Starting phenix.real_space_refine on Sat Sep 28 08:24:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/09_2024/8fok_29352.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/09_2024/8fok_29352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/09_2024/8fok_29352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/09_2024/8fok_29352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/09_2024/8fok_29352.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fok_29352/09_2024/8fok_29352.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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 P 34 5.49 5 S 94 5.16 5 C 11854 2.51 5 N 3234 2.21 5 O 3607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18827 Number of models: 1 Model: "" Number of chains: 7 Chain: "1" Number of atoms: 8250 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1046, 8242 Classifications: {'peptide': 1046} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 50, 'TRANS': 995} Chain breaks: 5 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Conformer: "B" Number of residues, atoms: 1046, 8242 Classifications: {'peptide': 1046} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 50, 'TRANS': 995} Chain breaks: 5 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 bond proxies already assigned to first conformer: 8385 Chain: "A" Number of atoms: 2866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2866 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 333} Chain breaks: 3 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3555 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 430, 3532 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 416} Chain breaks: 5 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 430, 3532 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 13, 'TRANS': 416} Chain breaks: 5 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 3581 Chain: "C" Number of atoms: 3428 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3414 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 433, 3414 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 3476 Chain: "T" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 415 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "P" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 305 Classifications: {'DNA': 4, 'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 13} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13324 SG CYS B 336 56.588 105.469 67.146 1.00 50.15 S ATOM 14113 SG CYS B 434 61.539 104.824 63.164 1.00 54.17 S ATOM 13981 SG CYS B 417 62.615 105.241 69.680 1.00 45.11 S ATOM 14430 SG CYS B 474 60.780 110.248 66.747 1.00 62.10 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASP 11414 " occ=0.25 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.75 residue: pdb=" N AASP C 263 " occ=0.30 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.70 residue: pdb=" N ACYS C 399 " occ=0.95 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.05 Time building chain proxies: 17.16, per 1000 atoms: 0.91 Number of scatterers: 18827 At special positions: 0 Unit cell: (95.22, 160.632, 163.944, 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) Fe 4 26.01 S 94 16.00 P 34 15.00 O 3607 8.00 N 3234 7.00 C 11854 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: 5.45 Conformation dependent library (CDL) restraints added in 4.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE1 SF4 B 601 " - pdb=" SG CYS B 336 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " pdb="FE3 SF4 B 601 " - pdb=" SG CYS B 417 " pdb="FE2 SF4 B 601 " - pdb=" SG CYS B 434 " Number of angles added : 12 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 19 sheets defined 50.3% alpha, 14.0% beta 5 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 6.61 Creating SS restraints... Processing helix chain '1' and resid 402 through 419 Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 480 through 489 Processing helix chain '1' and resid 597 through 606 Processing helix chain '1' and resid 615 through 631 Processing helix chain '1' and resid 643 through 656 Processing helix chain '1' and resid 659 through 664 Processing helix chain '1' and resid 682 through 691 Processing helix chain '1' and resid 701 through 708 Processing helix chain '1' and resid 715 through 724 Processing helix chain '1' and resid 738 through 743 Processing helix chain '1' and resid 744 through 768 Processing helix chain '1' and resid 769 through 782 Processing helix chain '1' and resid 784 through 790 Processing helix chain '1' and resid 793 through 807 Processing helix chain '1' and resid 867 through 877 Processing helix chain '1' and resid 904 through 925 removed outlier: 3.517A pdb=" N ARG 1 908 " --> pdb=" O GLY 1 904 " (cutoff:3.500A) Processing helix chain '1' and resid 933 through 953 removed outlier: 3.516A pdb=" N TYR 1 951 " --> pdb=" O ALA 1 947 " (cutoff:3.500A) Processing helix chain '1' and resid 963 through 988 Processing helix chain '1' and resid 1008 through 1025 removed outlier: 3.835A pdb=" N ALA 11012 " --> pdb=" O ASN 11008 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE 11015 " --> pdb=" O ASP 11011 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU 11025 " --> pdb=" O ARG 11021 " (cutoff:3.500A) Processing helix chain '1' and resid 1079 through 1095 Processing helix chain '1' and resid 1098 through 1119 Processing helix chain '1' and resid 1123 through 1128 removed outlier: 3.573A pdb=" N LYS 11128 " --> pdb=" O ASP 11125 " (cutoff:3.500A) Processing helix chain '1' and resid 1146 through 1159 removed outlier: 4.084A pdb=" N GLN 11150 " --> pdb=" O MET 11146 " (cutoff:3.500A) Processing helix chain '1' and resid 1189 through 1191 No H-bonds generated for 'chain '1' and resid 1189 through 1191' Processing helix chain '1' and resid 1195 through 1200 Processing helix chain '1' and resid 1201 through 1205 Processing helix chain '1' and resid 1209 through 1217 removed outlier: 3.530A pdb=" N TYR 11213 " --> pdb=" O ASP 11209 " (cutoff:3.500A) Processing helix chain '1' and resid 1218 through 1226 Processing helix chain '1' and resid 1233 through 1242 Processing helix chain '1' and resid 1244 through 1254 removed outlier: 4.125A pdb=" N TYR 11248 " --> pdb=" O ASP 11244 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG 11250 " --> pdb=" O LYS 11246 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG 11251 " --> pdb=" O LYS 11247 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU 11252 " --> pdb=" O TYR 11248 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY 11253 " --> pdb=" O PHE 11249 " (cutoff:3.500A) Processing helix chain '1' and resid 1266 through 1271 removed outlier: 3.534A pdb=" N ILE 11271 " --> pdb=" O LEU 11267 " (cutoff:3.500A) Processing helix chain '1' and resid 1272 through 1279 removed outlier: 4.533A pdb=" N ASP 11279 " --> pdb=" O GLU 11275 " (cutoff:3.500A) Processing helix chain '1' and resid 1322 through 1343 removed outlier: 4.305A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1381 through 1396 removed outlier: 3.710A pdb=" N PHE 11396 " --> pdb=" O PHE 11392 " (cutoff:3.500A) Processing helix chain '1' and resid 1397 through 1403 Processing helix chain '1' and resid 1423 through 1434 Processing helix chain '1' and resid 1434 through 1450 removed outlier: 3.663A pdb=" N VAL 11445 " --> pdb=" O GLY 11441 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 22 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 96 removed outlier: 4.958A pdb=" N ASP A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 removed outlier: 4.800A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 removed outlier: 4.179A pdb=" N ILE A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 210 through 229 Proline residue: A 222 - end of helix removed outlier: 4.128A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.768A pdb=" N GLU A 236 " --> pdb=" O ASN A 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.631A pdb=" N ASP A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 314 through 320 removed outlier: 4.326A pdb=" N THR A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 320' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 376 through 394 Processing helix chain 'B' and resid 43 through 55 Processing helix chain 'B' and resid 71 through 95 Processing helix chain 'B' and resid 98 through 113 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 120 through 138 removed outlier: 3.521A pdb=" N ARG B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 163 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 191 through 207 removed outlier: 4.728A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.673A pdb=" N ASN B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 278 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.719A pdb=" N GLU B 283 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 284 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 4.290A pdb=" N ILE B 290 " --> pdb=" O ARG B 286 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 334 through 348 Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 368 through 380 Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 450 Processing helix chain 'B' and resid 454 through 467 Processing helix chain 'B' and resid 469 through 482 Processing helix chain 'B' and resid 499 through 511 Processing helix chain 'C' and resid 253 through 277 removed outlier: 3.660A pdb=" N ILE C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 378 through 389 Processing helix chain 'C' and resid 410 through 423 Processing helix chain 'C' and resid 440 through 446 Processing helix chain 'C' and resid 460 through 469 Processing helix chain 'C' and resid 469 through 475 removed outlier: 3.580A pdb=" N THR C 475 " --> pdb=" O PRO C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 removed outlier: 3.560A pdb=" N ASP C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 554 Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 613 through 621 removed outlier: 3.790A pdb=" N LEU C 617 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 removed outlier: 3.616A pdb=" N PHE C 626 " --> pdb=" O VAL C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 697 Processing sheet with id=AA1, first strand: chain '1' and resid 515 through 519 removed outlier: 3.626A pdb=" N LEU 1 366 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS 1 373 " --> pdb=" O GLN 1 353 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN 1 353 " --> pdb=" O LYS 1 373 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 425 through 431 removed outlier: 7.583A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 609 through 612 removed outlier: 6.624A pdb=" N LEU 1 582 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG 1 611 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N THR 1 584 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN 1 554 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN 1 548 " --> pdb=" O GLN 1 554 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE 1 556 " --> pdb=" O LEU 1 546 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU 1 546 " --> pdb=" O ILE 1 556 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER 1 558 " --> pdb=" O GLN 1 544 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN 1 566 " --> pdb=" O LEU 1 536 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU 1 536 " --> pdb=" O ASN 1 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 854 through 856 removed outlier: 5.432A pdb=" N ILE 11034 " --> pdb=" O ASP 1 864 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASP 1 864 " --> pdb=" O ILE 11034 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN 11036 " --> pdb=" O VAL 1 862 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER 1 999 " --> pdb=" O GLY 1 995 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY 1 995 " --> pdb=" O SER 1 999 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET 11001 " --> pdb=" O VAL 1 993 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU 1 991 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 854 through 856 removed outlier: 13.566A pdb=" N ASP 11035 " --> pdb=" O LEU 11056 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N LEU 11056 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL 11037 " --> pdb=" O VAL 11054 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU 11052 " --> pdb=" O LYS 11039 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU 11041 " --> pdb=" O ALA 11050 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA 11050 " --> pdb=" O LEU 11041 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU 11043 " --> pdb=" O LYS 11048 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LYS 11048 " --> pdb=" O LEU 11043 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 1129 through 1132 Processing sheet with id=AA7, first strand: chain '1' and resid 1283 through 1286 removed outlier: 4.436A pdb=" N LEU 11283 " --> pdb=" O PHE 11296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 1305 through 1307 Processing sheet with id=AA9, first strand: chain '1' and resid 1356 through 1357 Processing sheet with id=AB1, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.752A pdb=" N PHE A 47 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 79 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 105 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.752A pdb=" N PHE A 47 " --> pdb=" O TYR A 59 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 79 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 108 through 112 removed outlier: 4.635A pdb=" N TRP A 159 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 181 through 182 removed outlier: 3.979A pdb=" N GLN B 181 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 302 removed outlier: 5.679A pdb=" N LEU C 316 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N PHE C 360 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG C 331 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL C 362 " --> pdb=" O ARG C 331 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ASP C 333 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER C 364 " --> pdb=" O ASP C 333 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL C 362 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS C 353 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 349 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 377 removed outlier: 4.291A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 681 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 515 through 517 removed outlier: 5.937A pdb=" N THR C 482 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS C 394 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ILE C 430 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE C 396 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE C 432 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C 398 " --> pdb=" O PHE C 432 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 531 through 533 removed outlier: 6.263A pdb=" N GLY C 532 " --> pdb=" O ILE C 632 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 578 through 579 removed outlier: 3.655A pdb=" N SER C 608 " --> pdb=" O ARG C 579 " (cutoff:3.500A) 897 hydrogen bonds defined for protein. 2551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 7.04 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.33: 3616 1.33 - 1.57: 15474 1.57 - 1.80: 164 1.80 - 2.04: 35 2.04 - 2.28: 13 Bond restraints: 19302 Sorted by residual: bond pdb=" CB PRO 1 894 " pdb=" CG PRO 1 894 " ideal model delta sigma weight residual 1.492 2.278 -0.786 5.00e-02 4.00e+02 2.47e+02 bond pdb=" C LEU 1 954 " pdb=" N GLY 1 955 " ideal model delta sigma weight residual 1.331 1.518 -0.187 1.46e-02 4.69e+03 1.64e+02 bond pdb=" CG PRO 1 894 " pdb=" CD PRO 1 894 " ideal model delta sigma weight residual 1.503 1.114 0.389 3.40e-02 8.65e+02 1.31e+02 bond pdb=" CG PRO 11266 " pdb=" CD PRO 11266 " ideal model delta sigma weight residual 1.503 1.181 0.322 3.40e-02 8.65e+02 8.98e+01 bond pdb=" CB PRO 11266 " pdb=" CG PRO 11266 " ideal model delta sigma weight residual 1.492 1.089 0.403 5.00e-02 4.00e+02 6.50e+01 ... (remaining 19297 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.46: 26277 16.46 - 32.92: 5 32.92 - 49.38: 1 49.38 - 65.84: 0 65.84 - 82.30: 1 Bond angle restraints: 26284 Sorted by residual: angle pdb=" CB PRO 1 894 " pdb=" CG PRO 1 894 " pdb=" CD PRO 1 894 " ideal model delta sigma weight residual 106.10 23.80 82.30 3.20e+00 9.77e-02 6.62e+02 angle pdb=" CA PRO 1 894 " pdb=" N PRO 1 894 " pdb=" CD PRO 1 894 " ideal model delta sigma weight residual 112.00 78.26 33.74 1.40e+00 5.10e-01 5.81e+02 angle pdb=" N PRO 11266 " pdb=" CD PRO 11266 " pdb=" CG PRO 11266 " ideal model delta sigma weight residual 103.20 75.01 28.19 1.50e+00 4.44e-01 3.53e+02 angle pdb=" CA PRO 11266 " pdb=" CB PRO 11266 " pdb=" CG PRO 11266 " ideal model delta sigma weight residual 104.50 73.13 31.37 1.90e+00 2.77e-01 2.73e+02 angle pdb=" N PRO 1 894 " pdb=" CD PRO 1 894 " pdb=" CG PRO 1 894 " ideal model delta sigma weight residual 103.20 122.16 -18.96 1.50e+00 4.44e-01 1.60e+02 ... (remaining 26279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.27: 11026 28.27 - 56.54: 593 56.54 - 84.81: 71 84.81 - 113.07: 9 113.07 - 141.34: 1 Dihedral angle restraints: 11700 sinusoidal: 5005 harmonic: 6695 Sorted by residual: dihedral pdb=" N PRO 1 894 " pdb=" CG PRO 1 894 " pdb=" CD PRO 1 894 " pdb=" CB PRO 1 894 " ideal model delta sinusoidal sigma weight residual 30.00 171.34 -141.34 1 1.50e+01 4.44e-03 7.60e+01 dihedral pdb=" N PRO 11266 " pdb=" CG PRO 11266 " pdb=" CD PRO 11266 " pdb=" CB PRO 11266 " ideal model delta sinusoidal sigma weight residual 30.00 97.28 -67.28 1 1.50e+01 4.44e-03 2.62e+01 dihedral pdb=" CA ALA C 349 " pdb=" C ALA C 349 " pdb=" N PHE C 350 " pdb=" CA PHE C 350 " ideal model delta harmonic sigma weight residual -180.00 -159.00 -21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 11697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2267 0.046 - 0.092: 495 0.092 - 0.138: 156 0.138 - 0.184: 5 0.184 - 0.230: 4 Chirality restraints: 2927 Sorted by residual: chirality pdb=" CG LEU C 510 " pdb=" CB LEU C 510 " pdb=" CD1 LEU C 510 " pdb=" CD2 LEU C 510 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU 1 449 " pdb=" CB LEU 1 449 " pdb=" CD1 LEU 1 449 " pdb=" CD2 LEU 1 449 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE 1 462 " pdb=" N ILE 1 462 " pdb=" C ILE 1 462 " pdb=" CB ILE 1 462 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 2924 not shown) Planarity restraints: 3278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU 1 954 " -0.034 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C LEU 1 954 " 0.110 2.00e-02 2.50e+03 pdb=" O LEU 1 954 " -0.043 2.00e-02 2.50e+03 pdb=" N GLY 1 955 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 1 902 " 0.023 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C ASP 1 902 " -0.095 2.00e-02 2.50e+03 pdb=" O ASP 1 902 " 0.040 2.00e-02 2.50e+03 pdb=" N GLN 1 903 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 633 " -0.085 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO C 634 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO C 634 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 634 " -0.064 5.00e-02 4.00e+02 ... (remaining 3275 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 431 2.69 - 3.24: 18537 3.24 - 3.80: 30370 3.80 - 4.35: 40086 4.35 - 4.90: 65493 Nonbonded interactions: 154917 Sorted by model distance: nonbonded pdb=" O THR 1 774 " pdb=" OG1 THR 1 778 " model vdw 2.141 3.040 nonbonded pdb=" OH TYR A 18 " pdb=" O PHE A 329 " model vdw 2.152 3.040 nonbonded pdb=" OH TYR B 51 " pdb=" OH TYR B 129 " model vdw 2.184 3.040 nonbonded pdb=" O TYR 1 859 " pdb=" OG1 THR 11004 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 209 " pdb=" OD1 ASP A 303 " model vdw 2.243 3.040 ... (remaining 154912 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 60.550 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 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 0.786 19302 Z= 0.643 Angle : 0.924 82.304 26284 Z= 0.471 Chirality : 0.042 0.230 2927 Planarity : 0.006 0.120 3278 Dihedral : 16.601 141.343 7356 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.15 % Allowed : 17.14 % Favored : 82.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2239 helix: 1.26 (0.16), residues: 1032 sheet: -0.23 (0.30), residues: 265 loop : 0.23 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 376 HIS 0.009 0.001 HIS A 27 PHE 0.021 0.002 PHE C 350 TYR 0.017 0.001 TYR 1 766 ARG 0.009 0.001 ARG 1 587 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.7815 (mt) cc_final: 0.7553 (mt) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.3336 time to fit residues: 54.7217 Evaluate side-chains 69 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 1244 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 385 GLN 1 523 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11433 GLN B 238 ASN B 401 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.798 19302 Z= 0.673 Angle : 0.883 81.262 26284 Z= 0.417 Chirality : 0.045 0.325 2927 Planarity : 0.005 0.094 3278 Dihedral : 10.122 84.260 2885 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.56 % Allowed : 16.09 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2239 helix: 1.43 (0.16), residues: 1030 sheet: -0.26 (0.31), residues: 256 loop : 0.28 (0.20), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 376 HIS 0.008 0.001 HIS 1 684 PHE 0.020 0.002 PHE B 399 TYR 0.023 0.002 TYR B 503 ARG 0.008 0.001 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 71 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8063 (mt) cc_final: 0.7739 (mt) REVERT: 1 883 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8342 (m) REVERT: 1 1001 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7348 (mmt) outliers start: 51 outliers final: 27 residues processed: 118 average time/residue: 0.3096 time to fit residues: 58.8669 Evaluate side-chains 95 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 467 SER Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1000 VAL Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1334 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain 1 residue 1440 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 224 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 428 GLN 1 844 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 19302 Z= 0.289 Angle : 0.599 15.154 26284 Z= 0.314 Chirality : 0.042 0.196 2927 Planarity : 0.005 0.112 3278 Dihedral : 10.019 83.512 2883 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.26 % Allowed : 16.24 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.18), residues: 2239 helix: 1.56 (0.16), residues: 1025 sheet: -0.24 (0.31), residues: 269 loop : 0.31 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 376 HIS 0.006 0.001 HIS 1 684 PHE 0.016 0.002 PHE B 399 TYR 0.017 0.001 TYR B 503 ARG 0.008 0.001 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 66 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8068 (mt) cc_final: 0.7777 (mt) REVERT: 1 883 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8341 (m) REVERT: 1 1330 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8290 (tp) outliers start: 45 outliers final: 31 residues processed: 110 average time/residue: 0.3207 time to fit residues: 58.0209 Evaluate side-chains 99 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 66 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 481 ILE Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 844 GLN Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 883 VAL Chi-restraints excluded: chain 1 residue 893 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1000 VAL Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1330 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.0470 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 40.0000 chunk 22 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 108 optimal weight: 0.0970 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 overall best weight: 2.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 754 ASN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11121 ASN B 221 GLN B 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19302 Z= 0.184 Angle : 0.529 10.545 26284 Z= 0.273 Chirality : 0.041 0.164 2927 Planarity : 0.005 0.072 3278 Dihedral : 9.871 81.518 2883 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.06 % Allowed : 16.44 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2239 helix: 1.77 (0.17), residues: 1018 sheet: -0.09 (0.31), residues: 271 loop : 0.47 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 671 HIS 0.006 0.001 HIS 1 684 PHE 0.012 0.001 PHE B 399 TYR 0.015 0.001 TYR B 503 ARG 0.006 0.000 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 69 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8036 (mt) cc_final: 0.7727 (mt) REVERT: 1 1001 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7305 (mmt) REVERT: 1 1330 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8180 (tp) outliers start: 41 outliers final: 25 residues processed: 109 average time/residue: 0.3228 time to fit residues: 56.4058 Evaluate side-chains 94 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 67 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1330 ILE Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 188 optimal weight: 0.0030 chunk 152 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 30.0000 chunk 197 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS 1 844 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19302 Z= 0.211 Angle : 0.525 10.218 26284 Z= 0.269 Chirality : 0.041 0.165 2927 Planarity : 0.004 0.063 3278 Dihedral : 9.812 79.823 2883 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.01 % Allowed : 16.39 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2239 helix: 1.78 (0.17), residues: 1026 sheet: -0.13 (0.31), residues: 264 loop : 0.45 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 1 671 HIS 0.005 0.001 HIS 1 684 PHE 0.012 0.001 PHE B 399 TYR 0.016 0.001 TYR B 503 ARG 0.009 0.000 ARG 1 459 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 66 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8043 (mt) cc_final: 0.7749 (mt) REVERT: 1 1001 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7278 (mmt) REVERT: 1 1073 MET cc_start: 0.7031 (mpp) cc_final: 0.6827 (mpp) REVERT: B 388 MET cc_start: 0.5016 (mmp) cc_final: 0.4726 (tpt) outliers start: 40 outliers final: 30 residues processed: 104 average time/residue: 0.2743 time to fit residues: 46.7446 Evaluate side-chains 97 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 66 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 402 THR Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1111 GLU Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 19302 Z= 0.251 Angle : 0.529 10.635 26284 Z= 0.272 Chirality : 0.041 0.166 2927 Planarity : 0.004 0.059 3278 Dihedral : 9.833 79.046 2883 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.06 % Allowed : 16.64 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.18), residues: 2239 helix: 1.78 (0.17), residues: 1027 sheet: -0.17 (0.31), residues: 264 loop : 0.46 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 671 HIS 0.010 0.001 HIS 1 407 PHE 0.013 0.001 PHE B 399 TYR 0.017 0.001 TYR B 503 ARG 0.007 0.000 ARG 1 975 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 66 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8086 (mt) cc_final: 0.7791 (mt) REVERT: 1 1001 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7283 (mmt) REVERT: B 388 MET cc_start: 0.5039 (mmp) cc_final: 0.4742 (tpt) outliers start: 41 outliers final: 31 residues processed: 105 average time/residue: 0.2838 time to fit residues: 49.1751 Evaluate side-chains 96 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 64 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 407 HIS Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 chunk 133 optimal weight: 0.4980 chunk 101 optimal weight: 7.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 407 HIS ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19302 Z= 0.199 Angle : 0.517 10.672 26284 Z= 0.265 Chirality : 0.040 0.159 2927 Planarity : 0.004 0.057 3278 Dihedral : 9.804 78.425 2883 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.85 % Allowed : 16.94 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2239 helix: 1.83 (0.17), residues: 1027 sheet: -0.13 (0.31), residues: 269 loop : 0.52 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 671 HIS 0.009 0.001 HIS 1 407 PHE 0.012 0.001 PHE B 399 TYR 0.016 0.001 TYR B 503 ARG 0.005 0.000 ARG 1 975 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 68 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 771 LEU cc_start: 0.8063 (mt) cc_final: 0.7783 (mt) REVERT: 1 1001 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7296 (mmt) REVERT: B 74 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7477 (mt0) REVERT: B 388 MET cc_start: 0.5083 (mmp) cc_final: 0.4795 (tpt) outliers start: 37 outliers final: 32 residues processed: 102 average time/residue: 0.2840 time to fit residues: 48.3749 Evaluate side-chains 99 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 65 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 402 THR Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 50.0000 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 20 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 736 GLN ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 19302 Z= 0.406 Angle : 0.621 11.566 26284 Z= 0.320 Chirality : 0.043 0.192 2927 Planarity : 0.005 0.057 3278 Dihedral : 10.057 77.864 2883 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.95 % Allowed : 17.49 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2239 helix: 1.56 (0.16), residues: 1027 sheet: -0.41 (0.31), residues: 279 loop : 0.42 (0.21), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 1 356 HIS 0.006 0.001 HIS C 606 PHE 0.017 0.002 PHE B 75 TYR 0.021 0.002 TYR B 503 ARG 0.008 0.001 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 64 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.5204 (ttt) cc_final: 0.4846 (ttt) REVERT: 1 1001 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7362 (mmt) REVERT: B 61 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.6900 (t80) REVERT: B 74 GLN cc_start: 0.7826 (OUTLIER) cc_final: 0.7464 (mt0) REVERT: B 388 MET cc_start: 0.5134 (mmp) cc_final: 0.4870 (tpt) outliers start: 39 outliers final: 35 residues processed: 100 average time/residue: 0.2798 time to fit residues: 45.7056 Evaluate side-chains 101 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 63 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 402 THR Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 4.9990 chunk 210 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 204 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 30.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19302 Z= 0.212 Angle : 0.536 10.897 26284 Z= 0.274 Chirality : 0.041 0.168 2927 Planarity : 0.004 0.056 3278 Dihedral : 9.917 78.041 2883 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.94 % Rotamer: Outliers : 2.06 % Allowed : 17.39 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.18), residues: 2239 helix: 1.74 (0.17), residues: 1026 sheet: -0.40 (0.31), residues: 282 loop : 0.55 (0.22), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 671 HIS 0.004 0.001 HIS 1 684 PHE 0.014 0.001 PHE B 399 TYR 0.016 0.001 TYR B 503 ARG 0.006 0.000 ARG 11076 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 66 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.5112 (ttt) cc_final: 0.4787 (ttt) REVERT: 1 1001 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7361 (mmt) REVERT: B 61 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6640 (t80) REVERT: B 388 MET cc_start: 0.5112 (mmp) cc_final: 0.4827 (tpt) outliers start: 41 outliers final: 34 residues processed: 105 average time/residue: 0.2928 time to fit residues: 50.7631 Evaluate side-chains 100 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 64 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 402 THR Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 19302 Z= 0.323 Angle : 0.574 11.127 26284 Z= 0.295 Chirality : 0.042 0.177 2927 Planarity : 0.004 0.057 3278 Dihedral : 10.025 76.737 2883 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.58 % Rotamer: Outliers : 1.85 % Allowed : 17.49 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.18), residues: 2239 helix: 1.63 (0.17), residues: 1029 sheet: -0.47 (0.31), residues: 268 loop : 0.49 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.005 0.001 HIS C 606 PHE 0.015 0.002 PHE B 399 TYR 0.019 0.001 TYR B 503 ARG 0.008 0.001 ARG 11076 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 64 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 354 MET cc_start: 0.5140 (ttt) cc_final: 0.4768 (ttt) REVERT: 1 1001 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.7417 (mmt) REVERT: B 61 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.6836 (t80) REVERT: B 388 MET cc_start: 0.4977 (mmp) cc_final: 0.4704 (tpt) outliers start: 37 outliers final: 34 residues processed: 98 average time/residue: 0.2911 time to fit residues: 47.2873 Evaluate side-chains 98 residues out of total 2055 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 62 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 402 THR Chi-restraints excluded: chain 1 residue 404 THR Chi-restraints excluded: chain 1 residue 528 THR Chi-restraints excluded: chain 1 residue 614 ASN Chi-restraints excluded: chain 1 residue 641 GLN Chi-restraints excluded: chain 1 residue 670 THR Chi-restraints excluded: chain 1 residue 855 LEU Chi-restraints excluded: chain 1 residue 860 VAL Chi-restraints excluded: chain 1 residue 861 LEU Chi-restraints excluded: chain 1 residue 896 VAL Chi-restraints excluded: chain 1 residue 951 TYR Chi-restraints excluded: chain 1 residue 957 VAL Chi-restraints excluded: chain 1 residue 991 LEU Chi-restraints excluded: chain 1 residue 1001 MET Chi-restraints excluded: chain 1 residue 1002 ILE Chi-restraints excluded: chain 1 residue 1007 ASP Chi-restraints excluded: chain 1 residue 1032 ILE Chi-restraints excluded: chain 1 residue 1068 VAL Chi-restraints excluded: chain 1 residue 1230 ASP Chi-restraints excluded: chain 1 residue 1274 VAL Chi-restraints excluded: chain 1 residue 1352 THR Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain B residue 55 TYR Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 137 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 480 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 648 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 874 GLN ** 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 = 0.3195 r_free = 0.3195 target = 0.038732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.029488 restraints weight = 380797.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.030882 restraints weight = 147181.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.031129 restraints weight = 78927.177| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 19302 Z= 0.283 Angle : 0.560 10.905 26284 Z= 0.286 Chirality : 0.042 0.177 2927 Planarity : 0.004 0.057 3278 Dihedral : 9.985 76.519 2883 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.90 % Allowed : 17.64 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2239 helix: 1.67 (0.17), residues: 1028 sheet: -0.47 (0.31), residues: 273 loop : 0.54 (0.22), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.005 0.001 HIS 1 684 PHE 0.015 0.001 PHE B 399 TYR 0.018 0.001 TYR B 503 ARG 0.007 0.000 ARG 11076 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2795.82 seconds wall clock time: 54 minutes 21.06 seconds (3261.06 seconds total)