163 Angle : 0.610 8.496 15910 Z= 0.306 Chirality : 0.039 0.193 1872 Planarity : 0.005 0.070 1976 Dihedral : 5.061 42.980 1692 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.87 % Allowed : 15.55 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.07 % 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: 0.23 (0.23), residues: 1446 helix: 0.83 (0.17), residues: 974 sheet: -1.00 (1.30), residues: 20 loop : -1.20 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 452 HIS 0.008 0.001 HIS C 108 PHE 0.020 0.001 PHE A 427 TYR 0.020 0.001 TYR A 150 ARG 0.006 0.000 ARG A 255 *********************** 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 217 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 194 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8659 (tt0) cc_final: 0.7928 (tm-30) REVERT: C 12 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8074 (tp30) REVERT: C 38 ARG cc_start: 0.8292 (ttm110) cc_final: 0.8075 (ptp-110) REVERT: C 125 MET cc_start: 0.7946 (mtt) cc_final: 0.7323 (mtt) REVERT: A 52 MET cc_start: 0.7479 (mtp) cc_final: 0.7156 (ttp) REVERT: A 220 LEU cc_start: 0.8459 (tp) cc_final: 0.8125 (mt) REVERT: A 268 VAL cc_start: 0.7999 (t) cc_final: 0.7497 (p) REVERT: A 364 MET cc_start: 0.6896 (tpp) cc_final: 0.6074 (ttt) REVERT: A 550 LYS cc_start: 0.7869 (ttmm) cc_final: 0.7569 (mmtp) REVERT: B 268 VAL cc_start: 0.7980 (t) cc_final: 0.7447 (p) REVERT: B 486 ARG cc_start: 0.7369 (mmm-85) cc_final: 0.7126 (mtt-85) REVERT: D 4 GLN cc_start: 0.8987 (tt0) cc_final: 0.8358 (tm-30) REVERT: D 83 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7397 (mp0) REVERT: D 125 MET cc_start: 0.7907 (mtt) cc_final: 0.7189 (mtp) REVERT: D 139 TYR cc_start: 0.7372 (t80) cc_final: 0.6875 (t80) outliers start: 23 outliers final: 21 residues processed: 207 average time/residue: 0.2329 time to fit residues: 69.2577 Evaluate side-chains 202 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain D residue 137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 7.9990 chunk 121 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 56 optimal weight: 0.0170 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- 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 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 moved from start: 0.5155 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= 0.227 Angle : 0.648 9.628 15910 Z= 0.324 Chirality : 0.041 0.197 1872 Planarity : 0.005 0.072 1976 Dihedral : 5.202 42.052 1692 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.28 % Allowed : 15.64 % Favored : 82.08 % 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: 0.18 (0.23), residues: 1446 helix: 0.80 (0.17), residues: 986 sheet: -0.92 (1.28), residues: 20 loop : -1.29 (0.33), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 452 HIS 0.007 0.001 HIS C 108 PHE 0.021 0.001 PHE A 427 TYR 0.022 0.001 TYR A 287 ARG 0.007 0.000 ARG A 255 *********************** 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 206 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8619 (tt0) cc_final: 0.7899 (tm-30) REVERT: C 8 GLU cc_start: 0.7344 (pm20) cc_final: 0.7078 (pm20) REVERT: C 12 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8013 (mm-30) REVERT: A 52 MET cc_start: 0.7483 (mtp) cc_final: 0.7166 (ttp) REVERT: A 268 VAL cc_start: 0.8108 (t) cc_final: 0.7634 (p) REVERT: A 364 MET cc_start: 0.7031 (tpp) cc_final: 0.6164 (ttt) REVERT: B 109 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.6535 (t-90) REVERT: B 268 VAL cc_start: 0.8046 (t) cc_final: 0.7495 (p) REVERT: B 329 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: B 486 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.7239 (mtt-85) REVERT: D 4 GLN cc_start: 0.8984 (tt0) cc_final: 0.8263 (tm-30) REVERT: D 83 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7549 (mp0) REVERT: D 125 MET cc_start: 0.7619 (mtt) cc_final: 0.6962 (mmm) outliers start: 28 outliers final: 22 residues processed: 199 average time/residue: 0.2203 time to fit residues: 64.0633 Evaluate side-chains 195 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 452 TRP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 493 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.2980 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** A 519 ASN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11708 Z= 0.167 Angle : 0.626 9.109 15910 Z= 0.312 Chirality : 0.040 0.194 1872 Planarity : 0.005 0.069 1976 Dihedral : 5.044 42.311 1692 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.87 % Allowed : 16.37 % Favored : 81.76 % 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: 0.44 (0.23), residues: 1446 helix: 1.00 (0.17), residues: 972 sheet: -0.97 (1.31), residues: 20 loop : -1.13 (0.33), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 452 HIS 0.007 0.001 HIS C 108 PHE 0.019 0.001 PHE A 427 TYR 0.020 0.001 TYR A 287 ARG 0.005 0.000 ARG A 255 ********************** 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 211 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 4 GLN cc_start: 0.8702 (tt0) cc_final: 0.7926 (tm-30) REVERT: C 8 GLU cc_start: 0.7381 (pm20) cc_final: 0.7119 (pm20) REVERT: C 12 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8107 (tp30) REVERT: C 125 MET cc_start: 0.7475 (mtt) cc_final: 0.6971 (mmm) REVERT: A 52 MET cc_start: 0.7427 (mtp) cc_final: 0.7090 (ttp) REVERT: A 268 VAL cc_start: 0.8022 (t) cc_final: 0.7536 (p) REVERT: A 364 MET cc_start: 0.6923 (tpp) cc_final: 0.6070 (ttt) REVERT: B 109 HIS cc_start: 0.6728 (OUTLIER) cc_final: 0.6525 (t-90) REVERT: B 268 VAL cc_start: 0.7972 (t) cc_final: 0.7415 (p) REVERT: B 329 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: B 486 ARG cc_start: 0.7437 (mmm-85) cc_final: 0.7200 (mtt-85) REVERT: D 4 GLN cc_start: 0.8990 (tt0) cc_final: 0.8347 (tm-30) REVERT: D 54 ASN cc_start: 0.8055 (m110) cc_final: 0.7843 (m110) REVERT: D 83 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7523 (mp0) REVERT: D 125 MET cc_start: 0.7572 (mtt) cc_final: 0.6932 (mmm) outliers start: 23 outliers final: 21 residues processed: 202 average time/residue: 0.2134 time to fit residues: 63.0341 Evaluate side-chains 201 residues out of total 1280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 455 TRP Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 HIS Chi-restraints excluded: chain B residue 141 CYS Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 361 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A 519 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.135324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098200 restraints weight = 23215.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100735 restraints weight = 13740.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102337 restraints weight = 10112.546| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11708 Z= 0.175 Angle : 0.629 10.320 15910 Z= 0.313 Chirality : 0.040 0.196 1872 Planarity : 0.005 0.070 1976 Dihedral : 5.001 41.459 1692 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.20 % Allowed : 15.80 % Favored : 82.00 % 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: 0.45 (0.23), residues: 1446 helix: 1.00 (0.17), residues: 984 sheet: -0.93 (1.29), residues: 20 loop : -1.17 (0.33), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 452 HIS 0.010 0.001 HIS C 108 PHE 0.020 0.001 PHE A 427 TYR 0.023 0.001 TYR A 181 ARG 0.006 0.000 ARG A 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2395.73 seconds wall clock time: 44 minutes 19.17 seconds (2659.17 seconds total)