Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 20:37:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/04_2023/7k01_22587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/04_2023/7k01_22587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/04_2023/7k01_22587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/04_2023/7k01_22587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/04_2023/7k01_22587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/04_2023/7k01_22587_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 5 6.06 5 S 123 5.16 5 C 13215 2.51 5 N 3745 2.21 5 O 3960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 282": "OE1" <-> "OE2" Residue "1 ARG 286": "NH1" <-> "NH2" Residue "4 GLU 55": "OE1" <-> "OE2" Residue "4 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 134": "OE1" <-> "OE2" Residue "4 ARG 175": "NH1" <-> "NH2" Residue "4 ARG 273": "NH1" <-> "NH2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "2 ARG 450": "NH1" <-> "NH2" Residue "0 GLU 85": "OE1" <-> "OE2" Residue "0 ARG 375": "NH1" <-> "NH2" Residue "0 GLU 421": "OE1" <-> "OE2" Residue "0 GLU 572": "OE1" <-> "OE2" Residue "6 ARG 378": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 21052 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2408 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 729 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 25, 'ASP:plan': 18, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 327 Chain: "4" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2041 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 11, 'TRANS': 272} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 85 Chain: "7" Number of atoms: 4447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4447 Classifications: {'peptide': 634} Incomplete info: {'backbone_only': 162} Link IDs: {'PTRANS': 26, 'TRANS': 607} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 1003 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 312 Chain: "5" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 498 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 62} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "2" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3011 Classifications: {'peptide': 460} Incomplete info: {'backbone_only': 154, 'truncation_to_alanine': 14} Link IDs: {'PTRANS': 17, 'TRANS': 442} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 727 Unresolved non-hydrogen angles: 1042 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 210 Planarities with less than four sites: {'GLN:plan1': 11, 'ARG:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 8, 'GLU:plan': 16, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 352 Chain: "0" Number of atoms: 6108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6108 Classifications: {'peptide': 754} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 721} Chain: "6" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2526 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 6, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 138 Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4244 SG CYS 4 289 54.958 56.600 110.902 1.00 0.00 S ATOM 4263 SG CYS 4 292 51.676 57.227 112.799 1.00 0.00 S ATOM 4348 SG CYS 4 305 53.623 53.966 112.924 1.00 0.00 S ATOM 4364 SG CYS 4 308 51.419 54.305 110.513 1.00 0.00 S ATOM 13343 SG CYS 0 115 55.562 28.673 48.346 1.00117.61 S ATOM 13343 SG CYS 0 115 55.562 28.673 48.346 1.00117.61 S ATOM 13670 SG CYS 0 156 57.397 24.619 47.475 1.00 90.79 S ATOM 13485 SG CYS 0 133 52.822 25.451 45.227 1.00 46.59 S ATOM 20726 SG CYS 6 403 27.695 79.689 110.997 1.00 0.00 S ATOM 20748 SG CYS 6 406 28.455 83.188 110.240 1.00 0.00 S ATOM 20915 SG CYS 6 437 27.581 80.989 107.263 1.00 0.00 S ATOM 20931 SG CYS 6 440 30.745 80.372 109.054 1.00 0.00 S ATOM 20873 SG CYS 6 429 30.429 67.904 110.392 1.00 0.00 S ATOM 20889 SG CYS 6 432 29.273 69.643 113.479 1.00 0.00 S ATOM 21009 SG CYS 6 451 32.826 70.408 112.300 1.00 0.00 S ATOM 21024 SG CYS 6 454 32.073 67.085 113.677 1.00 0.00 S ATOM 20371 SG CYS 6 349 71.715 69.148 112.948 1.00 0.00 S ATOM 20392 SG CYS 6 352 75.240 70.452 112.916 1.00 0.00 S ATOM 20461 SG CYS 6 363 73.968 69.215 109.815 1.00 0.00 S ATOM 20479 SG CYS 6 366 74.215 66.523 111.961 1.00 0.00 S ATOM 20288 SG CYS 6 336 75.695 80.367 107.015 1.00 30.00 S ATOM 20299 SG CYS 6 338 72.773 78.035 106.260 1.00 30.00 S ATOM 20426 SG CYS 6 357 72.028 81.591 107.319 1.00 30.00 S Time building chain proxies: 11.65, per 1000 atoms: 0.55 Number of scatterers: 21052 At special positions: 0 Unit cell: (106.24, 154.38, 156.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 Fe 4 26.01 S 123 16.00 O 3960 8.00 N 3745 7.00 C 13215 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: 9.96 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " Number of angles added : 9 Zn2+ tetrahedral coordination pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 403 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 437 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 429 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 352 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " Number of angles added : 27 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4962 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 11 sheets defined 45.9% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 Processing helix chain '1' and resid 189 through 197 Processing helix chain '1' and resid 206 through 224 removed outlier: 3.510A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) Proline residue: 1 215 - end of helix Processing helix chain '1' and resid 231 through 236 Processing helix chain '1' and resid 252 through 262 Processing helix chain '1' and resid 264 through 272 Processing helix chain '1' and resid 282 through 294 removed outlier: 3.697A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 329 removed outlier: 3.740A pdb=" N GLU 1 320 " --> pdb=" O THR 1 316 " (cutoff:3.500A) Processing helix chain '1' and resid 339 through 342 No H-bonds generated for 'chain '1' and resid 339 through 342' Processing helix chain '1' and resid 372 through 390 removed outlier: 3.949A pdb=" N LEU 1 389 " --> pdb=" O MET 1 385 " (cutoff:3.500A) Processing helix chain '1' and resid 468 through 482 Processing helix chain '1' and resid 497 through 515 Processing helix chain '1' and resid 541 through 564 Processing helix chain '1' and resid 576 through 604 Processing helix chain '1' and resid 607 through 638 Proline residue: 1 618 - end of helix Processing helix chain '4' and resid 34 through 42 Processing helix chain '4' and resid 50 through 67 Processing helix chain '4' and resid 117 through 134 Processing helix chain '4' and resid 138 through 142 Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 193 through 206 Processing helix chain '4' and resid 222 through 230 Processing helix chain '4' and resid 244 through 251 Processing helix chain '4' and resid 314 through 322 Processing helix chain '7' and resid 105 through 108 Processing helix chain '7' and resid 125 through 127 No H-bonds generated for 'chain '7' and resid 125 through 127' Processing helix chain '7' and resid 150 through 160 Processing helix chain '7' and resid 177 through 186 Processing helix chain '7' and resid 190 through 200 Processing helix chain '7' and resid 207 through 218 removed outlier: 3.516A pdb=" N ILE 7 218 " --> pdb=" O LYS 7 214 " (cutoff:3.500A) Processing helix chain '7' and resid 239 through 247 Processing helix chain '7' and resid 262 through 267 Processing helix chain '7' and resid 323 through 332 Processing helix chain '7' and resid 364 through 374 Processing helix chain '7' and resid 392 through 403 removed outlier: 4.428A pdb=" N GLY 7 396 " --> pdb=" O LYS 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 414 through 424 Processing helix chain '7' and resid 457 through 460 No H-bonds generated for 'chain '7' and resid 457 through 460' Processing helix chain '7' and resid 469 through 479 Processing helix chain '7' and resid 495 through 505 Processing helix chain '7' and resid 527 through 531 Processing helix chain '7' and resid 540 through 546 removed outlier: 3.962A pdb=" N GLN 7 545 " --> pdb=" O MET 7 541 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS 7 546 " --> pdb=" O GLU 7 542 " (cutoff:3.500A) Processing helix chain '7' and resid 563 through 571 Processing helix chain '7' and resid 575 through 582 removed outlier: 4.043A pdb=" N LEU 7 579 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 601 Processing helix chain '7' and resid 613 through 622 Processing helix chain '7' and resid 633 through 644 Processing helix chain '7' and resid 682 through 690 Processing helix chain '7' and resid 714 through 729 removed outlier: 3.795A pdb=" N TYR 7 717 " --> pdb=" O GLN 7 714 " (cutoff:3.500A) Processing helix chain '7' and resid 753 through 765 removed outlier: 3.566A pdb=" N LEU 7 765 " --> pdb=" O GLN 7 761 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 44 through 61 removed outlier: 4.314A pdb=" N GLU 5 48 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) Processing helix chain '2' and resid 10 through 16 Processing helix chain '2' and resid 19 through 26 Processing helix chain '2' and resid 29 through 36 Processing helix chain '2' and resid 41 through 50 Processing helix chain '2' and resid 59 through 64 Processing helix chain '2' and resid 71 through 84 Processing helix chain '2' and resid 102 through 112 Processing helix chain '2' and resid 120 through 122 No H-bonds generated for 'chain '2' and resid 120 through 122' Processing helix chain '2' and resid 136 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 193 Processing helix chain '2' and resid 197 through 210 Processing helix chain '2' and resid 218 through 230 Processing helix chain '2' and resid 244 through 255 Processing helix chain '2' and resid 273 through 280 removed outlier: 4.020A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 354 through 363 removed outlier: 4.226A pdb=" N PHE 2 363 " --> pdb=" O VAL 2 359 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 388 removed outlier: 4.008A pdb=" N ALA 2 386 " --> pdb=" O SER 2 382 " (cutoff:3.500A) Processing helix chain '2' and resid 395 through 402 Processing helix chain '2' and resid 409 through 416 Processing helix chain '2' and resid 435 through 447 Processing helix chain '2' and resid 465 through 478 Processing helix chain '2' and resid 496 through 506 Processing helix chain '0' and resid 19 through 33 Processing helix chain '0' and resid 48 through 62 Processing helix chain '0' and resid 76 through 97 Processing helix chain '0' and resid 118 through 122 Processing helix chain '0' and resid 126 through 136 Processing helix chain '0' and resid 141 through 147 Processing helix chain '0' and resid 158 through 168 removed outlier: 5.007A pdb=" N VAL 0 167 " --> pdb=" O TYR 0 163 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU 0 168 " --> pdb=" O ASN 0 164 " (cutoff:3.500A) Processing helix chain '0' and resid 178 through 187 Processing helix chain '0' and resid 192 through 201 removed outlier: 5.233A pdb=" N SER 0 201 " --> pdb=" O ARG 0 197 " (cutoff:3.500A) Processing helix chain '0' and resid 211 through 214 No H-bonds generated for 'chain '0' and resid 211 through 214' Processing helix chain '0' and resid 241 through 248 Processing helix chain '0' and resid 254 through 277 Processing helix chain '0' and resid 280 through 291 Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 323 through 326 Processing helix chain '0' and resid 328 through 346 Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 388 removed outlier: 3.897A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N CYS 0 377 " --> pdb=" O PRO 0 373 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 394 through 411 removed outlier: 4.790A pdb=" N ALA 0 398 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) Processing helix chain '0' and resid 425 through 427 No H-bonds generated for 'chain '0' and resid 425 through 427' Processing helix chain '0' and resid 442 through 452 removed outlier: 3.617A pdb=" N LYS 0 447 " --> pdb=" O ILE 0 444 " (cutoff:3.500A) Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 468 through 473 Processing helix chain '0' and resid 516 through 532 Processing helix chain '0' and resid 544 through 556 Processing helix chain '0' and resid 559 through 566 removed outlier: 3.738A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 591 Processing helix chain '0' and resid 605 through 609 removed outlier: 4.066A pdb=" N GLY 0 609 " --> pdb=" O LYS 0 605 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 605 through 609' Processing helix chain '0' and resid 634 through 645 Processing helix chain '0' and resid 650 through 669 removed outlier: 4.038A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 691 removed outlier: 3.512A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 695 through 700 removed outlier: 3.907A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 703 through 705 No H-bonds generated for 'chain '0' and resid 703 through 705' Processing helix chain '0' and resid 710 through 725 Processing helix chain '0' and resid 734 through 737 No H-bonds generated for 'chain '0' and resid 734 through 737' Processing helix chain '0' and resid 744 through 751 Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 201 removed outlier: 3.726A pdb=" N LYS 6 201 " --> pdb=" O LYS 6 197 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 223 removed outlier: 3.845A pdb=" N LEU 6 222 " --> pdb=" O ARG 6 218 " (cutoff:3.500A) Proline residue: 6 223 - end of helix Processing helix chain '6' and resid 248 through 257 Processing helix chain '6' and resid 271 through 280 Processing helix chain '6' and resid 294 through 305 Processing helix chain '6' and resid 374 through 383 Processing helix chain '6' and resid 419 through 422 No H-bonds generated for 'chain '6' and resid 419 through 422' Processing helix chain '6' and resid 438 through 446 Processing helix chain '6' and resid 452 through 455 No H-bonds generated for 'chain '6' and resid 452 through 455' Processing sheet with id= A, first strand: chain '4' and resid 26 through 31 removed outlier: 3.630A pdb=" N ALA 4 78 " --> pdb=" O ILE 4 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '4' and resid 176 through 182 removed outlier: 4.055A pdb=" N GLY 4 216 " --> pdb=" O VAL 4 238 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '7' and resid 382 through 385 Processing sheet with id= D, first strand: chain '7' and resid 484 through 487 removed outlier: 6.708A pdb=" N VAL 7 453 " --> pdb=" O VAL 7 409 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N CYS 7 411 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER 7 455 " --> pdb=" O CYS 7 411 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '7' and resid 732 through 734 removed outlier: 5.890A pdb=" N ALA 7 703 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA 7 555 " --> pdb=" O ALA 7 703 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE 7 705 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE 7 606 " --> pdb=" O ILE 7 671 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '5' and resid 8 through 11 Processing sheet with id= G, first strand: chain '0' and resid 456 through 459 removed outlier: 6.833A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '0' and resid 416 through 418 removed outlier: 3.616A pdb=" N THR 0 438 " --> pdb=" O LEU 0 417 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '0' and resid 537 through 541 removed outlier: 6.073A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '6' and resid 168 through 172 removed outlier: 3.682A pdb=" N LEU 6 126 " --> pdb=" O GLN 6 168 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY 6 170 " --> pdb=" O LEU 6 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU 6 233 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '6' and resid 322 through 324 removed outlier: 5.962A pdb=" N MET 6 369 " --> pdb=" O GLY 6 323 " (cutoff:3.500A) No H-bonds generated for sheet with id= K 881 hydrogen bonds defined for protein. 2457 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: 6.55 Time building geometry restraints manager: 10.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 8801 1.43 - 1.64: 12404 1.64 - 1.85: 182 1.85 - 2.06: 0 2.06 - 2.27: 12 Bond restraints: 21399 Sorted by residual: bond pdb=" C ASP 6 243 " pdb=" N PRO 6 244 " ideal model delta sigma weight residual 1.331 1.289 0.043 7.90e-03 1.60e+04 2.90e+01 bond pdb=" CA GLN 0 480 " pdb=" CB GLN 0 480 " ideal model delta sigma weight residual 1.528 1.451 0.077 2.61e-02 1.47e+03 8.78e+00 bond pdb=" CA LEU 1 389 " pdb=" C LEU 1 389 " ideal model delta sigma weight residual 1.523 1.489 0.034 1.34e-02 5.57e+03 6.55e+00 bond pdb=" CA ILE 1 337 " pdb=" CB ILE 1 337 " ideal model delta sigma weight residual 1.539 1.510 0.030 1.27e-02 6.20e+03 5.46e+00 bond pdb=" C LEU 0 621 " pdb=" N MET 0 622 " ideal model delta sigma weight residual 1.334 1.298 0.037 1.58e-02 4.01e+03 5.38e+00 ... (remaining 21394 not shown) Histogram of bond angle deviations from ideal: 73.64 - 85.73: 12 85.73 - 97.82: 0 97.82 - 109.92: 3347 109.92 - 122.01: 21421 122.01 - 134.10: 4073 Bond angle restraints: 28853 Sorted by residual: angle pdb=" N PRO 1 491 " pdb=" CA PRO 1 491 " pdb=" CB PRO 1 491 " ideal model delta sigma weight residual 103.25 111.45 -8.20 1.05e+00 9.07e-01 6.10e+01 angle pdb=" N LYS 1 390 " pdb=" CA LYS 1 390 " pdb=" C LYS 1 390 " ideal model delta sigma weight residual 113.38 104.02 9.36 1.23e+00 6.61e-01 5.78e+01 angle pdb=" N PRO 1 354 " pdb=" CA PRO 1 354 " pdb=" CB PRO 1 354 " ideal model delta sigma weight residual 103.25 110.83 -7.58 1.05e+00 9.07e-01 5.21e+01 angle pdb=" C LYS 1 238 " pdb=" N PRO 1 239 " pdb=" CA PRO 1 239 " ideal model delta sigma weight residual 119.84 112.18 7.66 1.25e+00 6.40e-01 3.75e+01 angle pdb=" C LEU 1 296 " pdb=" CA LEU 1 296 " pdb=" CB LEU 1 296 " ideal model delta sigma weight residual 117.23 109.45 7.78 1.36e+00 5.41e-01 3.27e+01 ... (remaining 28848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 11290 17.71 - 35.42: 973 35.42 - 53.12: 286 53.12 - 70.83: 65 70.83 - 88.54: 7 Dihedral angle restraints: 12621 sinusoidal: 4676 harmonic: 7945 Sorted by residual: dihedral pdb=" CA ARG 4 259 " pdb=" C ARG 4 259 " pdb=" N PRO 4 260 " pdb=" CA PRO 4 260 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LEU 6 372 " pdb=" C LEU 6 372 " pdb=" N SER 6 373 " pdb=" CA SER 6 373 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA VAL 0 167 " pdb=" C VAL 0 167 " pdb=" N GLU 0 168 " pdb=" CA GLU 0 168 " ideal model delta harmonic sigma weight residual 180.00 152.35 27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 12618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2327 0.048 - 0.096: 679 0.096 - 0.145: 151 0.145 - 0.193: 11 0.193 - 0.241: 5 Chirality restraints: 3173 Sorted by residual: chirality pdb=" CA PRO 1 491 " pdb=" N PRO 1 491 " pdb=" C PRO 1 491 " pdb=" CB PRO 1 491 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb="FE3 SF4 0 801 " pdb=" S1 SF4 0 801 " pdb=" S2 SF4 0 801 " pdb=" S4 SF4 0 801 " both_signs ideal model delta sigma weight residual False -10.55 -10.32 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ASN 1 277 " pdb=" N ASN 1 277 " pdb=" C ASN 1 277 " pdb=" CB ASN 1 277 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 3170 not shown) Planarity restraints: 3816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR 0 63 " 0.047 5.00e-02 4.00e+02 7.23e-02 8.35e+00 pdb=" N PRO 0 64 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO 0 64 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO 0 64 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS 1 238 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO 1 239 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO 1 239 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO 1 239 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG 7 681 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C ARG 7 681 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG 7 681 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN 7 682 " 0.013 2.00e-02 2.50e+03 ... (remaining 3813 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 604 2.61 - 3.18: 22333 3.18 - 3.75: 35574 3.75 - 4.33: 45983 4.33 - 4.90: 70789 Nonbonded interactions: 175283 Sorted by model distance: nonbonded pdb=" OG SER 0 378 " pdb=" OG1 THR 0 407 " model vdw 2.034 2.440 nonbonded pdb=" N ASP 2 61 " pdb=" OD1 ASP 2 61 " model vdw 2.078 2.520 nonbonded pdb=" O CYS 0 115 " pdb=" OG SER 0 121 " model vdw 2.082 2.440 nonbonded pdb=" O ILE 1 343 " pdb=" N ASP 1 345 " model vdw 2.087 2.520 nonbonded pdb=" O THR 6 116 " pdb=" OG1 THR 6 116 " model vdw 2.103 2.440 ... (remaining 175278 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 13.930 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 63.130 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.077 21399 Z= 0.560 Angle : 0.849 12.756 28853 Z= 0.489 Chirality : 0.047 0.241 3173 Planarity : 0.005 0.072 3816 Dihedral : 15.054 88.538 7659 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 30.22 Ramachandran Plot: Outliers : 1.77 % Allowed : 14.68 % Favored : 83.55 % Rotamer Outliers : 13.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % 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: -2.01 (0.16), residues: 2888 helix: 0.32 (0.14), residues: 1385 sheet: -2.84 (0.33), residues: 236 loop : -3.03 (0.17), residues: 1267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 142 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 267 outliers final: 135 residues processed: 388 average time/residue: 0.3015 time to fit residues: 186.2129 Evaluate side-chains 252 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 117 time to evaluate : 2.326 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 3 residues processed: 135 average time/residue: 0.2320 time to fit residues: 58.1224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 147 optimal weight: 7.9990 chunk 117 optimal weight: 30.0000 chunk 226 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 262 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 476 GLN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 480 GLN 6 227 HIS 6 375 HIS ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 21399 Z= 0.224 Angle : 0.682 11.995 28853 Z= 0.351 Chirality : 0.045 0.243 3173 Planarity : 0.005 0.063 3816 Dihedral : 5.742 30.453 3106 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.98 % Favored : 87.50 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2888 helix: 0.65 (0.14), residues: 1396 sheet: -2.86 (0.31), residues: 236 loop : -2.92 (0.17), residues: 1256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 146 time to evaluate : 2.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 26 residues processed: 203 average time/residue: 0.3071 time to fit residues: 102.1264 Evaluate side-chains 152 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 2.915 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 2 residues processed: 26 average time/residue: 0.2340 time to fit residues: 14.4637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 30.0000 chunk 81 optimal weight: 50.0000 chunk 218 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 72 optimal weight: 50.0000 chunk 262 optimal weight: 3.9990 chunk 284 optimal weight: 4.9990 chunk 234 optimal weight: 0.3980 chunk 260 optimal weight: 2.9990 chunk 89 optimal weight: 40.0000 chunk 210 optimal weight: 3.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 21 GLN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 21399 Z= 0.294 Angle : 0.663 11.680 28853 Z= 0.341 Chirality : 0.044 0.198 3173 Planarity : 0.004 0.063 3816 Dihedral : 5.513 31.855 3106 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.67 % Favored : 86.95 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.16), residues: 2888 helix: 0.79 (0.14), residues: 1389 sheet: -2.83 (0.31), residues: 239 loop : -2.90 (0.17), residues: 1260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 128 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 32 residues processed: 192 average time/residue: 0.3070 time to fit residues: 98.5338 Evaluate side-chains 156 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 2.844 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.2604 time to fit residues: 17.8594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 0.9990 chunk 197 optimal weight: 3.9990 chunk 136 optimal weight: 0.0770 chunk 29 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 263 optimal weight: 4.9990 chunk 279 optimal weight: 9.9990 chunk 137 optimal weight: 0.0980 chunk 250 optimal weight: 2.9990 chunk 75 optimal weight: 50.0000 overall best weight: 1.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 138 ASN ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 353 HIS 6 381 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5964 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 21399 Z= 0.187 Angle : 0.627 10.885 28853 Z= 0.316 Chirality : 0.043 0.183 3173 Planarity : 0.004 0.055 3816 Dihedral : 5.258 37.172 3106 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.22 % Favored : 88.43 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.16), residues: 2888 helix: 0.94 (0.14), residues: 1392 sheet: -2.61 (0.33), residues: 225 loop : -2.82 (0.17), residues: 1271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 140 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 186 average time/residue: 0.2954 time to fit residues: 92.3096 Evaluate side-chains 150 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2236 time to fit residues: 11.1589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 4 optimal weight: 0.0060 chunk 207 optimal weight: 4.9990 chunk 115 optimal weight: 50.0000 chunk 238 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 142 optimal weight: 0.3980 chunk 250 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 21399 Z= 0.196 Angle : 0.632 10.077 28853 Z= 0.316 Chirality : 0.043 0.351 3173 Planarity : 0.004 0.054 3816 Dihedral : 5.080 38.262 3106 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.39 % Favored : 88.26 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.16), residues: 2888 helix: 1.04 (0.14), residues: 1391 sheet: -2.49 (0.32), residues: 226 loop : -2.85 (0.17), residues: 1271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 142 time to evaluate : 2.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 19 residues processed: 175 average time/residue: 0.2907 time to fit residues: 86.6351 Evaluate side-chains 151 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 2.762 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2043 time to fit residues: 10.8755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 6.9990 chunk 251 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 68 optimal weight: 0.0170 chunk 279 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 ASN ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 21399 Z= 0.216 Angle : 0.627 12.008 28853 Z= 0.313 Chirality : 0.043 0.187 3173 Planarity : 0.004 0.053 3816 Dihedral : 5.038 38.230 3106 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.91 % Favored : 88.78 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2888 helix: 1.13 (0.15), residues: 1387 sheet: -2.45 (0.33), residues: 225 loop : -2.81 (0.17), residues: 1276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 2.897 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 164 average time/residue: 0.2936 time to fit residues: 81.5278 Evaluate side-chains 141 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2071 time to fit residues: 7.9116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 158 optimal weight: 0.0040 chunk 235 optimal weight: 4.9990 chunk 156 optimal weight: 40.0000 chunk 278 optimal weight: 4.9990 chunk 174 optimal weight: 30.0000 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 0.1980 overall best weight: 2.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 198 ASN ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 21399 Z= 0.222 Angle : 0.645 12.618 28853 Z= 0.319 Chirality : 0.043 0.352 3173 Planarity : 0.004 0.053 3816 Dihedral : 4.999 39.290 3106 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.11 % Favored : 88.57 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.16), residues: 2888 helix: 1.15 (0.15), residues: 1389 sheet: -2.49 (0.32), residues: 225 loop : -2.78 (0.17), residues: 1274 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 2.929 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 6 residues processed: 157 average time/residue: 0.3023 time to fit residues: 80.4834 Evaluate side-chains 137 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 2.881 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2005 time to fit residues: 5.9764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 218 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 258 ASN 4 198 ASN ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5942 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21399 Z= 0.192 Angle : 0.643 13.550 28853 Z= 0.317 Chirality : 0.043 0.305 3173 Planarity : 0.004 0.052 3816 Dihedral : 4.925 38.040 3106 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.32 % Favored : 89.40 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2888 helix: 1.13 (0.15), residues: 1398 sheet: -2.44 (0.32), residues: 225 loop : -2.77 (0.17), residues: 1265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 152 average time/residue: 0.2956 time to fit residues: 75.8459 Evaluate side-chains 137 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 2.770 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2768 time to fit residues: 6.3579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 1.9990 chunk 266 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 259 optimal weight: 0.7980 chunk 156 optimal weight: 40.0000 chunk 113 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 79 optimal weight: 40.0000 chunk 234 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 chunk 258 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 21399 Z= 0.185 Angle : 0.653 14.286 28853 Z= 0.319 Chirality : 0.043 0.372 3173 Planarity : 0.004 0.051 3816 Dihedral : 4.828 38.357 3106 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.46 % Favored : 89.27 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2888 helix: 1.14 (0.14), residues: 1404 sheet: -2.38 (0.33), residues: 227 loop : -2.76 (0.17), residues: 1257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 155 average time/residue: 0.2964 time to fit residues: 78.0263 Evaluate side-chains 137 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 2.818 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2840 time to fit residues: 6.8540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 1.9990 chunk 274 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 130 optimal weight: 0.0060 chunk 190 optimal weight: 0.9990 chunk 287 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 229 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 177 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 21399 Z= 0.175 Angle : 0.671 19.109 28853 Z= 0.324 Chirality : 0.043 0.383 3173 Planarity : 0.004 0.103 3816 Dihedral : 4.770 37.559 3106 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.76 % Favored : 89.96 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.16), residues: 2888 helix: 1.09 (0.14), residues: 1411 sheet: -2.28 (0.33), residues: 227 loop : -2.73 (0.17), residues: 1250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5776 Ramachandran restraints generated. 2888 Oldfield, 0 Emsley, 2888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 145 average time/residue: 0.2995 time to fit residues: 74.5759 Evaluate side-chains 138 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 135 time to evaluate : 2.940 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2485 time to fit residues: 5.1703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 70 optimal weight: 30.0000 chunk 211 optimal weight: 1.9990 chunk 33 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 258 ASN ** 4 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 375 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.081934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051659 restraints weight = 109732.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.053878 restraints weight = 70438.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053130 restraints weight = 39938.274| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.113 21399 Z= 0.387 Angle : 0.743 15.160 28853 Z= 0.367 Chirality : 0.046 0.385 3173 Planarity : 0.005 0.123 3816 Dihedral : 5.067 38.242 3106 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.81 % Favored : 87.92 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2888 helix: 1.02 (0.14), residues: 1414 sheet: -2.40 (0.33), residues: 227 loop : -2.74 (0.17), residues: 1247 =============================================================================== Job complete usr+sys time: 3581.13 seconds wall clock time: 69 minutes 40.29 seconds (4180.29 seconds total)