Starting phenix.real_space_refine on Mon Apr 8 19:34:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/04_2024/6owo_20215_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/04_2024/6owo_20215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/04_2024/6owo_20215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/04_2024/6owo_20215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/04_2024/6owo_20215_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owo_20215/04_2024/6owo_20215_updated.pdb" } resolution = 3.2 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 P 1 5.49 5 S 70 5.16 5 C 9146 2.51 5 N 2427 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 112": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14276 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4505 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 549} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4443 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 534} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3166 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 377} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "S" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1190 Classifications: {'peptide': 141} Link IDs: {'TRANS': 140} Chain: "N" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 7.71, per 1000 atoms: 0.54 Number of scatterers: 14276 At special positions: 0 Unit cell: (102.08, 109.04, 125.28, 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) S 70 16.00 P 1 15.00 O 2632 8.00 N 2427 7.00 C 9146 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: 5.22 Conformation dependent library (CDL) restraints added in 2.6 seconds 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 10 sheets defined 53.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.523A pdb=" N PHE A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 43 Processing helix chain 'A' and resid 52 through 68 removed outlier: 3.740A pdb=" N TYR A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 83 Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 106 through 121 removed outlier: 3.503A pdb=" N ASP A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.843A pdb=" N ALA A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 162 through 178 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.619A pdb=" N SER A 190 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A 193 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS A 194 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.594A pdb=" N SER A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 237 removed outlier: 3.770A pdb=" N SER A 227 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 232 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 234 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 237 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.577A pdb=" N GLN A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 removed outlier: 3.575A pdb=" N GLU A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 320 removed outlier: 3.774A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.675A pdb=" N GLN A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.585A pdb=" N LEU A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 355 " --> pdb=" O GLU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 379 removed outlier: 3.663A pdb=" N LYS A 367 " --> pdb=" O HIS A 363 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N THR A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 395 Processing helix chain 'A' and resid 402 through 413 Processing helix chain 'A' and resid 421 through 434 removed outlier: 3.669A pdb=" N GLU A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.778A pdb=" N VAL A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 471 removed outlier: 3.562A pdb=" N ARG A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 465 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 488 removed outlier: 3.704A pdb=" N PHE A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 507 removed outlier: 3.617A pdb=" N TYR A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 519 through 527 Processing helix chain 'A' and resid 535 through 551 removed outlier: 3.703A pdb=" N SER A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 removed outlier: 3.505A pdb=" N LYS A 556 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA A 557 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 559 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP A 561 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 574 through 588 Processing helix chain 'B' and resid 14 through 23 removed outlier: 3.897A pdb=" N GLU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.623A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 57 Proline residue: B 52 - end of helix removed outlier: 4.237A pdb=" N VAL B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN B 56 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 79 removed outlier: 3.601A pdb=" N ASN B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 removed outlier: 4.736A pdb=" N MET B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA B 87 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ASN B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N SER B 90 " --> pdb=" O MET B 86 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 111 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.604A pdb=" N THR B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.706A pdb=" N CYS B 129 " --> pdb=" O PRO B 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 129' Processing helix chain 'B' and resid 135 through 150 removed outlier: 3.698A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 169 removed outlier: 4.169A pdb=" N ASP B 163 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 164 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 189 removed outlier: 3.532A pdb=" N GLU B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 removed outlier: 4.955A pdb=" N ASN B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 228 removed outlier: 3.886A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 247 removed outlier: 3.507A pdb=" N CYS B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Proline residue: B 246 - end of helix Processing helix chain 'B' and resid 253 through 265 Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 285 through 293 removed outlier: 4.448A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.539A pdb=" N TYR B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 332 through 344 removed outlier: 3.945A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.830A pdb=" N ILE B 351 " --> pdb=" O GLN B 348 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ALA B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 353 " --> pdb=" O ASN B 350 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 355 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 358 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 359 " --> pdb=" O ALA B 356 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B 361 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 362 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 removed outlier: 3.884A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 401 removed outlier: 3.582A pdb=" N ALA B 388 " --> pdb=" O GLU B 385 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLU B 389 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 390 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 396 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 399 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 400 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 3.724A pdb=" N GLN B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 442 through 453 Processing helix chain 'B' and resid 462 through 470 removed outlier: 3.800A pdb=" N SER B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 494 Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.796A pdb=" N SER B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 532 removed outlier: 3.769A pdb=" N ARG B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 541 removed outlier: 3.866A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 566 removed outlier: 3.807A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 573 No H-bonds generated for 'chain 'B' and resid 570 through 573' Processing helix chain 'B' and resid 578 through 580 No H-bonds generated for 'chain 'B' and resid 578 through 580' Processing helix chain 'M' and resid 28 through 35 removed outlier: 3.515A pdb=" N PHE M 32 " --> pdb=" O ALA M 28 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG M 33 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 93 removed outlier: 3.753A pdb=" N CYS M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET M 89 " --> pdb=" O MET M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 101 No H-bonds generated for 'chain 'M' and resid 98 through 101' Processing helix chain 'M' and resid 105 through 114 removed outlier: 3.530A pdb=" N TYR M 109 " --> pdb=" O PHE M 105 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP M 113 " --> pdb=" O TYR M 109 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 131 No H-bonds generated for 'chain 'M' and resid 129 through 131' Processing helix chain 'M' and resid 415 through 417 No H-bonds generated for 'chain 'M' and resid 415 through 417' Processing helix chain 'S' and resid 25 through 39 removed outlier: 3.712A pdb=" N HIS S 36 " --> pdb=" O ILE S 32 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA S 37 " --> pdb=" O GLU S 33 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL S 38 " --> pdb=" O GLU S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 94 removed outlier: 3.556A pdb=" N HIS S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 105 Processing helix chain 'S' and resid 107 through 117 removed outlier: 3.662A pdb=" N THR S 112 " --> pdb=" O TYR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 139 removed outlier: 3.506A pdb=" N MET S 137 " --> pdb=" O LYS S 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 136 removed outlier: 3.610A pdb=" N LEU N 122 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP N 128 " --> pdb=" O ASP N 124 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'M' and resid 47 through 50 removed outlier: 3.514A pdb=" N ILE M 63 " --> pdb=" O ARG M 60 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'M' and resid 419 through 428 removed outlier: 3.504A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER M 204 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU M 271 " --> pdb=" O SER M 204 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 183 through 185 Processing sheet with id= D, first strand: chain 'M' and resid 262 through 265 Processing sheet with id= E, first strand: chain 'M' and resid 287 through 296 removed outlier: 3.854A pdb=" N LYS M 362 " --> pdb=" O SER M 309 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU M 371 " --> pdb=" O GLY M 332 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 316 through 318 Processing sheet with id= G, first strand: chain 'M' and resid 387 through 389 removed outlier: 3.547A pdb=" N SER M 387 " --> pdb=" O ARG M 323 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'S' and resid 49 through 52 removed outlier: 3.502A pdb=" N ARG S 60 " --> pdb=" O PHE S 67 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE S 4 " --> pdb=" O CYS S 70 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 42 through 44 removed outlier: 3.722A pdb=" N HIS N 17 " --> pdb=" O GLY N 108 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA N 103 " --> pdb=" O ILE N 95 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE N 91 " --> pdb=" O LEU N 107 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 8 through 13 removed outlier: 6.652A pdb=" N ILE N 48 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL N 12 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU N 46 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL N 54 " --> pdb=" O LYS N 51 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA N 69 " --> pdb=" O LEU N 59 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4071 1.33 - 1.45: 2185 1.45 - 1.57: 8167 1.57 - 1.69: 3 1.69 - 1.81: 105 Bond restraints: 14531 Sorted by residual: bond pdb=" OG1 TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.717 1.620 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" O1P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.525 1.612 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" O2P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.528 1.602 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C PHE N 76 " pdb=" N PRO N 77 " ideal model delta sigma weight residual 1.334 1.359 -0.025 8.40e-03 1.42e+04 9.13e+00 bond pdb=" O3P TPO M 156 " pdb=" P TPO M 156 " ideal model delta sigma weight residual 1.528 1.474 0.054 2.00e-02 2.50e+03 7.25e+00 ... (remaining 14526 not shown) Histogram of bond angle deviations from ideal: 97.64 - 105.57: 259 105.57 - 113.49: 8319 113.49 - 121.42: 7921 121.42 - 129.34: 3084 129.34 - 137.27: 80 Bond angle restraints: 19663 Sorted by residual: angle pdb=" N VAL A 555 " pdb=" CA VAL A 555 " pdb=" C VAL A 555 " ideal model delta sigma weight residual 113.43 106.70 6.73 1.09e+00 8.42e-01 3.82e+01 angle pdb=" C ARG M 60 " pdb=" N SER M 61 " pdb=" CA SER M 61 " ideal model delta sigma weight residual 121.54 131.21 -9.67 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C PHE S 52 " pdb=" N ARG S 53 " pdb=" CA ARG S 53 " ideal model delta sigma weight residual 121.54 131.10 -9.56 1.91e+00 2.74e-01 2.50e+01 angle pdb=" N PRO B 201 " pdb=" CA PRO B 201 " pdb=" C PRO B 201 " ideal model delta sigma weight residual 113.75 121.07 -7.32 1.49e+00 4.50e-01 2.41e+01 angle pdb=" C VAL N 73 " pdb=" N ASP N 74 " pdb=" CA ASP N 74 " ideal model delta sigma weight residual 121.54 130.78 -9.24 1.91e+00 2.74e-01 2.34e+01 ... (remaining 19658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 8426 14.94 - 29.88: 346 29.88 - 44.83: 101 44.83 - 59.77: 4 59.77 - 74.71: 2 Dihedral angle restraints: 8879 sinusoidal: 3602 harmonic: 5277 Sorted by residual: dihedral pdb=" CA ARG S 53 " pdb=" C ARG S 53 " pdb=" N ASN S 54 " pdb=" CA ASN S 54 " ideal model delta harmonic sigma weight residual 180.00 148.71 31.29 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" CA LYS B 29 " pdb=" C LYS B 29 " pdb=" N ARG B 30 " pdb=" CA ARG B 30 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ASN M 62 " pdb=" C ASN M 62 " pdb=" N ILE M 63 " pdb=" CA ILE M 63 " ideal model delta harmonic sigma weight residual -180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 8876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1723 0.060 - 0.119: 476 0.119 - 0.179: 68 0.179 - 0.238: 9 0.238 - 0.298: 2 Chirality restraints: 2278 Sorted by residual: chirality pdb=" CA PRO B 201 " pdb=" N PRO B 201 " pdb=" C PRO B 201 " pdb=" CB PRO B 201 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE N 21 " pdb=" CA ILE N 21 " pdb=" CG1 ILE N 21 " pdb=" CG2 ILE N 21 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ASP M 282 " pdb=" N ASP M 282 " pdb=" C ASP M 282 " pdb=" CB ASP M 282 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2275 not shown) Planarity restraints: 2496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 421 " -0.026 2.00e-02 2.50e+03 2.43e-02 1.48e+01 pdb=" CG TRP M 421 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP M 421 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP M 421 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 421 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP M 421 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 421 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 421 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP M 421 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE N 21 " 0.053 5.00e-02 4.00e+02 8.02e-02 1.03e+01 pdb=" N PRO N 22 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO N 22 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO N 22 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 361 " 0.016 2.00e-02 2.50e+03 1.89e-02 7.11e+00 pdb=" CG TYR B 361 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 361 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 361 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 361 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 361 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 361 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 361 " 0.001 2.00e-02 2.50e+03 ... (remaining 2493 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3765 2.79 - 3.32: 12856 3.32 - 3.84: 22789 3.84 - 4.37: 28307 4.37 - 4.90: 47334 Nonbonded interactions: 115051 Sorted by model distance: nonbonded pdb=" OH TYR A 95 " pdb=" OD2 ASP A 119 " model vdw 2.261 2.440 nonbonded pdb=" OH TYR M 20 " pdb=" O LEU M 112 " model vdw 2.266 2.440 nonbonded pdb=" OE1 GLU M 179 " pdb=" OH TYR M 277 " model vdw 2.271 2.440 nonbonded pdb=" NH1 ARG M 199 " pdb=" OE2 GLU M 273 " model vdw 2.279 2.520 nonbonded pdb=" O2P TPO M 156 " pdb=" OG SER N 87 " model vdw 2.306 2.440 ... (remaining 115046 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.020 Extract box with map and model: 6.680 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 39.430 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 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 : 0.009 0.097 14531 Z= 0.573 Angle : 0.987 14.175 19663 Z= 0.565 Chirality : 0.055 0.298 2278 Planarity : 0.007 0.080 2496 Dihedral : 9.504 74.710 5439 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 0.25 % Allowed : 1.71 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -4.78 (0.15), residues: 1749 helix: -4.19 (0.07), residues: 973 sheet: -0.99 (0.33), residues: 235 loop : -1.53 (0.23), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.005 TRP M 421 HIS 0.008 0.002 HIS A 363 PHE 0.043 0.004 PHE S 67 TYR 0.046 0.004 TYR B 361 ARG 0.009 0.001 ARG M 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 305 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 520 LEU cc_start: 0.8774 (tt) cc_final: 0.8303 (mp) REVERT: A 570 LYS cc_start: 0.8347 (mttt) cc_final: 0.8110 (tmtt) REVERT: A 585 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7724 (mtt180) REVERT: B 110 MET cc_start: 0.8984 (mtp) cc_final: 0.8726 (mtm) REVERT: B 458 ARG cc_start: 0.8333 (mmt180) cc_final: 0.7625 (ttt180) REVERT: B 467 GLU cc_start: 0.8305 (tp30) cc_final: 0.7825 (tp30) REVERT: M 218 ASP cc_start: 0.7988 (p0) cc_final: 0.7725 (p0) REVERT: N 95 ILE cc_start: 0.8705 (pp) cc_final: 0.8437 (pp) REVERT: N 137 LYS cc_start: 0.8545 (mptt) cc_final: 0.8069 (mptt) outliers start: 4 outliers final: 1 residues processed: 309 average time/residue: 0.3511 time to fit residues: 146.9381 Evaluate side-chains 158 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 194 HIS ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 179 ASN B 191 HIS B 250 HIS B 252 ASN B 353 GLN B 500 GLN M 38 HIS M 135 GLN M 310 ASN S 8 GLN N 123 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14531 Z= 0.205 Angle : 0.614 11.987 19663 Z= 0.330 Chirality : 0.043 0.183 2278 Planarity : 0.005 0.068 2496 Dihedral : 5.224 30.210 1936 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.71 % Allowed : 5.76 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.17), residues: 1749 helix: -1.79 (0.13), residues: 987 sheet: -0.38 (0.33), residues: 242 loop : -1.20 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 421 HIS 0.004 0.001 HIS S 85 PHE 0.018 0.002 PHE A 552 TYR 0.022 0.002 TYR A 478 ARG 0.008 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.8292 (pm20) cc_final: 0.7946 (pm20) REVERT: A 570 LYS cc_start: 0.8355 (mttt) cc_final: 0.8090 (tmtt) REVERT: B 67 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9056 (tttm) REVERT: B 83 MET cc_start: 0.8032 (tpp) cc_final: 0.7654 (tpp) REVERT: B 148 LEU cc_start: 0.8871 (tt) cc_final: 0.8653 (tt) REVERT: B 340 ASP cc_start: 0.8838 (t0) cc_final: 0.8444 (m-30) REVERT: B 458 ARG cc_start: 0.8321 (mmt180) cc_final: 0.7561 (ttt180) REVERT: B 467 GLU cc_start: 0.8245 (tp30) cc_final: 0.7880 (tp30) REVERT: M 85 MET cc_start: 0.8856 (tmm) cc_final: 0.8333 (tmm) REVERT: M 218 ASP cc_start: 0.7984 (p0) cc_final: 0.7678 (p0) REVERT: S 13 LYS cc_start: 0.9071 (ptmm) cc_final: 0.8848 (ptmm) REVERT: S 55 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.8148 (p90) outliers start: 27 outliers final: 21 residues processed: 209 average time/residue: 0.3067 time to fit residues: 91.3787 Evaluate side-chains 171 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 421 TRP Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 79 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 160 optimal weight: 0.3980 chunk 172 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN B 149 HIS ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14531 Z= 0.181 Angle : 0.538 10.827 19663 Z= 0.284 Chirality : 0.041 0.153 2278 Planarity : 0.004 0.059 2496 Dihedral : 4.699 29.830 1936 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.84 % Allowed : 7.85 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.19), residues: 1749 helix: -0.42 (0.16), residues: 987 sheet: -0.16 (0.33), residues: 244 loop : -0.76 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 421 HIS 0.003 0.001 HIS M 249 PHE 0.019 0.001 PHE S 4 TYR 0.023 0.001 TYR A 478 ARG 0.003 0.000 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 1.679 Fit side-chains REVERT: A 570 LYS cc_start: 0.8386 (mttt) cc_final: 0.8085 (tmtt) REVERT: B 83 MET cc_start: 0.8178 (tpp) cc_final: 0.7534 (tpp) REVERT: B 235 ARG cc_start: 0.8441 (ptm-80) cc_final: 0.8090 (mmp80) REVERT: B 340 ASP cc_start: 0.8860 (t0) cc_final: 0.8396 (m-30) REVERT: B 458 ARG cc_start: 0.8366 (mmt180) cc_final: 0.7600 (ttt180) REVERT: S 55 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7846 (p90) REVERT: S 61 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8289 (ttp80) outliers start: 29 outliers final: 18 residues processed: 198 average time/residue: 0.3147 time to fit residues: 88.0767 Evaluate side-chains 164 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain N residue 18 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 0.0970 chunk 170 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 307 ASN A 375 ASN M 103 ASN N 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14531 Z= 0.263 Angle : 0.566 10.443 19663 Z= 0.295 Chirality : 0.043 0.156 2278 Planarity : 0.004 0.054 2496 Dihedral : 4.619 26.074 1936 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.41 % Allowed : 8.23 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1749 helix: 0.19 (0.16), residues: 992 sheet: -0.00 (0.33), residues: 244 loop : -0.63 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 421 HIS 0.004 0.001 HIS M 57 PHE 0.019 0.002 PHE S 4 TYR 0.018 0.002 TYR A 53 ARG 0.004 0.000 ARG M 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 1.752 Fit side-chains REVERT: A 218 ASN cc_start: 0.9097 (OUTLIER) cc_final: 0.8635 (p0) REVERT: A 570 LYS cc_start: 0.8449 (mttt) cc_final: 0.8134 (tmtt) REVERT: B 83 MET cc_start: 0.8176 (tpp) cc_final: 0.7656 (tpp) REVERT: B 235 ARG cc_start: 0.8543 (ptm-80) cc_final: 0.8158 (mmp80) REVERT: B 340 ASP cc_start: 0.8837 (t0) cc_final: 0.8314 (m-30) REVERT: B 458 ARG cc_start: 0.8430 (mmt180) cc_final: 0.7746 (ttt180) REVERT: B 527 TRP cc_start: 0.8459 (t-100) cc_final: 0.8049 (t60) REVERT: S 55 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7682 (p90) REVERT: S 61 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8303 (ttp80) REVERT: N 39 GLN cc_start: 0.8383 (mp10) cc_final: 0.8061 (mp10) outliers start: 38 outliers final: 31 residues processed: 180 average time/residue: 0.3064 time to fit residues: 79.1318 Evaluate side-chains 178 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 0.0370 chunk 117 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN M 62 ASN M 365 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14531 Z= 0.150 Angle : 0.516 10.616 19663 Z= 0.267 Chirality : 0.041 0.148 2278 Planarity : 0.004 0.057 2496 Dihedral : 4.440 25.101 1936 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.41 % Allowed : 8.55 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1749 helix: 0.60 (0.17), residues: 992 sheet: 0.12 (0.34), residues: 244 loop : -0.51 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 421 HIS 0.002 0.001 HIS M 57 PHE 0.017 0.001 PHE S 4 TYR 0.018 0.001 TYR A 53 ARG 0.004 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8375 (mttt) cc_final: 0.8062 (tmtt) REVERT: B 21 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: B 83 MET cc_start: 0.8192 (tpp) cc_final: 0.7762 (tpp) REVERT: B 340 ASP cc_start: 0.8801 (t0) cc_final: 0.8281 (m-30) REVERT: B 458 ARG cc_start: 0.8499 (mmt180) cc_final: 0.7744 (ttt180) REVERT: B 527 TRP cc_start: 0.8448 (t-100) cc_final: 0.8027 (t60) REVERT: M 302 GLU cc_start: 0.8178 (pm20) cc_final: 0.7938 (pm20) REVERT: S 21 MET cc_start: 0.8588 (ttp) cc_final: 0.8344 (ptm) REVERT: S 55 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7148 (p90) REVERT: S 61 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.8244 (ttp80) REVERT: N 19 TYR cc_start: 0.8321 (m-80) cc_final: 0.8032 (m-80) REVERT: N 51 LYS cc_start: 0.6124 (tttp) cc_final: 0.5864 (mmtt) outliers start: 38 outliers final: 27 residues processed: 185 average time/residue: 0.2829 time to fit residues: 76.4613 Evaluate side-chains 181 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 61 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 170 optimal weight: 10.0000 chunk 141 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.0170 chunk 164 optimal weight: 0.0980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 389 ASN S 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14531 Z= 0.119 Angle : 0.497 10.666 19663 Z= 0.255 Chirality : 0.040 0.193 2278 Planarity : 0.003 0.058 2496 Dihedral : 4.185 24.517 1936 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 2.03 % Allowed : 8.87 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.20), residues: 1749 helix: 0.91 (0.17), residues: 988 sheet: 0.37 (0.34), residues: 233 loop : -0.39 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 421 HIS 0.002 0.000 HIS B 575 PHE 0.017 0.001 PHE S 4 TYR 0.017 0.001 TYR A 53 ARG 0.007 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7749 (p) REVERT: A 570 LYS cc_start: 0.8360 (mttt) cc_final: 0.8039 (tmtt) REVERT: B 21 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: B 83 MET cc_start: 0.8225 (tpp) cc_final: 0.7770 (tpp) REVERT: B 340 ASP cc_start: 0.8821 (t0) cc_final: 0.8272 (m-30) REVERT: B 458 ARG cc_start: 0.8519 (mmt180) cc_final: 0.7724 (ttt180) REVERT: B 527 TRP cc_start: 0.8434 (t-100) cc_final: 0.7980 (t60) REVERT: M 85 MET cc_start: 0.8842 (tmm) cc_final: 0.8408 (ttt) REVERT: M 302 GLU cc_start: 0.8132 (pm20) cc_final: 0.7902 (pm20) REVERT: S 55 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7177 (p90) REVERT: S 61 ARG cc_start: 0.8560 (ttp-110) cc_final: 0.8272 (ttp80) REVERT: S 93 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8338 (mm-30) REVERT: N 19 TYR cc_start: 0.8249 (m-80) cc_final: 0.7995 (m-80) REVERT: N 34 GLU cc_start: 0.7986 (mp0) cc_final: 0.7747 (mp0) outliers start: 32 outliers final: 22 residues processed: 206 average time/residue: 0.2933 time to fit residues: 86.7950 Evaluate side-chains 187 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 61 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 72 ASN M 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14531 Z= 0.207 Angle : 0.527 10.249 19663 Z= 0.271 Chirality : 0.042 0.166 2278 Planarity : 0.004 0.057 2496 Dihedral : 4.249 23.366 1936 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.66 % Allowed : 9.12 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1749 helix: 0.99 (0.17), residues: 988 sheet: 0.34 (0.33), residues: 238 loop : -0.30 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 421 HIS 0.003 0.001 HIS M 57 PHE 0.022 0.001 PHE M 81 TYR 0.014 0.001 TYR A 53 ARG 0.006 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 168 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 CYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7811 (p) REVERT: A 570 LYS cc_start: 0.8392 (mttt) cc_final: 0.8086 (tmtt) REVERT: B 21 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: B 83 MET cc_start: 0.8249 (tpp) cc_final: 0.7831 (tpp) REVERT: B 340 ASP cc_start: 0.8823 (t0) cc_final: 0.8278 (m-30) REVERT: B 458 ARG cc_start: 0.8555 (mmt180) cc_final: 0.7802 (ttt180) REVERT: B 527 TRP cc_start: 0.8452 (t-100) cc_final: 0.7991 (t60) REVERT: M 302 GLU cc_start: 0.8183 (pm20) cc_final: 0.7971 (pm20) REVERT: M 323 ARG cc_start: 0.8716 (ptp-110) cc_final: 0.8468 (mtp85) REVERT: S 55 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7091 (p90) REVERT: S 61 ARG cc_start: 0.8505 (ttp-110) cc_final: 0.8220 (ttp80) REVERT: S 93 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8393 (mm-30) REVERT: N 7 GLU cc_start: 0.7107 (pp20) cc_final: 0.6875 (pp20) REVERT: N 19 TYR cc_start: 0.8270 (m-80) cc_final: 0.8032 (m-80) REVERT: N 34 GLU cc_start: 0.7977 (mp0) cc_final: 0.7723 (mp0) outliers start: 42 outliers final: 37 residues processed: 194 average time/residue: 0.2736 time to fit residues: 77.0195 Evaluate side-chains 202 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 162 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 462 TRP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 275 MET Chi-restraints excluded: chain M residue 279 THR Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain N residue 8 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 61 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 0.0470 chunk 154 optimal weight: 0.7980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14531 Z= 0.138 Angle : 0.512 10.596 19663 Z= 0.263 Chirality : 0.041 0.167 2278 Planarity : 0.003 0.055 2496 Dihedral : 4.139 23.023 1936 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 2.15 % Allowed : 9.75 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1749 helix: 1.12 (0.17), residues: 995 sheet: 0.44 (0.33), residues: 238 loop : -0.31 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 421 HIS 0.006 0.001 HIS S 85 PHE 0.019 0.001 PHE A 552 TYR 0.014 0.001 TYR A 478 ARG 0.007 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 CYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7762 (p) REVERT: A 570 LYS cc_start: 0.8380 (mttt) cc_final: 0.8075 (tmtt) REVERT: B 21 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: B 83 MET cc_start: 0.8253 (tpp) cc_final: 0.7837 (tpp) REVERT: B 340 ASP cc_start: 0.8821 (t0) cc_final: 0.8265 (m-30) REVERT: B 458 ARG cc_start: 0.8587 (mmt180) cc_final: 0.7744 (ttt180) REVERT: B 527 TRP cc_start: 0.8439 (t-100) cc_final: 0.7966 (t60) REVERT: M 85 MET cc_start: 0.8772 (tmm) cc_final: 0.8429 (ttt) REVERT: M 323 ARG cc_start: 0.8664 (ptp-110) cc_final: 0.8452 (mtp85) REVERT: S 55 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7168 (p90) REVERT: S 93 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8333 (mm-30) REVERT: N 7 GLU cc_start: 0.7082 (pp20) cc_final: 0.6854 (pp20) REVERT: N 19 TYR cc_start: 0.8255 (m-80) cc_final: 0.8044 (m-80) REVERT: N 34 GLU cc_start: 0.7988 (mp0) cc_final: 0.7769 (mp0) outliers start: 34 outliers final: 29 residues processed: 204 average time/residue: 0.2826 time to fit residues: 83.7529 Evaluate side-chains 201 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 275 MET Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 54 ASN Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 61 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 0.6980 chunk 148 optimal weight: 0.0870 chunk 158 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 103 ASN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14531 Z= 0.140 Angle : 0.510 10.477 19663 Z= 0.261 Chirality : 0.041 0.167 2278 Planarity : 0.003 0.055 2496 Dihedral : 4.076 22.705 1936 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.74 % Favored : 97.20 % Rotamer: Outliers : 2.09 % Allowed : 9.69 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1749 helix: 1.24 (0.17), residues: 992 sheet: 0.53 (0.34), residues: 238 loop : -0.36 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 421 HIS 0.007 0.001 HIS S 85 PHE 0.021 0.001 PHE A 552 TYR 0.014 0.001 TYR A 478 ARG 0.006 0.000 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 LYS cc_start: 0.8369 (mttt) cc_final: 0.8065 (tmtt) REVERT: B 21 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: B 83 MET cc_start: 0.8270 (tpp) cc_final: 0.7865 (tpp) REVERT: B 458 ARG cc_start: 0.8602 (mmt180) cc_final: 0.7796 (ttt180) REVERT: B 527 TRP cc_start: 0.8390 (t-100) cc_final: 0.7905 (t60) REVERT: M 85 MET cc_start: 0.8758 (tmm) cc_final: 0.8508 (ttp) REVERT: S 55 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.7393 (p90) REVERT: S 93 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8314 (mm-30) REVERT: N 7 GLU cc_start: 0.7083 (pp20) cc_final: 0.6858 (pp20) REVERT: N 19 TYR cc_start: 0.8247 (m-80) cc_final: 0.8031 (m-80) REVERT: N 34 GLU cc_start: 0.7959 (mp0) cc_final: 0.7712 (mp0) outliers start: 33 outliers final: 27 residues processed: 196 average time/residue: 0.2919 time to fit residues: 82.8420 Evaluate side-chains 201 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 21 GLU Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 275 MET Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 36 HIS Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 61 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN B 203 ASN M 103 ASN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14531 Z= 0.238 Angle : 0.557 10.041 19663 Z= 0.286 Chirality : 0.042 0.190 2278 Planarity : 0.004 0.054 2496 Dihedral : 4.230 22.979 1936 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.97 % Favored : 96.97 % Rotamer: Outliers : 2.15 % Allowed : 9.44 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1749 helix: 1.14 (0.17), residues: 995 sheet: 0.54 (0.34), residues: 238 loop : -0.34 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 421 HIS 0.009 0.001 HIS S 85 PHE 0.017 0.002 PHE M 272 TYR 0.018 0.001 TYR A 478 ARG 0.007 0.000 ARG A 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 162 time to evaluate : 1.734 Fit side-chains revert: symmetry clash REVERT: A 282 GLU cc_start: 0.8092 (pm20) cc_final: 0.7595 (pm20) REVERT: A 570 LYS cc_start: 0.8444 (mttt) cc_final: 0.8134 (tmtt) REVERT: B 83 MET cc_start: 0.8275 (tpp) cc_final: 0.7899 (tpp) REVERT: B 458 ARG cc_start: 0.8619 (mmt180) cc_final: 0.7881 (ttt180) REVERT: B 527 TRP cc_start: 0.8493 (t-100) cc_final: 0.8043 (t60) REVERT: S 55 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7262 (p90) REVERT: S 93 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8426 (mm-30) REVERT: N 7 GLU cc_start: 0.7212 (pp20) cc_final: 0.6975 (pp20) REVERT: N 19 TYR cc_start: 0.8303 (m-80) cc_final: 0.7931 (m-80) REVERT: N 34 GLU cc_start: 0.8022 (mp0) cc_final: 0.7763 (mp0) outliers start: 34 outliers final: 28 residues processed: 182 average time/residue: 0.2886 time to fit residues: 75.7638 Evaluate side-chains 189 residues out of total 1587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 516 ARG Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain M residue 10 HIS Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 245 ASP Chi-restraints excluded: chain M residue 275 MET Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain S residue 13 LYS Chi-restraints excluded: chain S residue 25 ASP Chi-restraints excluded: chain S residue 55 PHE Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 101 LEU Chi-restraints excluded: chain S residue 126 THR Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 30 TYR Chi-restraints excluded: chain N residue 37 LEU Chi-restraints excluded: chain N residue 61 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 36 HIS N 39 GLN ** N 75 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 = 0.3419 r_free = 0.3419 target = 0.106788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.086102 restraints weight = 25107.818| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.27 r_work: 0.2924 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14531 Z= 0.217 Angle : 0.552 10.228 19663 Z= 0.282 Chirality : 0.042 0.169 2278 Planarity : 0.004 0.054 2496 Dihedral : 4.244 23.047 1936 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Rotamer: Outliers : 2.09 % Allowed : 9.37 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1749 helix: 1.17 (0.17), residues: 994 sheet: 0.53 (0.34), residues: 238 loop : -0.31 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 421 HIS 0.008 0.001 HIS S 85 PHE 0.020 0.001 PHE A 552 TYR 0.018 0.001 TYR A 478 ARG 0.008 0.000 ARG A 123 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.82 seconds wall clock time: 58 minutes 45.20 seconds (3525.20 seconds total)