Starting phenix.real_space_refine on Tue Nov 19 01:41:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/11_2024/8foc_29345.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/11_2024/8foc_29345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/11_2024/8foc_29345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/11_2024/8foc_29345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/11_2024/8foc_29345.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foc_29345/11_2024/8foc_29345.cif" } resolution = 3.7 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 97 5.16 5 C 11659 2.51 5 N 3156 2.21 5 O 3466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 18382 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3676 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 13, 'TRANS': 436} Chain breaks: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3257 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 375} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3412 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3388 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 433, 3388 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 5, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 3437 Chain: "1" Number of atoms: 8029 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1007, 7974 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Conformer: "B" Number of residues, atoms: 1007, 7974 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 bond proxies already assigned to first conformer: 8060 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 3311 SG CYS B 474 39.967 98.808 76.862 1.00 12.59 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AASP C 263 " occ=0.82 ... (14 atoms not shown) pdb=" OD2BASP C 263 " occ=0.18 residue: pdb=" N ACYS C 399 " occ=0.46 ... (10 atoms not shown) pdb=" SG BCYS C 399 " occ=0.54 residue: pdb=" N AASN 1 745 " occ=0.33 ... (14 atoms not shown) pdb=" ND2BASN 1 745 " occ=0.67 residue: pdb=" N AGLN 1 787 " occ=0.42 ... (16 atoms not shown) pdb=" NE2BGLN 1 787 " occ=0.58 residue: pdb=" N AGLN 1 941 " occ=0.48 ... (16 atoms not shown) pdb=" NE2BGLN 1 941 " occ=0.52 residue: pdb=" N AHIS 11044 " occ=0.09 ... (18 atoms not shown) pdb=" NE2BHIS 11044 " occ=0.91 residue: pdb=" N AASP 11414 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP 11414 " occ=0.55 Time building chain proxies: 14.34, per 1000 atoms: 0.78 Number of scatterers: 18382 At special positions: 0 Unit cell: (114.264, 145.728, 154.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 97 16.00 O 3466 8.00 N 3156 7.00 C 11659 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: 4.51 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 601 " pdb="FE4 SF4 B 601 " - pdb=" SG CYS B 474 " Number of angles added : 3 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4408 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 19 sheets defined 51.3% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... 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 139 removed outlier: 3.611A 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 208 removed outlier: 4.739A pdb=" N ALA B 201 " --> pdb=" O GLN B 197 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.551A pdb=" N GLN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 238 removed outlier: 3.806A pdb=" N ASN B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 282 Proline residue: B 279 - end of helix Processing helix chain 'B' and resid 287 through 298 removed outlier: 3.778A pdb=" N TYR B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 325 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 382 Processing helix chain 'B' and resid 387 through 395 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.696A pdb=" N TYR B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 451 Processing helix chain 'B' and resid 454 through 467 Processing helix chain 'B' and resid 469 through 483 Processing helix chain 'B' and resid 499 through 526 Processing helix chain 'A' and resid 11 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: 5.054A pdb=" N ASP A 94 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 removed outlier: 3.831A pdb=" N ASP A 118 " --> pdb=" O ASP A 115 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA A 119 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 121 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 151 removed outlier: 4.059A 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: 4.288A pdb=" N VAL A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 removed outlier: 3.664A 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 265 Processing helix chain 'A' and resid 269 through 285 removed outlier: 3.715A 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 315 through 320 removed outlier: 3.732A pdb=" N LYS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 320' Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 353 through 364 removed outlier: 3.516A pdb=" N LYS A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 372 through 402 Processing helix chain 'C' and resid 253 through 277 removed outlier: 3.703A 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 445 Processing helix chain 'C' and resid 460 through 469 Processing helix chain 'C' and resid 469 through 475 removed outlier: 3.709A pdb=" N THR C 475 " --> pdb=" O PRO C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 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: 5.072A pdb=" N GLY C 618 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 626 removed outlier: 3.511A pdb=" N PHE C 626 " --> pdb=" O VAL C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 697 Processing helix chain '1' and resid 402 through 419 removed outlier: 3.837A pdb=" N ILE 1 411 " --> pdb=" O HIS 1 407 " (cutoff:3.500A) Proline residue: 1 412 - end of helix Processing helix chain '1' and resid 480 through 489 Processing helix chain '1' and resid 521 through 523 No H-bonds generated for 'chain '1' and resid 521 through 523' Processing helix chain '1' and resid 597 through 606 Processing helix chain '1' and resid 615 through 631 removed outlier: 3.672A pdb=" N MET 1 619 " --> pdb=" O ASN 1 615 " (cutoff:3.500A) Processing helix chain '1' and resid 643 through 655 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 725 Processing helix chain '1' and resid 737 through 742 Processing helix chain '1' and resid 743 through 768 Processing helix chain '1' and resid 769 through 782 Processing helix chain '1' and resid 784 through 791 Processing helix chain '1' and resid 792 through 808 removed outlier: 4.495A pdb=" N ARG 1 796 " --> pdb=" O THR 1 792 " (cutoff:3.500A) Processing helix chain '1' and resid 867 through 876 Processing helix chain '1' and resid 904 through 927 removed outlier: 3.740A pdb=" N THR 1 926 " --> pdb=" O LYS 1 922 " (cutoff:3.500A) Processing helix chain '1' and resid 929 through 950 Processing helix chain '1' and resid 951 through 956 Processing helix chain '1' and resid 963 through 988 Processing helix chain '1' and resid 1008 through 1027 Processing helix chain '1' and resid 1079 through 1094 Processing helix chain '1' and resid 1100 through 1120 Processing helix chain '1' and resid 1123 through 1128 Processing helix chain '1' and resid 1136 through 1140 Processing helix chain '1' and resid 1146 through 1159 Processing helix chain '1' and resid 1196 through 1201 Processing helix chain '1' and resid 1202 through 1205 Processing helix chain '1' and resid 1209 through 1216 Processing helix chain '1' and resid 1218 through 1226 removed outlier: 3.872A pdb=" N ARG 11224 " --> pdb=" O ALA 11220 " (cutoff:3.500A) Processing helix chain '1' and resid 1322 through 1343 removed outlier: 4.106A pdb=" N GLN 11329 " --> pdb=" O GLN 11325 " (cutoff:3.500A) Processing helix chain '1' and resid 1381 through 1396 removed outlier: 3.830A pdb=" N PHE 11396 " --> pdb=" O PHE 11392 " (cutoff:3.500A) Processing helix chain '1' and resid 1397 through 1404 Processing helix chain '1' and resid 1423 through 1434 Processing helix chain '1' and resid 1434 through 1450 removed outlier: 4.157A pdb=" N TYR 11448 " --> pdb=" O VAL 11444 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 181 through 182 removed outlier: 4.218A pdb=" N GLN B 181 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 242 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 60 removed outlier: 5.541A pdb=" N ARG A 58 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET A 49 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 105 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 60 removed outlier: 5.541A pdb=" N ARG A 58 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET A 49 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU A 46 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 325 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 314 removed outlier: 4.648A pdb=" N ASP A 111 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TRP A 159 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 294 through 302 removed outlier: 5.424A pdb=" N LEU C 316 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LYS C 351 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE C 365 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ALA C 349 " --> pdb=" O ILE C 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AA7, first strand: chain 'C' and resid 375 through 377 removed outlier: 4.170A pdb=" N VAL C 689 " --> pdb=" O VAL C 683 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 681 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 515 through 517 removed outlier: 6.691A pdb=" N LYS C 394 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE C 430 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE C 396 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE C 432 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR C 398 " --> pdb=" O PHE C 432 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 522 through 526 removed outlier: 6.329A pdb=" N TYR C 530 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE C 632 " --> pdb=" O TYR C 530 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY C 532 " --> pdb=" O ILE C 632 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 578 through 579 Processing sheet with id=AB2, first strand: chain '1' and resid 515 through 519 removed outlier: 9.681A pdb=" N VAL 1 515 " --> pdb=" O CYS 1 379 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N SER 1 381 " --> pdb=" O VAL 1 515 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N VAL 1 517 " --> pdb=" O SER 1 381 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET 1 383 " --> pdb=" O VAL 1 517 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL 1 519 " --> pdb=" O MET 1 383 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLN 1 385 " --> pdb=" O VAL 1 519 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR 1 365 " --> pdb=" O GLU 1 361 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU 1 361 " --> pdb=" O THR 1 365 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE 1 367 " --> pdb=" O TYR 1 359 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR 1 359 " --> pdb=" O ILE 1 367 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE 1 369 " --> pdb=" O LEU 1 357 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS 1 373 " --> pdb=" O GLN 1 353 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN 1 353 " --> pdb=" O LYS 1 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1' and resid 425 through 431 removed outlier: 7.729A pdb=" N ASP 1 444 " --> pdb=" O PRO 1 397 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N HIS 1 473 " --> pdb=" O LEU 1 396 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '1' and resid 609 through 612 removed outlier: 6.811A pdb=" N LEU 1 582 " --> pdb=" O ARG 1 609 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ARG 1 611 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR 1 584 " --> pdb=" O ARG 1 611 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP 1 581 " --> pdb=" O ALA 1 563 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLN 1 554 " --> pdb=" O ASN 1 548 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN 1 548 " --> pdb=" O GLN 1 554 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE 1 556 " --> pdb=" O LEU 1 546 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LEU 1 546 " --> pdb=" O ILE 1 556 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER 1 558 " --> pdb=" O GLN 1 544 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN 1 566 " --> pdb=" O LEU 1 536 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU 1 536 " --> pdb=" O ASN 1 566 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '1' and resid 854 through 856 removed outlier: 3.819A pdb=" N ASP 11033 " --> pdb=" O ASP 1 864 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL 1 862 " --> pdb=" O ASP 11035 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL 11037 " --> pdb=" O VAL 1 860 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL 1 860 " --> pdb=" O VAL 11037 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP 11003 " --> pdb=" O VAL 1 992 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL 1 992 " --> pdb=" O ASP 11003 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1' and resid 854 through 856 removed outlier: 4.028A pdb=" N LYS 11040 " --> pdb=" O LEU 11052 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS 11048 " --> pdb=" O AHIS 11044 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '1' and resid 1129 through 1132 Processing sheet with id=AB8, first strand: chain '1' and resid 1283 through 1286 removed outlier: 4.500A pdb=" N LEU 11283 " --> pdb=" O PHE 11296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '1' and resid 1305 through 1308 Processing sheet with id=AC1, first strand: chain '1' and resid 1356 through 1357 965 hydrogen bonds defined for protein. 2726 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: 7.90 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 7746 1.42 - 1.63: 10884 1.63 - 1.85: 138 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 18780 Sorted by residual: bond pdb=" N PRO B 334 " pdb=" CD PRO B 334 " ideal model delta sigma weight residual 1.473 1.400 0.073 1.40e-02 5.10e+03 2.75e+01 bond pdb=" N PRO B 334 " pdb=" CA PRO B 334 " ideal model delta sigma weight residual 1.464 1.419 0.044 9.30e-03 1.16e+04 2.24e+01 bond pdb=" CG PRO A 374 " pdb=" CD PRO A 374 " ideal model delta sigma weight residual 1.503 1.345 0.158 3.40e-02 8.65e+02 2.17e+01 bond pdb=" N PRO 1 574 " pdb=" CA PRO 1 574 " ideal model delta sigma weight residual 1.464 1.422 0.041 9.30e-03 1.16e+04 1.95e+01 bond pdb=" CE1 HIS 1 803 " pdb=" NE2 HIS 1 803 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.64e+01 ... (remaining 18775 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 25138 2.53 - 5.06: 261 5.06 - 7.59: 25 7.59 - 10.12: 11 10.12 - 12.65: 3 Bond angle restraints: 25438 Sorted by residual: angle pdb=" N PRO A 374 " pdb=" CD PRO A 374 " pdb=" CG PRO A 374 " ideal model delta sigma weight residual 103.20 93.68 9.52 1.50e+00 4.44e-01 4.03e+01 angle pdb=" CA PRO A 374 " pdb=" CB PRO A 374 " pdb=" CG PRO A 374 " ideal model delta sigma weight residual 104.50 93.08 11.42 1.90e+00 2.77e-01 3.61e+01 angle pdb=" CA PRO 1 534 " pdb=" N PRO 1 534 " pdb=" CD PRO 1 534 " ideal model delta sigma weight residual 112.00 104.33 7.67 1.40e+00 5.10e-01 3.00e+01 angle pdb=" CA PRO A 374 " pdb=" N PRO A 374 " pdb=" CD PRO A 374 " ideal model delta sigma weight residual 112.00 104.79 7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" C ASN B 332 " pdb=" N TYR B 333 " pdb=" CA TYR B 333 " ideal model delta sigma weight residual 121.92 113.89 8.03 1.60e+00 3.91e-01 2.52e+01 ... (remaining 25433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10354 17.95 - 35.90: 871 35.90 - 53.85: 192 53.85 - 71.80: 40 71.80 - 89.75: 19 Dihedral angle restraints: 11476 sinusoidal: 4687 harmonic: 6789 Sorted by residual: dihedral pdb=" CA GLU 1 409 " pdb=" C GLU 1 409 " pdb=" N ILE 1 410 " pdb=" CA ILE 1 410 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA VAL 11362 " pdb=" C VAL 11362 " pdb=" N PHE 11363 " pdb=" CA PHE 11363 " ideal model delta harmonic sigma weight residual 180.00 160.27 19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA LEU 1 640 " pdb=" C LEU 1 640 " pdb=" N GLN 1 641 " pdb=" CA GLN 1 641 " ideal model delta harmonic sigma weight residual -180.00 -161.20 -18.80 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 11473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2187 0.048 - 0.097: 485 0.097 - 0.145: 130 0.145 - 0.194: 9 0.194 - 0.242: 4 Chirality restraints: 2815 Sorted by residual: chirality pdb=" CB ILE 1 507 " pdb=" CA ILE 1 507 " pdb=" CG1 ILE 1 507 " pdb=" CG2 ILE 1 507 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE 1 367 " pdb=" CA ILE 1 367 " pdb=" CG1 ILE 1 367 " pdb=" CG2 ILE 1 367 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ILE 11207 " pdb=" N ILE 11207 " pdb=" C ILE 11207 " pdb=" CB ILE 11207 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2812 not shown) Planarity restraints: 3315 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 470 " 0.071 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO C 471 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 471 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 471 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 1 450 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.75e+00 pdb=" N PRO 1 451 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO 1 451 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO 1 451 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 65 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.08e+00 pdb=" N PRO B 66 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " 0.039 5.00e-02 4.00e+02 ... (remaining 3312 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3278 2.77 - 3.30: 17867 3.30 - 3.83: 30521 3.83 - 4.37: 36213 4.37 - 4.90: 62047 Nonbonded interactions: 149926 Sorted by model distance: nonbonded pdb=" OD1 ASP B 416 " pdb=" OG1 THR B 419 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR A 122 " pdb=" O GLN A 232 " model vdw 2.236 3.040 nonbonded pdb=" O ALA C 444 " pdb=" NE2 GLN 11329 " model vdw 2.256 3.120 nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR A 190 " model vdw 2.265 3.040 nonbonded pdb=" O THR 1 708 " pdb=" OG1 THR 1 708 " model vdw 2.265 3.040 ... (remaining 149921 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: 0.830 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: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 52.530 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.120 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 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 : 0.005 0.158 18780 Z= 0.292 Angle : 0.672 12.648 25438 Z= 0.392 Chirality : 0.044 0.242 2815 Planarity : 0.005 0.103 3315 Dihedral : 14.503 89.747 7068 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.46 % Favored : 98.45 % Rotamer: Outliers : 0.39 % Allowed : 11.56 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.23 (0.17), residues: 2285 helix: 1.53 (0.16), residues: 1067 sheet: 0.11 (0.29), residues: 261 loop : 0.35 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 1 356 HIS 0.007 0.001 HIS B 401 PHE 0.034 0.002 PHE C 310 TYR 0.021 0.002 TYR B 333 ARG 0.004 0.000 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 333 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 ILE cc_start: 0.7821 (mt) cc_final: 0.7461 (mt) REVERT: C 262 ASP cc_start: 0.6287 (t0) cc_final: 0.5936 (t0) REVERT: C 332 LEU cc_start: 0.6445 (mt) cc_final: 0.5382 (tp) REVERT: C 356 ASN cc_start: 0.7335 (p0) cc_final: 0.6958 (p0) REVERT: C 514 ASN cc_start: 0.7061 (p0) cc_final: 0.6760 (p0) REVERT: 1 491 ILE cc_start: 0.7658 (mm) cc_final: 0.7328 (mt) REVERT: 1 703 MET cc_start: 0.7965 (tpp) cc_final: 0.7567 (tpp) REVERT: 1 713 SER cc_start: 0.7956 (p) cc_final: 0.7422 (t) REVERT: 1 783 ASN cc_start: 0.8032 (p0) cc_final: 0.7787 (p0) REVERT: 1 1302 SER cc_start: 0.8176 (t) cc_final: 0.7782 (m) outliers start: 8 outliers final: 1 residues processed: 338 average time/residue: 0.3291 time to fit residues: 170.2848 Evaluate side-chains 231 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 1322 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 206 optimal weight: 0.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS B 432 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN A 253 GLN A 373 GLN C 385 GLN C 693 ASN 1 473 HIS 1 683 ASN 1 736 GLN 1 776 GLN 1 779 ASN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 931 HIS 1 972 ASN 1 989 ASN 11337 HIS 11388 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 18780 Z= 0.318 Angle : 0.659 9.350 25438 Z= 0.339 Chirality : 0.046 0.200 2815 Planarity : 0.006 0.085 3315 Dihedral : 4.618 51.181 2502 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.31 % Allowed : 12.45 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.01 (0.17), residues: 2285 helix: 1.41 (0.15), residues: 1067 sheet: -0.26 (0.29), residues: 284 loop : 0.24 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 1 785 HIS 0.009 0.002 HIS 11337 PHE 0.030 0.002 PHE C 268 TYR 0.025 0.002 TYR B 333 ARG 0.008 0.001 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 410 ILE cc_start: 0.7894 (mt) cc_final: 0.7508 (mt) REVERT: C 262 ASP cc_start: 0.6511 (t0) cc_final: 0.6193 (t0) REVERT: C 332 LEU cc_start: 0.6591 (mt) cc_final: 0.5531 (tp) REVERT: 1 491 ILE cc_start: 0.7973 (mm) cc_final: 0.7659 (mt) REVERT: 1 906 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7236 (tt) outliers start: 47 outliers final: 34 residues processed: 278 average time/residue: 0.3069 time to fit residues: 137.0106 Evaluate side-chains 246 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 545 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 559 ILE Chi-restraints excluded: chain 1 residue 627 LEU Chi-restraints excluded: chain 1 residue 643 VAL Chi-restraints excluded: chain 1 residue 667 LEU Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 906 LEU Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1397 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 206 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 528 HIS A 253 GLN A 373 GLN 1 428 GLN 1 783 ASN 1 874 GLN 1 989 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18780 Z= 0.264 Angle : 0.598 10.498 25438 Z= 0.306 Chirality : 0.044 0.179 2815 Planarity : 0.005 0.068 3315 Dihedral : 4.351 19.013 2501 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.61 % Allowed : 12.99 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.92 (0.17), residues: 2285 helix: 1.43 (0.16), residues: 1075 sheet: -0.42 (0.29), residues: 265 loop : 0.09 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 134 HIS 0.008 0.001 HIS 11337 PHE 0.022 0.002 PHE C 268 TYR 0.024 0.002 TYR B 333 ARG 0.006 0.001 ARG C 559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 225 time to evaluate : 2.624 Fit side-chains revert: symmetry clash REVERT: B 122 GLU cc_start: 0.7367 (tp30) cc_final: 0.7058 (mt-10) REVERT: B 298 TYR cc_start: 0.5654 (t80) cc_final: 0.4636 (t80) REVERT: B 410 ILE cc_start: 0.7942 (mt) cc_final: 0.7555 (mt) REVERT: C 262 ASP cc_start: 0.6411 (t0) cc_final: 0.6103 (t0) REVERT: C 504 ILE cc_start: 0.8574 (mt) cc_final: 0.8180 (pt) REVERT: C 640 PHE cc_start: 0.8375 (p90) cc_final: 0.7956 (p90) REVERT: 1 491 ILE cc_start: 0.8009 (mm) cc_final: 0.7703 (mt) REVERT: 1 888 GLU cc_start: 0.6844 (mp0) cc_final: 0.6381 (mp0) REVERT: 1 1033 ASP cc_start: 0.6994 (p0) cc_final: 0.6246 (t70) outliers start: 53 outliers final: 37 residues processed: 262 average time/residue: 0.3255 time to fit residues: 135.8169 Evaluate side-chains 240 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 505 ASN Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 545 THR Chi-restraints excluded: chain 1 residue 601 LEU Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 988 MET Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain 1 residue 1440 THR Chi-restraints excluded: chain 1 residue 1443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 107 optimal weight: 0.0570 chunk 22 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 219 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 34 HIS A 253 GLN A 373 GLN 1 576 ASN 1 779 ASN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18780 Z= 0.187 Angle : 0.536 9.485 25438 Z= 0.273 Chirality : 0.042 0.168 2815 Planarity : 0.004 0.064 3315 Dihedral : 4.130 18.662 2501 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.46 % Allowed : 13.24 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.15 (0.17), residues: 2285 helix: 1.71 (0.16), residues: 1065 sheet: -0.45 (0.29), residues: 277 loop : 0.18 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.007 0.001 HIS 11337 PHE 0.018 0.002 PHE 1 485 TYR 0.023 0.001 TYR B 333 ARG 0.005 0.000 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 221 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6968 (m-10) REVERT: B 122 GLU cc_start: 0.7245 (tp30) cc_final: 0.7009 (mt-10) REVERT: B 127 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7255 (t0) REVERT: B 128 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.6484 (m-80) REVERT: B 298 TYR cc_start: 0.5619 (t80) cc_final: 0.4795 (t80) REVERT: B 410 ILE cc_start: 0.8007 (mt) cc_final: 0.7610 (mt) REVERT: C 262 ASP cc_start: 0.6367 (t0) cc_final: 0.6025 (t0) REVERT: C 640 PHE cc_start: 0.8348 (p90) cc_final: 0.8026 (p90) REVERT: 1 491 ILE cc_start: 0.7900 (mm) cc_final: 0.7583 (mt) REVERT: 1 888 GLU cc_start: 0.6880 (mp0) cc_final: 0.6497 (mp0) REVERT: 1 1033 ASP cc_start: 0.6898 (p0) cc_final: 0.6341 (t70) outliers start: 50 outliers final: 37 residues processed: 259 average time/residue: 0.3012 time to fit residues: 124.5274 Evaluate side-chains 237 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 601 LEU Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1322 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 0.6980 chunk 124 optimal weight: 0.0070 chunk 3 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 0.0000 chunk 187 optimal weight: 0.6980 chunk 151 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 overall best weight: 0.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN 1 783 ASN 1 989 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18780 Z= 0.152 Angle : 0.515 11.261 25438 Z= 0.261 Chirality : 0.041 0.166 2815 Planarity : 0.004 0.061 3315 Dihedral : 3.960 18.267 2501 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.31 % Allowed : 14.07 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.39 (0.18), residues: 2285 helix: 1.88 (0.16), residues: 1067 sheet: -0.29 (0.30), residues: 271 loop : 0.31 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 170 HIS 0.005 0.001 HIS 11337 PHE 0.023 0.001 PHE 1 485 TYR 0.023 0.001 TYR B 333 ARG 0.004 0.000 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: B 127 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7192 (t0) REVERT: B 128 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6478 (m-80) REVERT: B 410 ILE cc_start: 0.8009 (mt) cc_final: 0.7600 (mt) REVERT: C 262 ASP cc_start: 0.6199 (t0) cc_final: 0.5889 (t0) REVERT: C 640 PHE cc_start: 0.8364 (p90) cc_final: 0.8160 (p90) REVERT: 1 491 ILE cc_start: 0.7886 (mm) cc_final: 0.7666 (mt) REVERT: 1 865 PHE cc_start: 0.6177 (OUTLIER) cc_final: 0.5956 (m-80) REVERT: 1 888 GLU cc_start: 0.6961 (mp0) cc_final: 0.6613 (mp0) REVERT: 1 1033 ASP cc_start: 0.6818 (p0) cc_final: 0.6289 (t70) outliers start: 47 outliers final: 33 residues processed: 251 average time/residue: 0.2961 time to fit residues: 121.8284 Evaluate side-chains 227 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 601 LEU Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1081 LEU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1425 SER Chi-restraints excluded: chain 1 residue 1443 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 219 optimal weight: 0.5980 chunk 182 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN 1 989 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18780 Z= 0.180 Angle : 0.521 10.392 25438 Z= 0.264 Chirality : 0.041 0.162 2815 Planarity : 0.004 0.063 3315 Dihedral : 3.937 17.879 2501 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.71 % Allowed : 13.73 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 2285 helix: 1.85 (0.16), residues: 1067 sheet: -0.34 (0.30), residues: 271 loop : 0.32 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 134 HIS 0.006 0.001 HIS 11337 PHE 0.020 0.001 PHE 1 485 TYR 0.022 0.001 TYR B 333 ARG 0.004 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 199 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.7056 (m-10) REVERT: B 127 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7306 (t0) REVERT: B 128 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: B 410 ILE cc_start: 0.8044 (mt) cc_final: 0.7621 (mt) REVERT: A 361 MET cc_start: 0.6378 (mmm) cc_final: 0.6082 (mmm) REVERT: C 262 ASP cc_start: 0.6372 (t0) cc_final: 0.6057 (t0) REVERT: C 640 PHE cc_start: 0.8376 (p90) cc_final: 0.8165 (p90) REVERT: 1 491 ILE cc_start: 0.8042 (mm) cc_final: 0.7644 (mt) REVERT: 1 865 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5879 (m-80) REVERT: 1 888 GLU cc_start: 0.7048 (mp0) cc_final: 0.6705 (mp0) REVERT: 1 1033 ASP cc_start: 0.6797 (p0) cc_final: 0.6315 (t70) outliers start: 55 outliers final: 43 residues processed: 243 average time/residue: 0.2855 time to fit residues: 111.7058 Evaluate side-chains 238 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 601 LEU Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 875 GLU Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1081 LEU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1140 TYR Chi-restraints excluded: chain 1 residue 1443 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18780 Z= 0.226 Angle : 0.544 9.548 25438 Z= 0.278 Chirality : 0.043 0.228 2815 Planarity : 0.004 0.065 3315 Dihedral : 4.034 17.823 2501 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.00 % Allowed : 13.93 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.23 (0.18), residues: 2285 helix: 1.77 (0.16), residues: 1063 sheet: -0.50 (0.29), residues: 271 loop : 0.25 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 134 HIS 0.007 0.001 HIS 11337 PHE 0.029 0.002 PHE 1 485 TYR 0.022 0.002 TYR B 333 ARG 0.005 0.000 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 196 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.7143 (m-10) REVERT: B 127 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.7360 (t0) REVERT: B 128 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: B 199 VAL cc_start: 0.3946 (OUTLIER) cc_final: 0.3720 (m) REVERT: B 410 ILE cc_start: 0.8056 (mt) cc_final: 0.7611 (mt) REVERT: C 262 ASP cc_start: 0.6435 (t0) cc_final: 0.6149 (t0) REVERT: 1 491 ILE cc_start: 0.8030 (mm) cc_final: 0.7778 (mt) REVERT: 1 783 ASN cc_start: 0.7910 (p0) cc_final: 0.7511 (p0) REVERT: 1 865 PHE cc_start: 0.6192 (OUTLIER) cc_final: 0.5912 (m-80) REVERT: 1 1027 TYR cc_start: 0.5515 (m-80) cc_final: 0.5251 (m-80) REVERT: 1 1033 ASP cc_start: 0.6832 (p0) cc_final: 0.6428 (t70) outliers start: 61 outliers final: 49 residues processed: 245 average time/residue: 0.2823 time to fit residues: 112.2892 Evaluate side-chains 240 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 186 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 601 LEU Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 772 THR Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 875 GLU Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 1034 ILE Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1067 GLU Chi-restraints excluded: chain 1 residue 1081 LEU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1140 TYR Chi-restraints excluded: chain 1 residue 1377 ARG Chi-restraints excluded: chain 1 residue 1443 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 149 optimal weight: 0.0060 chunk 108 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 171 optimal weight: 0.6980 chunk 199 optimal weight: 8.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18780 Z= 0.149 Angle : 0.510 12.513 25438 Z= 0.258 Chirality : 0.041 0.193 2815 Planarity : 0.004 0.060 3315 Dihedral : 3.875 17.609 2501 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.51 % Allowed : 15.06 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.44 (0.18), residues: 2285 helix: 1.96 (0.16), residues: 1058 sheet: -0.39 (0.30), residues: 270 loop : 0.35 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 134 HIS 0.005 0.001 HIS 11337 PHE 0.027 0.001 PHE 1 485 TYR 0.021 0.001 TYR B 333 ARG 0.005 0.000 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7055 (m-10) REVERT: B 128 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6520 (m-80) REVERT: B 410 ILE cc_start: 0.8053 (mt) cc_final: 0.7650 (mt) REVERT: A 361 MET cc_start: 0.6308 (mmm) cc_final: 0.6055 (mmm) REVERT: C 262 ASP cc_start: 0.6336 (t0) cc_final: 0.6055 (t0) REVERT: 1 491 ILE cc_start: 0.7996 (mm) cc_final: 0.7712 (mt) REVERT: 1 783 ASN cc_start: 0.7813 (p0) cc_final: 0.7544 (p0) REVERT: 1 865 PHE cc_start: 0.6037 (OUTLIER) cc_final: 0.5715 (m-10) REVERT: 1 1027 TYR cc_start: 0.5376 (m-80) cc_final: 0.5134 (m-80) REVERT: 1 1033 ASP cc_start: 0.6751 (p0) cc_final: 0.6428 (t70) outliers start: 51 outliers final: 39 residues processed: 240 average time/residue: 0.2763 time to fit residues: 107.4961 Evaluate side-chains 229 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 187 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 601 LEU Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 1034 ILE Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1081 LEU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1140 TYR Chi-restraints excluded: chain 1 residue 1377 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 160 optimal weight: 0.5980 chunk 62 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 192 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN C 639 HIS ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN 11044 HIS B Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18780 Z= 0.299 Angle : 0.616 11.512 25438 Z= 0.315 Chirality : 0.045 0.189 2815 Planarity : 0.005 0.067 3315 Dihedral : 4.222 18.204 2501 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.51 % Allowed : 15.35 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 0.98 (0.18), residues: 2285 helix: 1.58 (0.16), residues: 1069 sheet: -0.78 (0.28), residues: 299 loop : 0.19 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 134 HIS 0.009 0.001 HIS 11337 PHE 0.028 0.002 PHE 1 485 TYR 0.022 0.002 TYR B 333 ARG 0.006 0.001 ARG C 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 2.374 Fit side-chains revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7222 (m-10) REVERT: B 128 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: B 298 TYR cc_start: 0.5952 (t80) cc_final: 0.5236 (t80) REVERT: C 262 ASP cc_start: 0.6410 (t0) cc_final: 0.6135 (t0) REVERT: C 504 ILE cc_start: 0.8483 (mt) cc_final: 0.8153 (pt) REVERT: 1 491 ILE cc_start: 0.8096 (mm) cc_final: 0.7865 (mt) REVERT: 1 783 ASN cc_start: 0.7925 (p0) cc_final: 0.7543 (p0) REVERT: 1 865 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: 1 866 ASN cc_start: 0.6641 (m-40) cc_final: 0.6416 (m110) REVERT: 1 1027 TYR cc_start: 0.5568 (m-80) cc_final: 0.5323 (m-80) REVERT: 1 1033 ASP cc_start: 0.6811 (p0) cc_final: 0.6528 (t70) outliers start: 51 outliers final: 42 residues processed: 225 average time/residue: 0.3066 time to fit residues: 110.4152 Evaluate side-chains 223 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 601 LEU Chi-restraints excluded: chain 1 residue 627 LEU Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 772 THR Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 875 GLU Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1081 LEU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1377 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18780 Z= 0.189 Angle : 0.547 11.796 25438 Z= 0.278 Chirality : 0.042 0.194 2815 Planarity : 0.004 0.063 3315 Dihedral : 4.045 18.001 2501 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.41 % Allowed : 15.45 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.15 (0.18), residues: 2285 helix: 1.78 (0.16), residues: 1057 sheet: -0.72 (0.29), residues: 300 loop : 0.22 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 134 HIS 0.006 0.001 HIS 11337 PHE 0.029 0.001 PHE 1 485 TYR 0.025 0.001 TYR B 333 ARG 0.010 0.000 ARG A 268 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4570 Ramachandran restraints generated. 2285 Oldfield, 0 Emsley, 2285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7163 (m-10) REVERT: B 128 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6474 (m-80) REVERT: B 134 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8206 (mm) REVERT: C 262 ASP cc_start: 0.6456 (t0) cc_final: 0.6199 (t0) REVERT: C 504 ILE cc_start: 0.8451 (mt) cc_final: 0.8113 (pt) REVERT: 1 491 ILE cc_start: 0.8026 (mm) cc_final: 0.7766 (mt) REVERT: 1 783 ASN cc_start: 0.7812 (p0) cc_final: 0.7382 (p0) REVERT: 1 865 PHE cc_start: 0.6030 (OUTLIER) cc_final: 0.5739 (m-10) REVERT: 1 1027 TYR cc_start: 0.5421 (m-80) cc_final: 0.5186 (m-80) REVERT: 1 1033 ASP cc_start: 0.6765 (p0) cc_final: 0.6512 (t70) REVERT: 1 1420 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6859 (tt0) outliers start: 49 outliers final: 41 residues processed: 231 average time/residue: 0.2843 time to fit residues: 106.1175 Evaluate side-chains 231 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 692 HIS Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 701 ASP Chi-restraints excluded: chain 1 residue 486 VAL Chi-restraints excluded: chain 1 residue 517 VAL Chi-restraints excluded: chain 1 residue 539 LEU Chi-restraints excluded: chain 1 residue 557 VAL Chi-restraints excluded: chain 1 residue 601 LEU Chi-restraints excluded: chain 1 residue 663 ILE Chi-restraints excluded: chain 1 residue 699 ILE Chi-restraints excluded: chain 1 residue 772 THR Chi-restraints excluded: chain 1 residue 858 ASN Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 875 GLU Chi-restraints excluded: chain 1 residue 891 ASP Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1081 LEU Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1377 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 158 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 GLN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.150191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138100 restraints weight = 103720.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140003 restraints weight = 105210.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139994 restraints weight = 57783.397| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3740 r_free = 0.3740 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18780 Z= 0.218 Angle : 0.562 11.721 25438 Z= 0.286 Chirality : 0.043 0.188 2815 Planarity : 0.004 0.063 3315 Dihedral : 4.063 17.877 2501 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.31 % Allowed : 15.75 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % 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: 1.10 (0.18), residues: 2285 helix: 1.75 (0.16), residues: 1057 sheet: -0.76 (0.29), residues: 300 loop : 0.18 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 134 HIS 0.007 0.001 HIS 11337 PHE 0.028 0.002 PHE 1 485 TYR 0.026 0.002 TYR B 333 ARG 0.013 0.000 ARG A 268 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.93 seconds wall clock time: 65 minutes 56.75 seconds (3956.75 seconds total)