Starting phenix.real_space_refine on Thu Sep 18 23:09:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k01_22587/09_2025/7k01_22587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k01_22587/09_2025/7k01_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/cci-nas-00/data/ceres_data/7k01_22587/09_2025/7k01_22587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k01_22587/09_2025/7k01_22587.map" model { file = "/net/cci-nas-00/data/ceres_data/7k01_22587/09_2025/7k01_22587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k01_22587/09_2025/7k01_22587.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 12, 'ASN:plan1': 25, 'TYR:plan': 7, 'PHE:plan': 2, 'ARG:plan': 6, 'GLN:plan1': 11, 'ASP:plan': 18, 'HIS:plan': 3} 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: {'TRP:plan': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'GLU:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} 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: {'ASP:plan': 14, 'PHE:plan': 7, 'ARG:plan': 9, 'HIS:plan': 6, 'TYR:plan': 6, 'TRP:plan': 1, 'GLU:plan': 8, 'GLN:plan1': 6, 'ASN:plan1': 3} 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: {'ASN:plan1': 2, 'TYR:plan': 1, '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: {'ASN:plan1': 11, 'GLU:plan': 16, 'GLN:plan1': 11, 'PHE:plan': 8, 'ASP:plan': 12, 'TYR:plan': 5, 'TRP:plan': 2, 'HIS:plan': 4, 'ARG:plan': 3} 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: {'ARG:plan': 4, 'PHE:plan': 6, 'GLU:plan': 8, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLN:plan1': 1} 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: 4.24, per 1000 atoms: 0.20 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 - 3.00 Amino acid : True - 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.4 microseconds 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... Secondary structure from input PDB file: 124 helices and 16 sheets defined 53.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain '1' and resid 170 through 177 Processing helix chain '1' and resid 177 through 188 Processing helix chain '1' and resid 188 through 198 Processing helix chain '1' and resid 205 through 225 removed outlier: 3.602A pdb=" N PHE 1 209 " --> pdb=" O PRO 1 205 " (cutoff:3.500A) 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 230 through 237 Processing helix chain '1' and resid 251 through 263 Processing helix chain '1' and resid 263 through 273 removed outlier: 3.792A pdb=" N LYS 1 267 " --> pdb=" O TYR 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 281 through 295 removed outlier: 3.697A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 309 through 330 removed outlier: 3.740A pdb=" N GLU 1 320 " --> pdb=" O THR 1 316 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU 1 330 " --> pdb=" O ASP 1 326 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 343 Processing helix chain '1' and resid 371 through 391 removed outlier: 3.949A pdb=" N LEU 1 389 " --> pdb=" O MET 1 385 " (cutoff:3.500A) Processing helix chain '1' and resid 467 through 483 Processing helix chain '1' and resid 496 through 516 Processing helix chain '1' and resid 540 through 565 Processing helix chain '1' and resid 575 through 605 Processing helix chain '1' and resid 606 through 639 Proline residue: 1 618 - end of helix Processing helix chain '4' and resid 33 through 43 Processing helix chain '4' and resid 50 through 68 removed outlier: 3.770A pdb=" N ASN 4 68 " --> pdb=" O HIS 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 135 Processing helix chain '4' and resid 137 through 143 removed outlier: 4.084A pdb=" N ASN 4 143 " --> pdb=" O GLN 4 139 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 167 Processing helix chain '4' and resid 192 through 207 Processing helix chain '4' and resid 221 through 231 Processing helix chain '4' and resid 244 through 252 Processing helix chain '4' and resid 313 through 322 Processing helix chain '7' and resid 104 through 109 Processing helix chain '7' and resid 124 through 128 Processing helix chain '7' and resid 149 through 161 Processing helix chain '7' and resid 176 through 187 removed outlier: 3.877A pdb=" N GLY 7 187 " --> pdb=" O ALA 7 183 " (cutoff:3.500A) Processing helix chain '7' and resid 189 through 201 Processing helix chain '7' and resid 206 through 219 removed outlier: 3.516A pdb=" N ILE 7 218 " --> pdb=" O LYS 7 214 " (cutoff:3.500A) Processing helix chain '7' and resid 238 through 248 removed outlier: 3.625A pdb=" N LEU 7 242 " --> pdb=" O GLN 7 238 " (cutoff:3.500A) Processing helix chain '7' and resid 262 through 268 Processing helix chain '7' and resid 322 through 333 Processing helix chain '7' and resid 363 through 375 removed outlier: 3.613A pdb=" N GLY 7 375 " --> pdb=" O SER 7 371 " (cutoff:3.500A) Processing helix chain '7' and resid 391 through 404 removed outlier: 4.481A pdb=" N VAL 7 395 " --> pdb=" O GLY 7 391 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY 7 396 " --> pdb=" O LYS 7 392 " (cutoff:3.500A) Processing helix chain '7' and resid 413 through 425 Processing helix chain '7' and resid 457 through 461 Processing helix chain '7' and resid 468 through 480 Processing helix chain '7' and resid 494 through 506 removed outlier: 4.079A pdb=" N PHE 7 498 " --> pdb=" O PRO 7 494 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 532 Processing helix chain '7' and resid 539 through 544 Processing helix chain '7' and resid 562 through 572 Processing helix chain '7' and resid 576 through 583 removed outlier: 4.048A pdb=" N LEU 7 580 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) Processing helix chain '7' and resid 584 through 602 Processing helix chain '7' and resid 612 through 623 Processing helix chain '7' and resid 632 through 645 Processing helix chain '7' and resid 681 through 691 removed outlier: 3.675A pdb=" N LEU 7 691 " --> pdb=" O LEU 7 687 " (cutoff:3.500A) Processing helix chain '7' and resid 715 through 730 Processing helix chain '7' and resid 752 through 766 removed outlier: 3.566A pdb=" N LEU 7 765 " --> pdb=" O GLN 7 761 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS 7 766 " --> pdb=" O GLU 7 762 " (cutoff:3.500A) Processing helix chain '5' and resid 13 through 27 Processing helix chain '5' and resid 43 through 62 removed outlier: 3.789A pdb=" N VAL 5 47 " --> pdb=" O ASN 5 43 " (cutoff:3.500A) 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 9 through 17 removed outlier: 3.506A pdb=" N TYR 2 13 " --> pdb=" O SER 2 9 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE 2 17 " --> pdb=" O TYR 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 27 Processing helix chain '2' and resid 28 through 37 Processing helix chain '2' and resid 40 through 51 Processing helix chain '2' and resid 59 through 65 Processing helix chain '2' and resid 70 through 85 Processing helix chain '2' and resid 101 through 113 Processing helix chain '2' and resid 119 through 123 removed outlier: 4.261A pdb=" N VAL 2 123 " --> pdb=" O SER 2 120 " (cutoff:3.500A) Processing helix chain '2' and resid 135 through 152 Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 185 through 194 Processing helix chain '2' and resid 196 through 211 Processing helix chain '2' and resid 217 through 231 removed outlier: 3.874A pdb=" N LEU 2 231 " --> pdb=" O MET 2 227 " (cutoff:3.500A) Processing helix chain '2' and resid 243 through 256 Processing helix chain '2' and resid 272 through 280 removed outlier: 4.181A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 353 through 362 Processing helix chain '2' and resid 379 through 389 removed outlier: 4.008A pdb=" N ALA 2 386 " --> pdb=" O SER 2 382 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN 2 389 " --> pdb=" O ARG 2 385 " (cutoff:3.500A) Processing helix chain '2' and resid 394 through 403 removed outlier: 3.844A pdb=" N ALA 2 398 " --> pdb=" O ASP 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 404 through 407 Processing helix chain '2' and resid 408 through 417 Processing helix chain '2' and resid 434 through 448 Processing helix chain '2' and resid 464 through 479 Processing helix chain '2' and resid 495 through 507 Processing helix chain '0' and resid 18 through 34 removed outlier: 3.665A pdb=" N VAL 0 34 " --> pdb=" O LYS 0 30 " (cutoff:3.500A) Processing helix chain '0' and resid 47 through 63 removed outlier: 3.550A pdb=" N SER 0 51 " --> pdb=" O GLY 0 47 " (cutoff:3.500A) Processing helix chain '0' and resid 75 through 98 Processing helix chain '0' and resid 117 through 123 removed outlier: 3.777A pdb=" N GLU 0 123 " --> pdb=" O GLU 0 119 " (cutoff:3.500A) Processing helix chain '0' and resid 125 through 137 Processing helix chain '0' and resid 140 through 148 Processing helix chain '0' and resid 157 through 165 Processing helix chain '0' and resid 177 through 188 Processing helix chain '0' and resid 191 through 200 Processing helix chain '0' and resid 210 through 215 Processing helix chain '0' and resid 240 through 249 Processing helix chain '0' and resid 253 through 278 Processing helix chain '0' and resid 279 through 292 removed outlier: 3.736A pdb=" N GLY 0 292 " --> pdb=" O LYS 0 288 " (cutoff:3.500A) Processing helix chain '0' and resid 294 through 299 Processing helix chain '0' and resid 322 through 326 Processing helix chain '0' and resid 327 through 347 Processing helix chain '0' and resid 355 through 367 Processing helix chain '0' and resid 370 through 376 removed outlier: 3.897A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) Processing helix chain '0' and resid 376 through 389 Processing helix chain '0' and resid 393 through 395 No H-bonds generated for 'chain '0' and resid 393 through 395' Processing helix chain '0' and resid 396 through 412 Processing helix chain '0' and resid 424 through 428 Processing helix chain '0' and resid 442 through 453 removed outlier: 3.819A pdb=" N ILE 0 446 " --> pdb=" O ALA 0 442 " (cutoff:3.500A) Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 467 through 474 Processing helix chain '0' and resid 515 through 533 removed outlier: 3.608A pdb=" N VAL 0 519 " --> pdb=" O ASP 0 515 " (cutoff:3.500A) Processing helix chain '0' and resid 543 through 557 Processing helix chain '0' and resid 558 through 567 removed outlier: 3.829A pdb=" N GLU 0 562 " --> pdb=" O GLY 0 558 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL 0 563 " --> pdb=" O ILE 0 559 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 592 Processing helix chain '0' and resid 604 through 610 removed outlier: 3.911A pdb=" N GLU 0 608 " --> pdb=" O GLY 0 604 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY 0 609 " --> pdb=" O LYS 0 605 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE 0 610 " --> pdb=" O VAL 0 606 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 604 through 610' Processing helix chain '0' and resid 633 through 646 Processing helix chain '0' and resid 649 through 667 Processing helix chain '0' and resid 668 through 670 No H-bonds generated for 'chain '0' and resid 668 through 670' Processing helix chain '0' and resid 685 through 690 removed outlier: 3.986A pdb=" N LYS 0 689 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG 0 690 " --> pdb=" O PHE 0 686 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 685 through 690' Processing helix chain '0' and resid 694 through 701 removed outlier: 3.907A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 702 through 706 Processing helix chain '0' and resid 709 through 726 Processing helix chain '0' and resid 733 through 738 removed outlier: 3.685A pdb=" N SER 0 737 " --> pdb=" O GLN 0 733 " (cutoff:3.500A) Processing helix chain '0' and resid 743 through 752 Processing helix chain '6' and resid 133 through 138 Processing helix chain '6' and resid 144 through 164 removed outlier: 4.031A pdb=" N MET 6 148 " --> pdb=" O ASN 6 144 " (cutoff:3.500A) Processing helix chain '6' and resid 188 through 201 removed outlier: 3.931A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS 6 201 " --> pdb=" O LYS 6 197 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 221 Processing helix chain '6' and resid 246 through 257 removed outlier: 4.083A pdb=" N THR 6 250 " --> pdb=" O ASP 6 246 " (cutoff:3.500A) Processing helix chain '6' and resid 270 through 281 Processing helix chain '6' and resid 293 through 306 removed outlier: 4.001A pdb=" N THR 6 306 " --> pdb=" O ASN 6 302 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 384 removed outlier: 3.676A pdb=" N MET 6 384 " --> pdb=" O TYR 6 380 " (cutoff:3.500A) Processing helix chain '6' and resid 418 through 423 removed outlier: 4.224A pdb=" N THR 6 423 " --> pdb=" O GLY 6 419 " (cutoff:3.500A) Processing helix chain '6' and resid 437 through 447 Processing helix chain '6' and resid 451 through 456 removed outlier: 3.508A pdb=" N SER 6 456 " --> pdb=" O PRO 6 452 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '4' and resid 73 through 76 removed outlier: 6.397A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '4' and resid 179 through 182 removed outlier: 4.055A pdb=" N GLY 4 216 " --> pdb=" O VAL 4 238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '4' and resid 295 through 296 removed outlier: 4.261A pdb=" N MET 6 369 " --> pdb=" O LYS 6 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '7' and resid 382 through 385 Processing sheet with id=AA5, first strand: chain '7' and resid 453 through 456 removed outlier: 6.743A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE 7 408 " --> pdb=" O ILE 7 486 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '7' and resid 651 through 654 removed outlier: 6.743A pdb=" N ILE 7 605 " --> pdb=" O ILE 7 652 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU 7 654 " --> pdb=" O ILE 7 605 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL 7 607 " --> pdb=" O LEU 7 654 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN 7 553 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N SER 7 707 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA 7 555 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL 7 552 " --> pdb=" O ALA 7 732 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LYS 7 734 " --> pdb=" O VAL 7 552 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N CYS 7 554 " --> pdb=" O LYS 7 734 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '7' and resid 558 through 559 Processing sheet with id=AA8, first strand: chain '5' and resid 33 through 36 removed outlier: 6.231A pdb=" N HIS 5 39 " --> pdb=" O LEU 5 35 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN 5 11 " --> pdb=" O ILE 2 452 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE 2 452 " --> pdb=" O GLN 5 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 57 through 58 Processing sheet with id=AB1, first strand: chain '2' and resid 457 through 458 removed outlier: 3.645A pdb=" N SER 2 457 " --> pdb=" O ILE 2 493 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE 2 493 " --> pdb=" O SER 2 457 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '0' and resid 3 through 4 removed outlier: 3.658A pdb=" N PHE 0 3 " --> pdb=" O VAL 0 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '0' and resid 105 through 108 removed outlier: 6.620A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 207 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE 0 69 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N TYR 0 208 " --> pdb=" O ILE 0 69 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR 0 71 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE 0 70 " --> pdb=" O ILE 0 233 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASP 0 235 " --> pdb=" O ILE 0 70 " (cutoff:3.500A) 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) removed outlier: 3.666A pdb=" N SER 0 460 " --> pdb=" O LEU 0 40 " (cutoff:3.500A) Processing sheet with id=AB4, 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=AB5, first strand: chain '0' and resid 537 through 541 removed outlier: 6.448A pdb=" N MET 0 537 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER 0 600 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL 0 539 " --> pdb=" O SER 0 600 " (cutoff:3.500A) 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) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain '6' and resid 181 through 186 removed outlier: 5.766A pdb=" N GLN 6 184 " --> pdb=" O ILE 6 171 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE 6 171 " --> pdb=" O GLN 6 184 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU 6 126 " --> pdb=" O GLY 6 170 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ILE 6 172 " --> pdb=" O LEU 6 126 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU 6 128 " --> pdb=" O ILE 6 172 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU 6 233 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N LYS 6 262 " --> pdb=" O ARG 6 230 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL 6 232 " --> pdb=" O LYS 6 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '6' and resid 347 through 348 1042 hydrogen bonds defined for protein. 3057 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: 3.43 Time building geometry restraints manager: 2.44 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: 0.00 - 2.55: 28275 2.55 - 5.10: 510 5.10 - 7.65: 53 7.65 - 10.20: 14 10.20 - 12.76: 1 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: 575 2.61 - 3.18: 22166 3.18 - 3.75: 35419 3.75 - 4.33: 45716 4.33 - 4.90: 70763 Nonbonded interactions: 174639 Sorted by model distance: nonbonded pdb=" OG SER 0 378 " pdb=" OG1 THR 0 407 " model vdw 2.034 3.040 nonbonded pdb=" N ASP 2 61 " pdb=" OD1 ASP 2 61 " model vdw 2.078 3.120 nonbonded pdb=" O CYS 0 115 " pdb=" OG SER 0 121 " model vdw 2.082 3.040 nonbonded pdb=" O ILE 1 343 " pdb=" N ASP 1 345 " model vdw 2.087 3.120 nonbonded pdb=" O THR 6 116 " pdb=" OG1 THR 6 116 " model vdw 2.103 3.040 ... (remaining 174634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.080 ------------------------------------------------------------------------------- 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 0.091 21422 Z= 0.407 Angle : 1.084 71.031 28889 Z= 0.494 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 : 30.20 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG 0 513 TYR 0.024 0.002 TYR 0 629 PHE 0.023 0.002 PHE 2 492 TRP 0.010 0.002 TRP 7 558 HIS 0.008 0.001 HIS 4 64 Details of bonding type rmsd covalent geometry : bond 0.00841 (21399) covalent geometry : angle 0.84912 (28853) hydrogen bonds : bond 0.15400 ( 1042) hydrogen bonds : angle 6.63997 ( 3057) metal coordination : bond 0.02696 ( 23) metal coordination : angle 19.10374 ( 36) *********************** 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 to be fit. rotamer outliers: 267 poor density : 142 time to evaluate : 0.858 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: 0.1357 time to fit residues: 84.5434 Evaluate side-chains 268 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 118 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** 1 262 ASN ** 7 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 476 GLN 6 227 HIS 6 375 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.082522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.055103 restraints weight = 109811.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053736 restraints weight = 90798.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054153 restraints weight = 69055.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054163 restraints weight = 61739.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054212 restraints weight = 53017.490| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21422 Z= 0.168 Angle : 0.938 65.044 28889 Z= 0.379 Chirality : 0.046 0.176 3173 Planarity : 0.005 0.072 3816 Dihedral : 10.632 84.229 3401 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.08 % Favored : 87.43 % Rotamer: Outliers : 7.31 % Allowed : 18.42 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.16), residues: 2888 helix: 0.75 (0.14), residues: 1411 sheet: -2.95 (0.31), residues: 231 loop : -2.97 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 4 273 TYR 0.022 0.002 TYR 6 380 PHE 0.025 0.002 PHE 2 45 TRP 0.025 0.003 TRP 2 201 HIS 0.006 0.001 HIS 0 294 Details of bonding type rmsd covalent geometry : bond 0.00359 (21399) covalent geometry : angle 0.72631 (28853) hydrogen bonds : bond 0.04350 ( 1042) hydrogen bonds : angle 5.34108 ( 3057) metal coordination : bond 0.01706 ( 23) metal coordination : angle 16.84554 ( 36) *********************** 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 296 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 148 time to evaluate : 0.588 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: 1 597 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: 4 225 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8201 (tm-30) REVERT: 7 716 MET cc_start: 0.9051 (mmm) cc_final: 0.8765 (mmm) REVERT: 5 27 MET cc_start: 0.7866 (ppp) cc_final: 0.7578 (ppp) REVERT: 2 67 ASN cc_start: 0.9244 (OUTLIER) cc_final: 0.8921 (p0) REVERT: 2 286 ARG cc_start: 0.4599 (OUTLIER) cc_final: 0.4234 (tmm160) REVERT: 0 241 ASP cc_start: 0.9057 (p0) cc_final: 0.8747 (p0) REVERT: 0 401 ASP cc_start: 0.9498 (OUTLIER) cc_final: 0.9276 (m-30) REVERT: 6 118 TYR cc_start: 0.4834 (OUTLIER) cc_final: 0.2524 (p90) REVERT: 6 136 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8155 (mtp) REVERT: 6 142 ARG cc_start: 0.8842 (mmp80) cc_final: 0.8354 (mmp80) REVERT: 6 254 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9382 (mp) REVERT: 6 274 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9182 (tmtt) REVERT: 6 353 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8477 (t-90) outliers start: 148 outliers final: 93 residues processed: 284 average time/residue: 0.1196 time to fit residues: 55.7654 Evaluate side-chains 233 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 131 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 382 SER Chi-restraints excluded: chain 1 residue 597 PHE Chi-restraints excluded: chain 4 residue 26 LEU 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 212 VAL Chi-restraints excluded: chain 4 residue 258 LEU Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 274 THR 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 620 LEU Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 7 residue 701 PHE 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 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 110 SER 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 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 284 ASP Chi-restraints excluded: chain 0 residue 318 THR Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 401 ASP Chi-restraints excluded: chain 0 residue 419 ILE 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 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 654 LEU Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 705 ASP Chi-restraints excluded: chain 0 residue 710 THR 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 118 TYR Chi-restraints excluded: chain 6 residue 122 ILE Chi-restraints excluded: chain 6 residue 136 MET Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 6 residue 202 GLN 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 274 LYS 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 353 HIS 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 107 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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** 1 262 ASN 4 198 ASN ** 7 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 161 ASN ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 480 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.081826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054784 restraints weight = 109401.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.053708 restraints weight = 84393.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.053835 restraints weight = 66874.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053735 restraints weight = 61377.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053869 restraints weight = 50211.073| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21422 Z= 0.191 Angle : 0.870 59.746 28889 Z= 0.357 Chirality : 0.045 0.213 3173 Planarity : 0.004 0.060 3816 Dihedral : 8.888 57.993 3269 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.08 % Favored : 87.53 % Rotamer: Outliers : 7.16 % Allowed : 19.31 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.16), residues: 2888 helix: 0.94 (0.14), residues: 1412 sheet: -2.78 (0.32), residues: 229 loop : -2.94 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 680 TYR 0.025 0.002 TYR 7 677 PHE 0.016 0.001 PHE 2 492 TRP 0.008 0.001 TRP 7 482 HIS 0.006 0.001 HIS 4 64 Details of bonding type rmsd covalent geometry : bond 0.00418 (21399) covalent geometry : angle 0.68928 (28853) hydrogen bonds : bond 0.03988 ( 1042) hydrogen bonds : angle 5.10182 ( 3057) metal coordination : bond 0.01424 ( 23) metal coordination : angle 15.03477 ( 36) *********************** 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 286 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 141 time to evaluate : 0.826 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: 1 597 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: 4 225 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8251 (tm-30) REVERT: 4 254 ILE cc_start: 0.8836 (pp) cc_final: 0.8611 (pp) REVERT: 7 425 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8913 (mm) REVERT: 2 67 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8920 (p0) REVERT: 2 97 MET cc_start: 0.9330 (mmm) cc_final: 0.8970 (mmm) REVERT: 0 76 MET cc_start: 0.8512 (ppp) cc_final: 0.8035 (tmm) REVERT: 0 136 MET cc_start: 0.8714 (tpp) cc_final: 0.8494 (tpp) REVERT: 0 155 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.8942 (mp) REVERT: 0 241 ASP cc_start: 0.9092 (p0) cc_final: 0.8694 (p0) REVERT: 0 435 MET cc_start: 0.8951 (tpp) cc_final: 0.8730 (mmm) REVERT: 0 742 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8441 (tp30) REVERT: 6 118 TYR cc_start: 0.4663 (OUTLIER) cc_final: 0.2419 (p90) REVERT: 6 142 ARG cc_start: 0.8849 (mmp80) cc_final: 0.8488 (mmp80) REVERT: 6 254 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9378 (mp) REVERT: 6 274 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9007 (tptm) REVERT: 6 353 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8452 (t70) REVERT: 6 380 TYR cc_start: 0.8193 (m-80) cc_final: 0.7963 (m-80) outliers start: 145 outliers final: 104 residues processed: 274 average time/residue: 0.1246 time to fit residues: 56.2220 Evaluate side-chains 243 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 130 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 553 LEU 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 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 212 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 258 LEU 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 357 LYS Chi-restraints excluded: chain 7 residue 425 LEU 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 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 14 LEU Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 28 SER Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 67 ASN Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 95 THR 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 371 VAL Chi-restraints excluded: chain 2 residue 383 ILE 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 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 254 THR 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 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 556 THR 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 601 VAL 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 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 742 GLU Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 118 TYR 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 194 ASP Chi-restraints excluded: chain 6 residue 202 GLN 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 274 LYS Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 292 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 92 optimal weight: 30.0000 chunk 213 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 108 optimal weight: 40.0000 chunk 227 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 468 HIS ** 2 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 21 GLN ** 0 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.081445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.054045 restraints weight = 110334.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.053144 restraints weight = 85854.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053140 restraints weight = 62702.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053429 restraints weight = 52896.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053856 restraints weight = 47439.135| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21422 Z= 0.213 Angle : 0.843 55.549 28889 Z= 0.354 Chirality : 0.045 0.170 3173 Planarity : 0.004 0.059 3816 Dihedral : 8.588 57.983 3253 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.33 % Favored : 87.29 % Rotamer: Outliers : 7.21 % Allowed : 19.95 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.16), residues: 2888 helix: 0.98 (0.14), residues: 1415 sheet: -2.85 (0.32), residues: 232 loop : -2.91 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 680 TYR 0.020 0.002 TYR 2 13 PHE 0.016 0.001 PHE 2 492 TRP 0.008 0.001 TRP 7 482 HIS 0.006 0.001 HIS 4 64 Details of bonding type rmsd covalent geometry : bond 0.00465 (21399) covalent geometry : angle 0.68950 (28853) hydrogen bonds : bond 0.03880 ( 1042) hydrogen bonds : angle 5.03670 ( 3057) metal coordination : bond 0.01519 ( 23) metal coordination : angle 13.77400 ( 36) *********************** 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 282 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 136 time to evaluate : 0.890 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: 0.8826 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: 4 225 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8310 (tm-30) REVERT: 7 425 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8902 (mm) REVERT: 7 716 MET cc_start: 0.9189 (mmm) cc_final: 0.8917 (mmm) REVERT: 2 67 ASN cc_start: 0.9288 (OUTLIER) cc_final: 0.8918 (p0) REVERT: 0 76 MET cc_start: 0.8569 (ppp) cc_final: 0.8155 (tmm) REVERT: 0 241 ASP cc_start: 0.9155 (p0) cc_final: 0.8793 (p0) REVERT: 0 435 MET cc_start: 0.9028 (tpp) cc_final: 0.8780 (mmm) REVERT: 0 512 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8174 (mm) REVERT: 0 742 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8419 (tp30) REVERT: 6 118 TYR cc_start: 0.4712 (OUTLIER) cc_final: 0.2503 (p90) REVERT: 6 142 ARG cc_start: 0.8885 (mmp80) cc_final: 0.8495 (mmp80) REVERT: 6 353 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8502 (t70) REVERT: 6 375 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7566 (m-70) outliers start: 146 outliers final: 112 residues processed: 270 average time/residue: 0.1306 time to fit residues: 57.9226 Evaluate side-chains 253 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 133 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain 1 residue 553 LEU Chi-restraints excluded: chain 1 residue 558 CYS 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 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 212 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 258 LEU 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 357 LYS Chi-restraints excluded: chain 7 residue 425 LEU 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 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 14 LEU Chi-restraints excluded: chain 2 residue 16 GLU Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 67 ASN Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 88 ILE Chi-restraints excluded: chain 2 residue 95 THR 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 371 VAL Chi-restraints excluded: chain 2 residue 383 ILE 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 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 254 THR 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 477 THR Chi-restraints excluded: chain 0 residue 487 LEU Chi-restraints excluded: chain 0 residue 512 ILE 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 556 THR 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 601 VAL 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 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 742 GLU Chi-restraints excluded: chain 0 residue 747 HIS Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 141 LEU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 158 HIS Chi-restraints excluded: chain 6 residue 161 PHE Chi-restraints excluded: chain 6 residue 166 ILE Chi-restraints excluded: chain 6 residue 194 ASP Chi-restraints excluded: chain 6 residue 202 GLN Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 239 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 292 LEU 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 353 HIS Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 375 HIS Chi-restraints excluded: chain 6 residue 381 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 86 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 253 optimal weight: 0.7980 chunk 282 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 72 optimal weight: 40.0000 chunk 268 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 188 ASN 1 258 ASN ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 431 GLN ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 382 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.082941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055279 restraints weight = 108303.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.054279 restraints weight = 80538.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.054263 restraints weight = 65655.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054462 restraints weight = 54990.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054631 restraints weight = 47104.816| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21422 Z= 0.125 Angle : 0.757 43.962 28889 Z= 0.328 Chirality : 0.043 0.242 3173 Planarity : 0.004 0.053 3816 Dihedral : 8.005 59.754 3241 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.05 % Favored : 88.61 % Rotamer: Outliers : 5.88 % Allowed : 21.58 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.16), residues: 2888 helix: 1.05 (0.14), residues: 1431 sheet: -2.88 (0.32), residues: 231 loop : -2.79 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 0 67 TYR 0.026 0.001 TYR 6 380 PHE 0.013 0.001 PHE 2 492 TRP 0.010 0.001 TRP 0 696 HIS 0.005 0.001 HIS 7 468 Details of bonding type rmsd covalent geometry : bond 0.00271 (21399) covalent geometry : angle 0.65029 (28853) hydrogen bonds : bond 0.03455 ( 1042) hydrogen bonds : angle 4.76422 ( 3057) metal coordination : bond 0.00861 ( 23) metal coordination : angle 11.00516 ( 36) *********************** 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 266 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 147 time to evaluate : 0.884 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: 1 551 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7580 (ttp-170) REVERT: 1 597 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8080 (m-80) REVERT: 7 425 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8836 (mm) REVERT: 7 449 GLU cc_start: -0.0345 (OUTLIER) cc_final: -0.0690 (mt-10) REVERT: 7 716 MET cc_start: 0.9340 (mmm) cc_final: 0.9095 (mmm) REVERT: 2 67 ASN cc_start: 0.9281 (OUTLIER) cc_final: 0.8958 (p0) REVERT: 2 97 MET cc_start: 0.9292 (mmm) cc_final: 0.8753 (mmm) REVERT: 2 286 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.3958 (tmm160) REVERT: 0 76 MET cc_start: 0.8509 (ppp) cc_final: 0.8103 (tmm) REVERT: 0 346 MET cc_start: 0.8938 (mmm) cc_final: 0.8564 (mmm) REVERT: 0 435 MET cc_start: 0.8972 (tpp) cc_final: 0.8689 (mmm) REVERT: 0 568 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8473 (mp) REVERT: 0 742 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: 6 118 TYR cc_start: 0.4759 (OUTLIER) cc_final: 0.2392 (p90) REVERT: 6 142 ARG cc_start: 0.8821 (mmp80) cc_final: 0.8514 (mmp80) REVERT: 6 353 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.8415 (t70) REVERT: 6 380 TYR cc_start: 0.8146 (m-80) cc_final: 0.7942 (m-80) outliers start: 119 outliers final: 81 residues processed: 257 average time/residue: 0.1386 time to fit residues: 58.0059 Evaluate side-chains 224 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 133 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 551 ARG 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 212 VAL Chi-restraints excluded: chain 4 residue 236 LEU Chi-restraints excluded: chain 4 residue 273 ARG Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 425 LEU 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 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU 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 67 ASN 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 286 ARG Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 383 ILE Chi-restraints excluded: chain 2 residue 411 LEU Chi-restraints excluded: chain 2 residue 450 ARG Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 101 GLU 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 221 ARG Chi-restraints excluded: chain 0 residue 231 ILE Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 254 THR 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 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 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 649 ARG Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 0 residue 669 VAL Chi-restraints excluded: chain 0 residue 680 VAL 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 742 GLU Chi-restraints excluded: chain 0 residue 747 HIS 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 222 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 292 LEU 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 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 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 138 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 195 optimal weight: 0.9980 chunk 263 optimal weight: 8.9990 chunk 243 optimal weight: 0.9990 chunk 232 optimal weight: 0.0980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.083404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053317 restraints weight = 107571.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055171 restraints weight = 65558.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055447 restraints weight = 39129.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055421 restraints weight = 39362.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.055357 restraints weight = 30549.880| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21422 Z= 0.118 Angle : 0.725 32.117 28889 Z= 0.325 Chirality : 0.043 0.362 3173 Planarity : 0.004 0.050 3816 Dihedral : 7.471 56.830 3216 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.66 % Favored : 88.99 % Rotamer: Outliers : 5.53 % Allowed : 21.78 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.16), residues: 2888 helix: 1.14 (0.14), residues: 1438 sheet: -2.90 (0.30), residues: 238 loop : -2.74 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 0 67 TYR 0.028 0.001 TYR 4 193 PHE 0.024 0.001 PHE 7 446 TRP 0.009 0.001 TRP 0 696 HIS 0.006 0.001 HIS 6 375 Details of bonding type rmsd covalent geometry : bond 0.00255 (21399) covalent geometry : angle 0.66218 (28853) hydrogen bonds : bond 0.03329 ( 1042) hydrogen bonds : angle 4.61224 ( 3057) metal coordination : bond 0.00691 ( 23) metal coordination : angle 8.39808 ( 36) *********************** 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 255 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 143 time to evaluate : 0.734 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: 0.8618 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: 7 425 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8753 (mm) REVERT: 7 578 MET cc_start: -0.3362 (tpt) cc_final: -0.3764 (tpt) REVERT: 7 716 MET cc_start: 0.9345 (mmm) cc_final: 0.9027 (mmm) REVERT: 2 67 ASN cc_start: 0.9325 (OUTLIER) cc_final: 0.8987 (p0) REVERT: 2 286 ARG cc_start: 0.4173 (OUTLIER) cc_final: 0.3628 (tmm160) REVERT: 0 76 MET cc_start: 0.8384 (ppp) cc_final: 0.7968 (tmm) REVERT: 0 199 MET cc_start: 0.8768 (mmm) cc_final: 0.8520 (tpp) REVERT: 0 346 MET cc_start: 0.8769 (mmm) cc_final: 0.8369 (mmm) REVERT: 0 435 MET cc_start: 0.8926 (tpp) cc_final: 0.8683 (mmm) REVERT: 6 118 TYR cc_start: 0.4674 (OUTLIER) cc_final: 0.2395 (p90) REVERT: 6 142 ARG cc_start: 0.8591 (mmp80) cc_final: 0.8389 (mmp80) REVERT: 6 353 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8434 (t70) REVERT: 6 369 MET cc_start: 0.8260 (tpt) cc_final: 0.8055 (tpt) outliers start: 112 outliers final: 78 residues processed: 244 average time/residue: 0.1380 time to fit residues: 54.5779 Evaluate side-chains 216 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 132 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain 1 residue 516 HIS 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 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 212 VAL Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 425 LEU 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 541 MET Chi-restraints excluded: chain 7 residue 549 ILE 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 14 LEU Chi-restraints excluded: chain 2 residue 67 ASN Chi-restraints excluded: chain 2 residue 87 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 383 ILE Chi-restraints excluded: chain 2 residue 453 THR Chi-restraints excluded: chain 2 residue 464 THR Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 157 GLU Chi-restraints excluded: chain 0 residue 170 TYR 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 254 THR Chi-restraints excluded: chain 0 residue 318 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 556 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 680 VAL Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 747 HIS 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 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 239 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 274 LYS Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 292 LEU 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 353 HIS Chi-restraints excluded: chain 6 residue 362 VAL Chi-restraints excluded: chain 6 residue 381 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 233 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 250 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 174 optimal weight: 20.0000 chunk 259 optimal weight: 2.9990 chunk 82 optimal weight: 50.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** 5 22 GLN 0 138 ASN ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 382 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.082737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.052586 restraints weight = 108541.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054782 restraints weight = 64887.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054018 restraints weight = 37869.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.054407 restraints weight = 38196.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054304 restraints weight = 32711.940| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21422 Z= 0.150 Angle : 0.715 28.049 28889 Z= 0.328 Chirality : 0.043 0.193 3173 Planarity : 0.004 0.100 3816 Dihedral : 7.146 57.646 3198 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.80 % Favored : 88.92 % Rotamer: Outliers : 5.23 % Allowed : 22.47 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.16), residues: 2888 helix: 1.23 (0.14), residues: 1438 sheet: -2.84 (0.31), residues: 233 loop : -2.73 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 2 450 TYR 0.025 0.001 TYR 6 380 PHE 0.023 0.001 PHE 1 321 TRP 0.032 0.001 TRP 7 558 HIS 0.006 0.001 HIS 6 375 Details of bonding type rmsd covalent geometry : bond 0.00331 (21399) covalent geometry : angle 0.65893 (28853) hydrogen bonds : bond 0.03382 ( 1042) hydrogen bonds : angle 4.61647 ( 3057) metal coordination : bond 0.00935 ( 23) metal coordination : angle 7.87028 ( 36) *********************** 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 242 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 136 time to evaluate : 0.912 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: 0.8701 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: 7 425 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8764 (mm) REVERT: 7 716 MET cc_start: 0.9363 (mmm) cc_final: 0.9115 (mmm) REVERT: 2 67 ASN cc_start: 0.9347 (OUTLIER) cc_final: 0.8978 (p0) REVERT: 2 286 ARG cc_start: 0.4332 (OUTLIER) cc_final: 0.3721 (tmm160) REVERT: 0 76 MET cc_start: 0.8418 (ppp) cc_final: 0.7982 (tmm) REVERT: 0 642 MET cc_start: 0.9076 (tpp) cc_final: 0.8835 (tpp) REVERT: 6 118 TYR cc_start: 0.4609 (OUTLIER) cc_final: 0.2461 (p90) REVERT: 6 142 ARG cc_start: 0.8729 (mmp80) cc_final: 0.8462 (mmp80) REVERT: 6 353 HIS cc_start: 0.8990 (OUTLIER) cc_final: 0.8509 (t70) outliers start: 106 outliers final: 86 residues processed: 232 average time/residue: 0.1337 time to fit residues: 51.5622 Evaluate side-chains 226 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 134 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain 1 residue 516 HIS Chi-restraints excluded: chain 1 residue 558 CYS 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 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 212 VAL Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 293 LEU Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 425 LEU 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 541 MET Chi-restraints excluded: chain 7 residue 549 ILE 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 67 ASN Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 95 THR 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 383 ILE Chi-restraints excluded: chain 2 residue 453 THR Chi-restraints excluded: chain 2 residue 464 THR Chi-restraints excluded: chain 0 residue 32 LEU Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 101 GLU 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 231 ILE Chi-restraints excluded: chain 0 residue 248 LEU Chi-restraints excluded: chain 0 residue 254 THR Chi-restraints excluded: chain 0 residue 318 THR 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 556 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 680 VAL 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 729 ASP Chi-restraints excluded: chain 0 residue 747 HIS 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 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 239 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 274 LYS Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 292 LEU 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 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 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 184 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 228 optimal weight: 0.9990 chunk 245 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** 0 21 GLN ** 0 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 ASN ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 566 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.083538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.053511 restraints weight = 108003.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055479 restraints weight = 65392.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.055154 restraints weight = 37105.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055358 restraints weight = 38372.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.055307 restraints weight = 32732.042| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21422 Z= 0.118 Angle : 0.716 22.269 28889 Z= 0.328 Chirality : 0.044 0.365 3173 Planarity : 0.004 0.090 3816 Dihedral : 6.934 59.091 3196 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.32 % Favored : 89.44 % Rotamer: Outliers : 4.99 % Allowed : 22.91 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.16), residues: 2888 helix: 1.26 (0.14), residues: 1437 sheet: -2.69 (0.31), residues: 231 loop : -2.70 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 450 TYR 0.033 0.001 TYR 2 13 PHE 0.024 0.001 PHE 1 321 TRP 0.020 0.001 TRP 7 558 HIS 0.007 0.001 HIS 6 375 Details of bonding type rmsd covalent geometry : bond 0.00255 (21399) covalent geometry : angle 0.67355 (28853) hydrogen bonds : bond 0.03257 ( 1042) hydrogen bonds : angle 4.55929 ( 3057) metal coordination : bond 0.00621 ( 23) metal coordination : angle 6.93318 ( 36) *********************** 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 245 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 144 time to evaluate : 0.888 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: 0.8638 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: 4 137 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8562 (mtmm) REVERT: 4 271 ASP cc_start: 0.7311 (m-30) cc_final: 0.6919 (t70) REVERT: 7 425 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8721 (mm) REVERT: 7 716 MET cc_start: 0.9384 (mmm) cc_final: 0.9153 (mmm) REVERT: 2 67 ASN cc_start: 0.9327 (OUTLIER) cc_final: 0.8717 (p0) REVERT: 2 97 MET cc_start: 0.9184 (mmm) cc_final: 0.8606 (mmm) REVERT: 2 286 ARG cc_start: 0.4157 (OUTLIER) cc_final: 0.3608 (tmm160) REVERT: 0 76 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7961 (tmm) REVERT: 0 199 MET cc_start: 0.8712 (mmm) cc_final: 0.8421 (tpp) REVERT: 0 435 MET cc_start: 0.8952 (mmm) cc_final: 0.8579 (mmm) REVERT: 0 642 MET cc_start: 0.9068 (tpp) cc_final: 0.8850 (tpp) REVERT: 6 118 TYR cc_start: 0.4719 (OUTLIER) cc_final: 0.2445 (p90) REVERT: 6 142 ARG cc_start: 0.8590 (mmp80) cc_final: 0.8361 (mmp80) REVERT: 6 166 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8767 (mp) REVERT: 6 353 HIS cc_start: 0.8930 (OUTLIER) cc_final: 0.8481 (t70) outliers start: 101 outliers final: 76 residues processed: 232 average time/residue: 0.1345 time to fit residues: 51.6761 Evaluate side-chains 225 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 140 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain 1 residue 516 HIS 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 212 VAL Chi-restraints excluded: chain 4 residue 244 LEU Chi-restraints excluded: chain 4 residue 261 ILE Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 425 LEU 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 541 MET Chi-restraints excluded: chain 7 residue 549 ILE Chi-restraints excluded: chain 7 residue 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 60 LEU 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 279 THR Chi-restraints excluded: chain 2 residue 286 ARG Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 383 ILE Chi-restraints excluded: chain 2 residue 453 THR Chi-restraints excluded: chain 2 residue 464 THR Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 148 ASP Chi-restraints excluded: chain 0 residue 157 GLU 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 318 THR 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 556 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 680 VAL 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 118 TYR 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 222 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 270 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 292 LEU 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 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 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 140 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 240 optimal weight: 0.6980 chunk 274 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.083343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055432 restraints weight = 107632.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055293 restraints weight = 78678.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.055289 restraints weight = 58777.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.055303 restraints weight = 55575.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055370 restraints weight = 45731.549| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21422 Z= 0.126 Angle : 0.714 19.123 28889 Z= 0.330 Chirality : 0.044 0.402 3173 Planarity : 0.004 0.087 3816 Dihedral : 6.817 58.148 3192 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.25 % Favored : 89.51 % Rotamer: Outliers : 4.49 % Allowed : 23.36 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.16), residues: 2888 helix: 1.31 (0.14), residues: 1444 sheet: -2.64 (0.32), residues: 232 loop : -2.70 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 450 TYR 0.028 0.001 TYR 6 380 PHE 0.028 0.001 PHE 0 334 TRP 0.018 0.001 TRP 7 558 HIS 0.006 0.001 HIS 6 375 Details of bonding type rmsd covalent geometry : bond 0.00279 (21399) covalent geometry : angle 0.67909 (28853) hydrogen bonds : bond 0.03234 ( 1042) hydrogen bonds : angle 4.51742 ( 3057) metal coordination : bond 0.00677 ( 23) metal coordination : angle 6.30929 ( 36) *********************** 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 232 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 141 time to evaluate : 0.934 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: 0.8589 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: 4 271 ASP cc_start: 0.7518 (m-30) cc_final: 0.7117 (t70) REVERT: 7 425 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8671 (mm) REVERT: 7 449 GLU cc_start: -0.0574 (OUTLIER) cc_final: -0.0816 (mt-10) REVERT: 7 716 MET cc_start: 0.9375 (mmm) cc_final: 0.9091 (mmm) REVERT: 2 67 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8954 (p0) REVERT: 2 97 MET cc_start: 0.9216 (mmm) cc_final: 0.8690 (mmm) REVERT: 2 286 ARG cc_start: 0.3951 (OUTLIER) cc_final: 0.3396 (tmm160) REVERT: 0 76 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7946 (tmm) REVERT: 0 136 MET cc_start: 0.8699 (tpp) cc_final: 0.8433 (tpp) REVERT: 0 199 MET cc_start: 0.8624 (mmm) cc_final: 0.8360 (tpp) REVERT: 0 435 MET cc_start: 0.8853 (mmm) cc_final: 0.8503 (mmm) REVERT: 6 118 TYR cc_start: 0.4693 (OUTLIER) cc_final: 0.2358 (p90) REVERT: 6 142 ARG cc_start: 0.8673 (mmp80) cc_final: 0.8381 (mmp80) REVERT: 6 166 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8730 (mp) REVERT: 6 353 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.8361 (t70) outliers start: 91 outliers final: 72 residues processed: 223 average time/residue: 0.1370 time to fit residues: 50.3530 Evaluate side-chains 220 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 139 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain 1 residue 516 HIS 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 30 ILE Chi-restraints excluded: chain 4 residue 163 ILE 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 261 ILE Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 425 LEU 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 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 51 VAL 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 279 THR Chi-restraints excluded: chain 2 residue 286 ARG Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 383 ILE Chi-restraints excluded: chain 2 residue 453 THR Chi-restraints excluded: chain 2 residue 464 THR Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 157 GLU 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 318 THR 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 539 VAL Chi-restraints excluded: chain 0 residue 556 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 680 VAL Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 747 HIS 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 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 239 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 270 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 292 LEU 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 353 HIS 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 235 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 141 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 160 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 190 optimal weight: 0.0570 chunk 91 optimal weight: 20.0000 chunk 260 optimal weight: 2.9990 overall best weight: 1.4302 ------------------------------------------------------------------------------- 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** ** 0 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.083380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056013 restraints weight = 108027.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.055083 restraints weight = 80201.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.055527 restraints weight = 54958.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.055698 restraints weight = 46933.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055921 restraints weight = 42339.820| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21422 Z= 0.130 Angle : 0.725 17.600 28889 Z= 0.335 Chirality : 0.044 0.417 3173 Planarity : 0.004 0.084 3816 Dihedral : 6.596 57.449 3182 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.94 % Favored : 89.82 % Rotamer: Outliers : 4.15 % Allowed : 23.70 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.16), residues: 2888 helix: 1.34 (0.14), residues: 1444 sheet: -2.61 (0.32), residues: 233 loop : -2.70 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 450 TYR 0.037 0.001 TYR 6 380 PHE 0.024 0.001 PHE 0 334 TRP 0.017 0.001 TRP 7 558 HIS 0.017 0.001 HIS 6 382 Details of bonding type rmsd covalent geometry : bond 0.00287 (21399) covalent geometry : angle 0.69333 (28853) hydrogen bonds : bond 0.03229 ( 1042) hydrogen bonds : angle 4.50823 ( 3057) metal coordination : bond 0.00700 ( 23) metal coordination : angle 6.03701 ( 36) ********************** 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 227 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 143 time to evaluate : 0.901 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: 0.8528 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: 4 266 ASN cc_start: 0.8472 (t0) cc_final: 0.8248 (t0) REVERT: 4 271 ASP cc_start: 0.7502 (m-30) cc_final: 0.7161 (t0) REVERT: 7 425 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8653 (mm) REVERT: 7 716 MET cc_start: 0.9353 (mmm) cc_final: 0.9051 (mmm) REVERT: 2 67 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8927 (p0) REVERT: 2 97 MET cc_start: 0.9209 (mmm) cc_final: 0.8698 (mmm) REVERT: 2 286 ARG cc_start: 0.3891 (OUTLIER) cc_final: 0.3331 (tmm160) REVERT: 0 76 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7938 (tmm) REVERT: 0 199 MET cc_start: 0.8635 (mmm) cc_final: 0.8410 (tpp) REVERT: 0 435 MET cc_start: 0.8833 (mmm) cc_final: 0.8487 (mmm) REVERT: 6 118 TYR cc_start: 0.4668 (OUTLIER) cc_final: 0.2387 (p90) REVERT: 6 142 ARG cc_start: 0.8672 (mmp80) cc_final: 0.8384 (mmp80) REVERT: 6 148 MET cc_start: 0.8712 (ttm) cc_final: 0.8354 (ttm) REVERT: 6 152 TYR cc_start: 0.9037 (m-80) cc_final: 0.8684 (m-80) REVERT: 6 166 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8746 (mp) REVERT: 6 322 MET cc_start: 0.8825 (pmm) cc_final: 0.8515 (pmm) REVERT: 6 353 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8356 (t70) outliers start: 84 outliers final: 71 residues processed: 219 average time/residue: 0.1351 time to fit residues: 49.1210 Evaluate side-chains 217 residues out of total 2645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 138 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain 1 residue 516 HIS Chi-restraints excluded: chain 1 residue 558 CYS 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 163 ILE 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 261 ILE Chi-restraints excluded: chain 4 residue 274 THR Chi-restraints excluded: chain 7 residue 357 LYS Chi-restraints excluded: chain 7 residue 425 LEU 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 692 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 2 residue 51 VAL 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 279 THR Chi-restraints excluded: chain 2 residue 286 ARG Chi-restraints excluded: chain 2 residue 348 TYR Chi-restraints excluded: chain 2 residue 383 ILE Chi-restraints excluded: chain 2 residue 453 THR Chi-restraints excluded: chain 2 residue 464 THR Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 0 residue 76 MET Chi-restraints excluded: chain 0 residue 101 GLU Chi-restraints excluded: chain 0 residue 130 ASP Chi-restraints excluded: chain 0 residue 157 GLU 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 318 THR Chi-restraints excluded: chain 0 residue 355 THR Chi-restraints excluded: chain 0 residue 462 THR Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 556 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 680 VAL Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 0 residue 721 LEU Chi-restraints excluded: chain 0 residue 747 HIS 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 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 239 LEU Chi-restraints excluded: chain 6 residue 263 VAL Chi-restraints excluded: chain 6 residue 266 LEU Chi-restraints excluded: chain 6 residue 270 VAL Chi-restraints excluded: chain 6 residue 290 ILE Chi-restraints excluded: chain 6 residue 292 LEU 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 353 HIS Chi-restraints excluded: chain 6 residue 363 CYS Chi-restraints excluded: chain 6 residue 381 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 99 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 195 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 283 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 4 optimal weight: 0.2980 chunk 199 optimal weight: 0.4980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.083061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.052937 restraints weight = 108045.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055435 restraints weight = 66740.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054817 restraints weight = 35321.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054964 restraints weight = 32208.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.054916 restraints weight = 32438.810| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21422 Z= 0.147 Angle : 0.735 16.984 28889 Z= 0.339 Chirality : 0.044 0.426 3173 Planarity : 0.004 0.084 3816 Dihedral : 6.579 59.029 3181 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.18 % Favored : 89.58 % Rotamer: Outliers : 4.25 % Allowed : 23.70 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.16), residues: 2888 helix: 1.37 (0.14), residues: 1443 sheet: -2.58 (0.32), residues: 233 loop : -2.70 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 0 67 TYR 0.037 0.001 TYR 6 380 PHE 0.021 0.001 PHE 0 334 TRP 0.016 0.001 TRP 7 558 HIS 0.007 0.001 HIS 6 375 Details of bonding type rmsd covalent geometry : bond 0.00326 (21399) covalent geometry : angle 0.70400 (28853) hydrogen bonds : bond 0.03266 ( 1042) hydrogen bonds : angle 4.50655 ( 3057) metal coordination : bond 0.00830 ( 23) metal coordination : angle 6.00721 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4003.46 seconds wall clock time: 70 minutes 2.31 seconds (4202.31 seconds total)