Starting phenix.real_space_refine on Sun Feb 18 06:18:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/02_2024/7k01_22587_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/02_2024/7k01_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_22587/02_2024/7k01_22587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/02_2024/7k01_22587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/02_2024/7k01_22587_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k01_22587/02_2024/7k01_22587_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 11.27, per 1000 atoms: 0.54 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: 9.08 Conformation dependent library (CDL) restraints added in 4.2 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: 4.41 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: 5.99 Time building geometry restraints manager: 9.68 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: 3.310 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: 13.380 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 64.010 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.690 ------------------------------------------------------------------------------- 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 % Allowed : 14.47 % Favored : 72.35 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 7 558 HIS 0.008 0.001 HIS 4 64 PHE 0.023 0.002 PHE 2 492 TYR 0.024 0.002 TYR 0 629 ARG 0.006 0.001 ARG 0 513 *********************** 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 : 2.627 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 REVERT: 1 597 PHE cc_start: 0.5618 (OUTLIER) cc_final: 0.5326 (m-80) REVERT: 4 86 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8253 (mp) REVERT: 7 578 MET cc_start: -0.0460 (tpp) cc_final: -0.1368 (mmt) REVERT: 7 622 MET cc_start: 0.6659 (ppp) cc_final: 0.6115 (ppp) REVERT: 2 67 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8282 (p0) REVERT: 2 112 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6717 (mp) REVERT: 0 198 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7158 (ptt-90) REVERT: 0 379 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: 0 382 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7796 (t) REVERT: 0 512 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7747 (mm) REVERT: 0 562 GLU cc_start: 0.7147 (tp30) cc_final: 0.6697 (tp30) REVERT: 0 568 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7534 (mp) REVERT: 0 745 ILE cc_start: 0.6512 (OUTLIER) cc_final: 0.6136 (pt) REVERT: 6 118 TYR cc_start: 0.4406 (OUTLIER) cc_final: 0.3836 (t80) REVERT: 6 136 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8260 (mtp) REVERT: 6 142 ARG cc_start: 0.9051 (mmp80) cc_final: 0.8671 (mmp80) REVERT: 6 216 MET cc_start: 0.8508 (ttm) cc_final: 0.8286 (ttt) REVERT: 6 254 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8715 (mp) REVERT: 6 274 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8810 (tptm) REVERT: 6 353 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7552 (t70) outliers start: 267 outliers final: 135 residues processed: 388 average time/residue: 0.3207 time to fit residues: 200.8219 Evaluate side-chains 268 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 118 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 279 LYS Chi-restraints excluded: chain 1 residue 282 GLU Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 382 SER Chi-restraints excluded: chain 1 residue 558 CYS Chi-restraints excluded: chain 1 residue 597 PHE Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 86 LEU Chi-restraints excluded: chain 4 residue 137 LYS Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 180 THR Chi-restraints excluded: chain 4 residue 204 THR Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 234 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 248 LEU Chi-restraints excluded: chain 4 residue 260 PRO Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 297 SER Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 677 TYR Chi-restraints excluded: chain 7 residue 680 ARG Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 8 HIS Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 14 LEU Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 60 LEU Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 67 ASN Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 100 LEU Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain 2 residue 286 ARG Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 352 ASN Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 413 GLU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 2 residue 476 GLN Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 28 ILE Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 66 HIS Chi-restraints excluded: chain 0 residue 72 CYS Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 127 THR Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 131 GLU Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 157 GLU Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 196 VAL Chi-restraints excluded: chain 0 residue 198 ARG Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 207 ILE Chi-restraints excluded: chain 0 residue 208 TYR Chi-restraints excluded: chain 0 residue 218 ILE Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 273 GLU Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 379 GLU Chi-restraints excluded: chain 0 residue 382 SER Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 512 ILE Chi-restraints excluded: chain 0 residue 515 ASP Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 537 MET Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 545 LEU Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 563 VAL Chi-restraints excluded: chain 0 residue 568 LEU Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 597 ILE Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 654 LEU Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 659 MET Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 710 THR Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 125 SER Chi-restraints excluded: chain 6 residue 136 MET Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 161 PHE Chi-restraints excluded: chain 6 residue 164 ASN Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 6 residue 202 GLN Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 254 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 274 LYS Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 311 ASN Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 353 HIS Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 406 CYS Chi-restraints excluded: chain 6 residue 444 ILE Chi-restraints excluded: chain 6 residue 448 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 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: 3.9990 chunk 87 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 168 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** 6 227 HIS 6 375 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6018 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21399 Z= 0.208 Angle : 0.665 12.598 28853 Z= 0.341 Chirality : 0.044 0.252 3173 Planarity : 0.005 0.063 3816 Dihedral : 10.632 84.771 3401 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.12 % Favored : 87.40 % Rotamer: Outliers : 8.10 % Allowed : 18.72 % Favored : 73.19 % 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: -1.68 (0.16), residues: 2888 helix: 0.67 (0.14), residues: 1397 sheet: -2.83 (0.31), residues: 246 loop : -2.95 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 2 201 HIS 0.004 0.001 HIS 0 294 PHE 0.022 0.002 PHE 2 45 TYR 0.020 0.001 TYR 6 380 ARG 0.010 0.000 ARG 4 273 *********************** 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 310 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 146 time to evaluate : 2.819 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: 1 597 PHE cc_start: 0.5403 (OUTLIER) cc_final: 0.5100 (m-80) REVERT: 7 578 MET cc_start: -0.0813 (tpp) cc_final: -0.1216 (mmt) REVERT: 7 622 MET cc_start: 0.6515 (ppp) cc_final: 0.5988 (ppp) REVERT: 2 67 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8165 (p0) REVERT: 2 286 ARG cc_start: 0.2892 (OUTLIER) cc_final: 0.2658 (tmm160) REVERT: 0 241 ASP cc_start: 0.8731 (p0) cc_final: 0.8438 (p0) REVERT: 0 346 MET cc_start: 0.7303 (tpp) cc_final: 0.7049 (tpp) REVERT: 0 382 SER cc_start: 0.7928 (OUTLIER) cc_final: 0.7529 (t) REVERT: 0 568 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7752 (mp) REVERT: 0 745 ILE cc_start: 0.6214 (OUTLIER) cc_final: 0.5893 (pt) REVERT: 6 118 TYR cc_start: 0.4363 (OUTLIER) cc_final: 0.2702 (p90) REVERT: 6 142 ARG cc_start: 0.8983 (mmp80) cc_final: 0.8521 (mmp80) REVERT: 6 216 MET cc_start: 0.8270 (ttm) cc_final: 0.8029 (ttt) REVERT: 6 254 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8690 (mp) REVERT: 6 275 GLU cc_start: 0.7870 (tp30) cc_final: 0.7577 (tp30) outliers start: 164 outliers final: 110 residues processed: 298 average time/residue: 0.2905 time to fit residues: 142.0625 Evaluate side-chains 245 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 127 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 315 LEU Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 382 SER Chi-restraints excluded: chain 1 residue 597 PHE Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 137 LYS Chi-restraints excluded: chain 4 residue 163 ILE Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 247 TYR Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 444 GLU Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 680 ARG Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 8 HIS Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 14 LEU Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 67 ASN Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 100 LEU Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 286 ARG Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 72 CYS Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 157 GLU Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 218 ILE Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 382 SER Chi-restraints excluded: chain 0 residue 438 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 506 ILE Chi-restraints excluded: chain 0 residue 533 THR Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 563 VAL Chi-restraints excluded: chain 0 residue 568 LEU Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 654 LEU Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 122 ILE Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 6 residue 202 GLN Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 254 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 356 VAL Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 383 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 429 CYS Chi-restraints excluded: chain 6 residue 448 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 145 optimal weight: 9.9990 chunk 81 optimal weight: 30.0000 chunk 218 optimal weight: 0.0370 chunk 178 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 262 optimal weight: 5.9990 chunk 284 optimal weight: 4.9990 chunk 234 optimal weight: 0.9990 chunk 260 optimal weight: 0.9990 chunk 89 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- 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** ** 7 462 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21399 Z= 0.210 Angle : 0.630 11.909 28853 Z= 0.321 Chirality : 0.043 0.205 3173 Planarity : 0.004 0.059 3816 Dihedral : 9.012 59.451 3297 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.02 % Favored : 87.64 % Rotamer: Outliers : 7.80 % Allowed : 18.57 % Favored : 73.63 % 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: -1.42 (0.16), residues: 2888 helix: 0.92 (0.14), residues: 1391 sheet: -2.60 (0.32), residues: 237 loop : -2.86 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 7 482 HIS 0.006 0.001 HIS 7 676 PHE 0.014 0.001 PHE 2 492 TYR 0.024 0.001 TYR 6 380 ARG 0.003 0.000 ARG 0 221 *********************** 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 294 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 136 time to evaluate : 2.627 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: 1 597 PHE cc_start: 0.5323 (OUTLIER) cc_final: 0.5110 (m-80) REVERT: 7 578 MET cc_start: -0.0774 (tpp) cc_final: -0.1104 (tpt) REVERT: 7 622 MET cc_start: 0.6510 (ppp) cc_final: 0.5902 (ppp) REVERT: 2 67 ASN cc_start: 0.8470 (OUTLIER) cc_final: 0.8238 (p0) REVERT: 2 97 MET cc_start: 0.8984 (mmm) cc_final: 0.8773 (mmm) REVERT: 0 68 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7669 (mmmm) REVERT: 0 70 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.9005 (mm) REVERT: 0 76 MET cc_start: 0.7874 (ppp) cc_final: 0.7621 (tmm) REVERT: 0 155 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8860 (mp) REVERT: 0 568 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7601 (mp) REVERT: 0 745 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5911 (pt) REVERT: 6 118 TYR cc_start: 0.4216 (OUTLIER) cc_final: 0.2615 (p90) REVERT: 6 142 ARG cc_start: 0.9008 (mmp80) cc_final: 0.8643 (mmp80) REVERT: 6 275 GLU cc_start: 0.7869 (tp30) cc_final: 0.7587 (tp30) outliers start: 158 outliers final: 106 residues processed: 282 average time/residue: 0.3033 time to fit residues: 139.5107 Evaluate side-chains 243 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 129 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 315 LEU Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 1 residue 597 PHE Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 137 LYS Chi-restraints excluded: chain 4 residue 163 ILE Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 247 TYR Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 7 residue 323 VAL Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 444 GLU Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 680 ARG Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 8 HIS Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 14 LEU Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 67 ASN Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 100 LEU Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 279 THR Chi-restraints excluded: chain 2 residue 286 ARG Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 352 ASN Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 68 LYS Chi-restraints excluded: chain 0 residue 70 ILE Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 127 THR Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 254 THR Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 315 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 568 LEU Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 620 VAL Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 669 VAL Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 712 MET Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 383 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 448 LEU Chi-restraints excluded: chain 6 residue 451 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 259 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 125 optimal weight: 30.0000 chunk 176 optimal weight: 0.0570 chunk 263 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 75 optimal weight: 50.0000 overall best weight: 1.2106 ------------------------------------------------------------------------------- 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 21 GLN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 138 ASN ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 480 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21399 Z= 0.178 Angle : 0.619 11.060 28853 Z= 0.311 Chirality : 0.043 0.181 3173 Planarity : 0.004 0.054 3816 Dihedral : 8.449 59.375 3266 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.84 % Favored : 88.82 % Rotamer: Outliers : 6.86 % Allowed : 19.56 % Favored : 73.58 % 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: -1.24 (0.16), residues: 2888 helix: 1.10 (0.14), residues: 1385 sheet: -2.60 (0.32), residues: 234 loop : -2.79 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 7 482 HIS 0.005 0.001 HIS 0 238 PHE 0.016 0.001 PHE 0 334 TYR 0.032 0.001 TYR 6 380 ARG 0.003 0.000 ARG 0 221 *********************** 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 278 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 139 time to evaluate : 2.718 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: 4 225 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7428 (tm-30) REVERT: 7 578 MET cc_start: -0.0670 (tpp) cc_final: -0.1584 (mtp) REVERT: 7 622 MET cc_start: 0.6452 (ppp) cc_final: 0.5858 (ppp) REVERT: 2 67 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8215 (p0) REVERT: 0 70 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8999 (mm) REVERT: 0 76 MET cc_start: 0.7853 (ppp) cc_final: 0.7608 (tmm) REVERT: 0 346 MET cc_start: 0.7062 (mmm) cc_final: 0.6446 (mmm) REVERT: 0 745 ILE cc_start: 0.6269 (OUTLIER) cc_final: 0.5904 (pt) REVERT: 6 118 TYR cc_start: 0.4276 (OUTLIER) cc_final: 0.2663 (p90) REVERT: 6 142 ARG cc_start: 0.9040 (mmp80) cc_final: 0.8677 (mmp80) REVERT: 6 275 GLU cc_start: 0.7804 (tp30) cc_final: 0.7534 (tp30) outliers start: 139 outliers final: 101 residues processed: 265 average time/residue: 0.3095 time to fit residues: 133.1400 Evaluate side-chains 240 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 135 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 558 CYS Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 137 LYS Chi-restraints excluded: chain 4 residue 163 ILE Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 247 TYR Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 288 ILE Chi-restraints excluded: chain 7 residue 323 VAL Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 444 GLU Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 514 THR Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 680 ARG Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 14 LEU Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 67 ASN Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 100 LEU Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 371 VAL Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 70 ILE Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 127 THR Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 155 LEU Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 419 ILE Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 519 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 601 VAL Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 669 VAL Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 336 CYS Chi-restraints excluded: chain 6 residue 353 HIS Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 383 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 232 optimal weight: 3.9990 chunk 158 optimal weight: 0.0270 chunk 4 optimal weight: 0.7980 chunk 207 optimal weight: 7.9990 chunk 115 optimal weight: 50.0000 chunk 238 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 142 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 overall best weight: 1.5442 ------------------------------------------------------------------------------- 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** 2 352 ASN ** 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** ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21399 Z= 0.189 Angle : 0.618 10.993 28853 Z= 0.307 Chirality : 0.043 0.336 3173 Planarity : 0.004 0.053 3816 Dihedral : 8.010 59.570 3245 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.98 % Favored : 88.68 % Rotamer: Outliers : 6.72 % Allowed : 19.95 % Favored : 73.33 % 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: -1.17 (0.16), residues: 2888 helix: 1.16 (0.14), residues: 1388 sheet: -2.45 (0.32), residues: 227 loop : -2.80 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP 7 427 HIS 0.006 0.001 HIS 6 375 PHE 0.020 0.001 PHE 1 597 TYR 0.029 0.001 TYR 6 380 ARG 0.003 0.000 ARG 0 221 *********************** 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 275 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 139 time to evaluate : 2.678 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: 4 225 GLN cc_start: 0.7621 (tm-30) cc_final: 0.7410 (tm-30) REVERT: 7 578 MET cc_start: -0.0762 (tpp) cc_final: -0.1482 (mtp) REVERT: 7 622 MET cc_start: 0.6429 (ppp) cc_final: 0.5788 (ppp) REVERT: 0 346 MET cc_start: 0.6996 (mmm) cc_final: 0.6628 (mmm) REVERT: 0 745 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.6007 (pt) REVERT: 6 118 TYR cc_start: 0.4232 (OUTLIER) cc_final: 0.2664 (p90) REVERT: 6 142 ARG cc_start: 0.9038 (mmp80) cc_final: 0.8711 (mmp80) REVERT: 6 254 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8541 (mp) REVERT: 6 275 GLU cc_start: 0.7809 (tp30) cc_final: 0.7543 (tp30) outliers start: 136 outliers final: 106 residues processed: 262 average time/residue: 0.2920 time to fit residues: 125.0545 Evaluate side-chains 239 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 130 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 558 CYS Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 137 LYS Chi-restraints excluded: chain 4 residue 163 ILE Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 247 TYR Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 7 residue 323 VAL Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 444 GLU Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 680 ARG Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 14 LEU Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain 2 residue 208 LEU Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 352 ASN Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 2 residue 453 THR Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 72 CYS Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 127 THR Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 206 ILE Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 519 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 601 VAL Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 254 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 383 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 448 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 93 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 232 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 0 164 ASN ** 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: 0.5998 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21399 Z= 0.249 Angle : 0.626 11.181 28853 Z= 0.313 Chirality : 0.043 0.183 3173 Planarity : 0.004 0.054 3816 Dihedral : 7.888 59.924 3233 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.98 % Favored : 88.68 % Rotamer: Outliers : 6.62 % Allowed : 20.64 % Favored : 72.74 % 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: -1.12 (0.16), residues: 2888 helix: 1.22 (0.15), residues: 1387 sheet: -2.48 (0.32), residues: 226 loop : -2.78 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 7 427 HIS 0.006 0.001 HIS 6 375 PHE 0.025 0.001 PHE 7 643 TYR 0.029 0.001 TYR 6 380 ARG 0.004 0.000 ARG 0 221 *********************** 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 270 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 136 time to evaluate : 2.650 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: 4 252 MET cc_start: 0.8287 (mmm) cc_final: 0.8013 (mmp) REVERT: 7 445 MET cc_start: -0.1702 (ptt) cc_final: -0.2000 (ptt) REVERT: 7 578 MET cc_start: -0.0620 (tpp) cc_final: -0.1308 (mtp) REVERT: 7 622 MET cc_start: 0.6332 (ppp) cc_final: 0.5763 (ppp) REVERT: 2 97 MET cc_start: 0.9026 (mmm) cc_final: 0.8752 (mmm) REVERT: 2 399 TYR cc_start: 0.8470 (t80) cc_final: 0.8268 (t80) REVERT: 0 346 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6479 (mmm) REVERT: 0 745 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.5939 (pt) REVERT: 6 118 TYR cc_start: 0.4261 (OUTLIER) cc_final: 0.2709 (p90) REVERT: 6 142 ARG cc_start: 0.9067 (mmp80) cc_final: 0.8738 (mmp80) REVERT: 6 254 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8578 (mp) REVERT: 6 275 GLU cc_start: 0.7857 (tp30) cc_final: 0.7573 (tp30) REVERT: 6 322 MET cc_start: 0.6456 (pmm) cc_final: 0.6170 (pmm) outliers start: 134 outliers final: 104 residues processed: 258 average time/residue: 0.2992 time to fit residues: 126.4736 Evaluate side-chains 238 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 130 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 558 CYS Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 137 LYS Chi-restraints excluded: chain 4 residue 163 ILE Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 247 TYR Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 7 residue 323 VAL Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 444 GLU Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 680 ARG Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 2 residue 453 THR Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 72 CYS Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 127 THR Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 218 ILE Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 346 MET Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 519 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 545 LEU Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 601 VAL Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 669 VAL Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 241 THR Chi-restraints excluded: chain 6 residue 254 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 383 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 448 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 269 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 158 optimal weight: 0.0770 chunk 235 optimal weight: 1.9990 chunk 156 optimal weight: 40.0000 chunk 278 optimal weight: 0.8980 chunk 174 optimal weight: 30.0000 chunk 169 optimal weight: 0.9980 chunk 128 optimal weight: 0.0470 overall best weight: 0.8038 ------------------------------------------------------------------------------- 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** ** 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** 6 381 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5925 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21399 Z= 0.168 Angle : 0.629 13.087 28853 Z= 0.309 Chirality : 0.043 0.342 3173 Planarity : 0.004 0.051 3816 Dihedral : 7.579 57.715 3226 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.28 % Favored : 89.44 % Rotamer: Outliers : 5.43 % Allowed : 21.98 % Favored : 72.59 % 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: -1.11 (0.16), residues: 2888 helix: 1.19 (0.14), residues: 1394 sheet: -2.35 (0.33), residues: 227 loop : -2.77 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP 7 427 HIS 0.007 0.001 HIS 2 403 PHE 0.020 0.001 PHE 7 643 TYR 0.042 0.001 TYR 6 380 ARG 0.003 0.000 ARG 0 221 *********************** 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 256 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 146 time to evaluate : 2.939 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: 4 252 MET cc_start: 0.8294 (mmm) cc_final: 0.8013 (mmp) REVERT: 7 449 GLU cc_start: -0.0895 (OUTLIER) cc_final: -0.1408 (mt-10) REVERT: 7 578 MET cc_start: -0.0635 (tpp) cc_final: -0.1212 (mtp) REVERT: 7 622 MET cc_start: 0.6365 (ppp) cc_final: 0.5771 (ppp) REVERT: 2 97 MET cc_start: 0.8972 (mmm) cc_final: 0.8770 (mmm) REVERT: 0 346 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6339 (mmm) REVERT: 0 745 ILE cc_start: 0.6248 (OUTLIER) cc_final: 0.5846 (pt) REVERT: 6 118 TYR cc_start: 0.4246 (OUTLIER) cc_final: 0.2631 (p90) REVERT: 6 142 ARG cc_start: 0.9033 (mmp80) cc_final: 0.8709 (mmp80) REVERT: 6 275 GLU cc_start: 0.7797 (tp30) cc_final: 0.7529 (tp30) REVERT: 6 322 MET cc_start: 0.6469 (pmm) cc_final: 0.6143 (pmm) outliers start: 110 outliers final: 91 residues processed: 243 average time/residue: 0.3116 time to fit residues: 123.3080 Evaluate side-chains 233 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 138 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 163 ILE Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 247 TYR Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 7 residue 323 VAL Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 444 GLU Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 72 CYS Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 346 MET Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 419 ILE Chi-restraints excluded: chain 0 residue 456 VAL Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 519 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 545 LEU Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 202 GLN Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 383 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 448 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 218 optimal weight: 0.0170 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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** ** 7 551 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 353 HIS ** 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: 0.5985 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21399 Z= 0.249 Angle : 0.650 13.030 28853 Z= 0.321 Chirality : 0.043 0.367 3173 Planarity : 0.004 0.108 3816 Dihedral : 7.440 59.244 3216 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.87 % Favored : 88.82 % Rotamer: Outliers : 5.93 % Allowed : 21.68 % Favored : 72.40 % 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: -1.03 (0.16), residues: 2888 helix: 1.27 (0.15), residues: 1392 sheet: -2.31 (0.33), residues: 225 loop : -2.75 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP 7 427 HIS 0.006 0.001 HIS 6 375 PHE 0.025 0.001 PHE 1 321 TYR 0.041 0.001 TYR 6 380 ARG 0.004 0.000 ARG 0 221 *********************** 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 252 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 132 time to evaluate : 2.612 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: 4 86 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8009 (mp) REVERT: 7 449 GLU cc_start: -0.0975 (OUTLIER) cc_final: -0.1523 (mt-10) REVERT: 7 578 MET cc_start: -0.0771 (tpp) cc_final: -0.1281 (mtp) REVERT: 7 622 MET cc_start: 0.6234 (ppp) cc_final: 0.5681 (ppp) REVERT: 0 136 MET cc_start: 0.8363 (tpp) cc_final: 0.7932 (tpp) REVERT: 0 346 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6364 (mmm) REVERT: 0 745 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.5846 (pt) REVERT: 6 118 TYR cc_start: 0.4213 (OUTLIER) cc_final: 0.2668 (p90) REVERT: 6 142 ARG cc_start: 0.9068 (mmp80) cc_final: 0.8735 (mmp80) REVERT: 6 254 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8525 (mp) REVERT: 6 275 GLU cc_start: 0.7862 (tp30) cc_final: 0.7586 (tp30) REVERT: 6 322 MET cc_start: 0.6510 (pmm) cc_final: 0.6126 (pmm) REVERT: 6 353 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.7546 (t70) outliers start: 120 outliers final: 102 residues processed: 242 average time/residue: 0.3056 time to fit residues: 122.7312 Evaluate side-chains 241 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 132 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 558 CYS Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 86 LEU Chi-restraints excluded: chain 4 residue 163 ILE Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 211 ASP Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 247 TYR Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 7 residue 323 VAL Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 427 TRP Chi-restraints excluded: chain 7 residue 444 GLU Chi-restraints excluded: chain 7 residue 449 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 523 LYS Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 10 VAL Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 72 CYS Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 218 ILE Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 249 SER Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 346 MET Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 519 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 545 LEU Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 601 VAL Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 202 GLN Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 241 THR Chi-restraints excluded: chain 6 residue 254 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 353 HIS Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 383 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 448 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 243 optimal weight: 10.0000 chunk 259 optimal weight: 3.9990 chunk 156 optimal weight: 40.0000 chunk 113 optimal weight: 50.0000 chunk 203 optimal weight: 2.9990 chunk 79 optimal weight: 50.0000 chunk 234 optimal weight: 0.0770 chunk 245 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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** ** 7 551 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21399 Z= 0.189 Angle : 0.647 14.683 28853 Z= 0.315 Chirality : 0.043 0.382 3173 Planarity : 0.004 0.099 3816 Dihedral : 7.342 58.078 3216 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.32 % Favored : 89.37 % Rotamer: Outliers : 5.28 % Allowed : 22.81 % Favored : 71.90 % 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: -1.04 (0.16), residues: 2888 helix: 1.23 (0.15), residues: 1399 sheet: -2.26 (0.34), residues: 226 loop : -2.75 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP 7 427 HIS 0.011 0.001 HIS 6 353 PHE 0.023 0.001 PHE 1 321 TYR 0.044 0.001 TYR 6 380 ARG 0.003 0.000 ARG 0 221 *********************** 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 250 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 143 time to evaluate : 2.796 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: 7 578 MET cc_start: -0.0871 (tpp) cc_final: -0.1351 (mtp) REVERT: 7 622 MET cc_start: 0.6236 (ppp) cc_final: 0.5664 (ppp) REVERT: 0 136 MET cc_start: 0.8390 (tpp) cc_final: 0.7926 (tpp) REVERT: 0 346 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.5979 (mmm) REVERT: 0 745 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.5868 (pt) REVERT: 6 118 TYR cc_start: 0.4262 (OUTLIER) cc_final: 0.2712 (p90) REVERT: 6 142 ARG cc_start: 0.9028 (mmp80) cc_final: 0.8712 (mmp80) REVERT: 6 254 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8571 (mp) REVERT: 6 275 GLU cc_start: 0.7824 (tp30) cc_final: 0.7555 (tp30) REVERT: 6 322 MET cc_start: 0.6556 (pmm) cc_final: 0.6118 (pmm) REVERT: 6 353 HIS cc_start: 0.7682 (OUTLIER) cc_final: 0.7469 (t70) outliers start: 107 outliers final: 97 residues processed: 238 average time/residue: 0.2921 time to fit residues: 113.7219 Evaluate side-chains 240 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 138 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 163 ILE Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 247 TYR Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 7 residue 323 VAL Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 427 TRP Chi-restraints excluded: chain 7 residue 444 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 523 LYS Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 72 CYS Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 346 MET Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 519 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 545 LEU Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 601 VAL Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 202 GLN Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 254 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 353 HIS Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 383 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 170 optimal weight: 10.0000 chunk 274 optimal weight: 0.0980 chunk 167 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 190 optimal weight: 6.9990 chunk 287 optimal weight: 3.9990 chunk 264 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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** ** 7 366 GLN ** 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 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 353 HIS ** 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: 0.6012 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21399 Z= 0.299 Angle : 0.693 17.390 28853 Z= 0.340 Chirality : 0.044 0.387 3173 Planarity : 0.004 0.109 3816 Dihedral : 7.343 58.073 3209 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.18 % Favored : 88.54 % Rotamer: Outliers : 5.48 % Allowed : 22.52 % Favored : 72.00 % 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: -1.07 (0.16), residues: 2888 helix: 1.21 (0.14), residues: 1398 sheet: -2.37 (0.33), residues: 227 loop : -2.74 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP 7 427 HIS 0.006 0.001 HIS 4 267 PHE 0.022 0.001 PHE 1 321 TYR 0.037 0.002 TYR 6 380 ARG 0.005 0.000 ARG 6 120 ********************** 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 245 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 134 time to evaluate : 2.565 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: 4 86 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8037 (mp) REVERT: 7 445 MET cc_start: -0.1728 (ptt) cc_final: -0.2137 (ptt) REVERT: 7 578 MET cc_start: -0.0923 (tpp) cc_final: -0.1362 (mtp) REVERT: 7 622 MET cc_start: 0.6180 (ppp) cc_final: 0.5607 (ppp) REVERT: 0 136 MET cc_start: 0.8416 (tpp) cc_final: 0.7950 (tpp) REVERT: 0 346 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6201 (mmm) REVERT: 6 118 TYR cc_start: 0.4288 (OUTLIER) cc_final: 0.2685 (p90) REVERT: 6 142 ARG cc_start: 0.9091 (mmp80) cc_final: 0.8774 (mmp80) REVERT: 6 254 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8549 (mp) REVERT: 6 275 GLU cc_start: 0.7880 (tp30) cc_final: 0.7586 (tp30) REVERT: 6 322 MET cc_start: 0.6604 (pmm) cc_final: 0.6166 (pmm) REVERT: 6 353 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7479 (t70) outliers start: 111 outliers final: 102 residues processed: 234 average time/residue: 0.2931 time to fit residues: 113.5585 Evaluate side-chains 239 residues out of total 2645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 132 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 185 LEU Chi-restraints excluded: chain 1 residue 214 ILE Chi-restraints excluded: chain 1 residue 263 TYR Chi-restraints excluded: chain 1 residue 266 VAL Chi-restraints excluded: chain 1 residue 287 PHE Chi-restraints excluded: chain 1 residue 346 ASP Chi-restraints excluded: chain 1 residue 558 CYS Chi-restraints excluded: chain 1 residue 563 HIS Chi-restraints excluded: chain 4 residue 27 THR Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 86 LEU Chi-restraints excluded: chain 4 residue 163 ILE Chi-restraints excluded: chain 4 residue 176 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 4 residue 212 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 247 TYR Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 4 residue 276 CYS Chi-restraints excluded: chain 7 residue 323 VAL Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 427 TRP Chi-restraints excluded: chain 7 residue 444 GLU Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain 7 residue 518 VAL Chi-restraints excluded: chain 7 residue 523 LYS Chi-restraints excluded: chain 7 residue 541 MET Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 583 MET Chi-restraints excluded: chain 7 residue 620 LEU Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 11 THR Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 95 THR Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 0 residue 6 ASP Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 72 CYS Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 127 THR Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 170 TYR Chi-restraints excluded: chain 0 residue 218 ILE Chi-restraints excluded: chain 0 residue 221 ARG Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 255 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 346 MET Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 519 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 545 LEU Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 599 LEU Chi-restraints excluded: chain 0 residue 601 VAL Chi-restraints excluded: chain 0 residue 614 HIS Chi-restraints excluded: chain 0 residue 649 ARG Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 674 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 683 ASP Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 116 THR Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 191 ASP Chi-restraints excluded: chain 6 residue 202 GLN Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 241 THR Chi-restraints excluded: chain 6 residue 254 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 293 ASP Chi-restraints excluded: chain 6 residue 297 LEU Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 326 THR Chi-restraints excluded: chain 6 residue 353 HIS Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 381 HIS Chi-restraints excluded: chain 6 residue 382 HIS Chi-restraints excluded: chain 6 residue 383 LEU Chi-restraints excluded: chain 6 residue 384 MET Chi-restraints excluded: chain 6 residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 182 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 211 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 chunk 235 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** ** 7 366 GLN ** 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.083372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.055483 restraints weight = 107819.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054849 restraints weight = 80307.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054970 restraints weight = 61093.644| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21399 Z= 0.189 Angle : 0.674 16.238 28853 Z= 0.327 Chirality : 0.043 0.367 3173 Planarity : 0.004 0.091 3816 Dihedral : 7.157 57.878 3205 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.08 % Favored : 89.61 % Rotamer: Outliers : 5.14 % Allowed : 23.11 % Favored : 71.75 % 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: -1.03 (0.16), residues: 2888 helix: 1.24 (0.15), residues: 1396 sheet: -2.28 (0.33), residues: 228 loop : -2.72 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP 7 427 HIS 0.006 0.001 HIS 6 375 PHE 0.021 0.001 PHE 1 321 TYR 0.042 0.001 TYR 6 380 ARG 0.005 0.000 ARG 2 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.09 seconds wall clock time: 74 minutes 20.51 seconds (4460.51 seconds total)