Starting phenix.real_space_refine on Mon Jun 16 03:14:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8foc_29345/06_2025/8foc_29345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8foc_29345/06_2025/8foc_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/cci-nas-00/data/ceres_data/8foc_29345/06_2025/8foc_29345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8foc_29345/06_2025/8foc_29345.map" model { file = "/net/cci-nas-00/data/ceres_data/8foc_29345/06_2025/8foc_29345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8foc_29345/06_2025/8foc_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-5710/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: 15.70, per 1000 atoms: 0.85 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: 4.41 Conformation dependent library (CDL) restraints added in 3.9 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: 2.19 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: 7.09 Time building geometry restraints manager: 5.26 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: 1.060 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: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 53.510 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.070 ------------------------------------------------------------------------------- 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 18781 Z= 0.247 Angle : 0.708 26.809 25441 Z= 0.393 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 Details of bonding type rmsd hydrogen bonds : bond 0.14750 ( 954) hydrogen bonds : angle 6.61139 ( 2726) metal coordination : bond 0.12155 ( 1) metal coordination : angle 20.48001 ( 3) covalent geometry : bond 0.00463 (18780) covalent geometry : angle 0.67213 (25438) *********************** 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 : 1.831 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: 0.3124 time to fit residues: 160.5081 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 : 1.937 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.151678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138776 restraints weight = 105055.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.140583 restraints weight = 114797.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140891 restraints weight = 60411.303| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.137 | | 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) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 18781 Z= 0.215 Angle : 0.679 19.046 25441 Z= 0.340 Chirality : 0.046 0.200 2815 Planarity : 0.006 0.085 3315 Dihedral : 4.618 51.180 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 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 954) hydrogen bonds : angle 5.41790 ( 2726) metal coordination : bond 0.00748 ( 1) metal coordination : angle 15.31945 ( 3) covalent geometry : bond 0.00491 (18780) covalent geometry : angle 0.65878 (25438) *********************** 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 292 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 1.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 410 ILE cc_start: 0.7875 (mt) cc_final: 0.7490 (mt) REVERT: C 262 ASP cc_start: 0.6464 (t0) cc_final: 0.6107 (t0) REVERT: C 332 LEU cc_start: 0.6400 (mt) cc_final: 0.5425 (tp) REVERT: 1 491 ILE cc_start: 0.7965 (mm) cc_final: 0.7661 (mt) REVERT: 1 906 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7350 (tt) outliers start: 47 outliers final: 34 residues processed: 279 average time/residue: 0.3209 time to fit residues: 144.6491 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 : 2.968 ------------------------------------------------------------------------------- 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 139 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.152241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140218 restraints weight = 101630.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.141843 restraints weight = 113377.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142022 restraints weight = 55996.805| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3766 r_free = 0.3766 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18781 Z= 0.144 Angle : 0.577 16.849 25441 Z= 0.287 Chirality : 0.043 0.171 2815 Planarity : 0.005 0.069 3315 Dihedral : 4.230 19.080 2501 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.07 % Allowed : 13.29 % Favored : 84.65 % 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: 1.18 (0.17), residues: 2285 helix: 1.65 (0.16), residues: 1065 sheet: -0.15 (0.29), residues: 269 loop : 0.18 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 134 HIS 0.009 0.001 HIS 11337 PHE 0.019 0.002 PHE 1 485 TYR 0.023 0.002 TYR B 333 ARG 0.006 0.000 ARG 11442 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 954) hydrogen bonds : angle 5.14747 ( 2726) metal coordination : bond 0.00915 ( 1) metal coordination : angle 13.45569 ( 3) covalent geometry : bond 0.00329 (18780) covalent geometry : angle 0.55831 (25438) *********************** 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 269 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 410 ILE cc_start: 0.7940 (mt) cc_final: 0.7541 (mt) REVERT: A 174 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6531 (mtmm) REVERT: C 262 ASP cc_start: 0.6413 (t0) cc_final: 0.6094 (t0) REVERT: 1 491 ILE cc_start: 0.7964 (mm) cc_final: 0.7650 (mt) REVERT: 1 888 GLU cc_start: 0.6647 (mp0) cc_final: 0.6187 (mp0) outliers start: 42 outliers final: 29 residues processed: 256 average time/residue: 0.2778 time to fit residues: 112.8273 Evaluate side-chains 233 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 294 LEU Chi-restraints excluded: chain B residue 420 ILE 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 174 LYS 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 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 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 559 ILE 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 1443 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 89 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 155 optimal weight: 0.4980 chunk 48 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 253 GLN A 373 GLN 1 576 ASN 1 779 ASN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.153301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142180 restraints weight = 99917.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143694 restraints weight = 111920.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.143863 restraints weight = 49492.052| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18781 Z= 0.112 Angle : 0.530 13.219 25441 Z= 0.265 Chirality : 0.042 0.187 2815 Planarity : 0.004 0.062 3315 Dihedral : 3.998 18.370 2501 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.26 % Allowed : 13.53 % Favored : 84.20 % 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: 1.36 (0.18), residues: 2285 helix: 1.84 (0.16), residues: 1069 sheet: -0.16 (0.30), residues: 269 loop : 0.25 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 170 HIS 0.006 0.001 HIS 11337 PHE 0.023 0.001 PHE 1 485 TYR 0.024 0.001 TYR B 333 ARG 0.005 0.000 ARG C 513 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 954) hydrogen bonds : angle 4.86152 ( 2726) metal coordination : bond 0.00774 ( 1) metal coordination : angle 10.28428 ( 3) covalent geometry : bond 0.00251 (18780) covalent geometry : angle 0.51812 (25438) *********************** 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 268 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: B 410 ILE cc_start: 0.7944 (mt) cc_final: 0.7567 (mt) REVERT: A 355 ILE cc_start: 0.6579 (tp) cc_final: 0.6238 (pt) REVERT: C 262 ASP cc_start: 0.6165 (t0) cc_final: 0.5834 (t0) REVERT: C 640 PHE cc_start: 0.8307 (p90) cc_final: 0.8048 (p90) REVERT: C 649 VAL cc_start: 0.8566 (t) cc_final: 0.8365 (p) REVERT: 1 491 ILE cc_start: 0.7886 (mm) cc_final: 0.7598 (mt) REVERT: 1 865 PHE cc_start: 0.6117 (OUTLIER) cc_final: 0.5770 (m-80) REVERT: 1 888 GLU cc_start: 0.6675 (mp0) cc_final: 0.6323 (mp0) REVERT: 1 1438 MET cc_start: 0.8240 (mmm) cc_final: 0.8027 (mtp) outliers start: 46 outliers final: 31 residues processed: 255 average time/residue: 0.2741 time to fit residues: 111.9920 Evaluate side-chains 224 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 858 ASN Chi-restraints excluded: chain 1 residue 865 PHE Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1140 TYR Chi-restraints excluded: chain 1 residue 1322 THR Chi-restraints excluded: chain 1 residue 1443 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 176 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.0670 chunk 102 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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 ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 874 GLN 1 989 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.149893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.135990 restraints weight = 115263.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138492 restraints weight = 109149.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138517 restraints weight = 62135.357| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18781 Z= 0.180 Angle : 0.604 18.303 25441 Z= 0.299 Chirality : 0.044 0.169 2815 Planarity : 0.005 0.068 3315 Dihedral : 4.196 22.914 2501 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.05 % Allowed : 13.39 % 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: 1.09 (0.17), residues: 2285 helix: 1.63 (0.16), residues: 1067 sheet: -0.50 (0.29), residues: 275 loop : 0.17 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 671 HIS 0.009 0.001 HIS 11337 PHE 0.024 0.002 PHE C 268 TYR 0.023 0.002 TYR B 333 ARG 0.005 0.000 ARG C 322 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 954) hydrogen bonds : angle 5.02895 ( 2726) metal coordination : bond 0.01273 ( 1) metal coordination : angle 14.04069 ( 3) covalent geometry : bond 0.00412 (18780) covalent geometry : angle 0.58496 (25438) *********************** 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 275 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.7107 (m-10) REVERT: B 127 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7456 (t0) REVERT: B 128 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.6556 (m-80) REVERT: B 298 TYR cc_start: 0.5901 (t80) cc_final: 0.4984 (t80) REVERT: B 410 ILE cc_start: 0.7981 (mt) cc_final: 0.7572 (mt) REVERT: C 262 ASP cc_start: 0.6384 (t0) cc_final: 0.6018 (t0) REVERT: C 640 PHE cc_start: 0.8435 (p90) cc_final: 0.8186 (p90) REVERT: 1 491 ILE cc_start: 0.8035 (mm) cc_final: 0.7770 (mt) REVERT: 1 671 TRP cc_start: 0.7121 (m-90) cc_final: 0.6807 (m-90) REVERT: 1 865 PHE cc_start: 0.6217 (OUTLIER) cc_final: 0.5937 (m-80) REVERT: 1 888 GLU cc_start: 0.6999 (mp0) cc_final: 0.6634 (mp0) REVERT: 1 1438 MET cc_start: 0.8287 (mmm) cc_final: 0.7992 (mtp) outliers start: 62 outliers final: 45 residues processed: 259 average time/residue: 0.2895 time to fit residues: 118.7632 Evaluate side-chains 242 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 2.111 ------------------------------------------------------------------------------- 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 85 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 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 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 545 THR 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 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 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 190 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 171 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 1 576 ASN ** 1 783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 989 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138044 restraints weight = 102679.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139969 restraints weight = 109863.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.140203 restraints weight = 57891.791| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3735 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3735 r_free = 0.3735 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3735 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18781 Z= 0.142 Angle : 0.558 16.590 25441 Z= 0.276 Chirality : 0.042 0.162 2815 Planarity : 0.004 0.064 3315 Dihedral : 4.110 19.249 2501 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.66 % Allowed : 13.93 % Favored : 83.42 % 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: 1.16 (0.18), residues: 2285 helix: 1.74 (0.16), residues: 1062 sheet: -0.59 (0.29), residues: 279 loop : 0.21 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 134 HIS 0.006 0.001 HIS 11337 PHE 0.022 0.002 PHE 1 485 TYR 0.020 0.001 TYR B 333 ARG 0.006 0.000 ARG 11442 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 954) hydrogen bonds : angle 4.92146 ( 2726) metal coordination : bond 0.01034 ( 1) metal coordination : angle 12.75389 ( 3) covalent geometry : bond 0.00326 (18780) covalent geometry : angle 0.54103 (25438) *********************** 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 258 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.7071 (m-10) REVERT: B 127 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7241 (t0) REVERT: B 128 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.6532 (m-80) REVERT: B 410 ILE cc_start: 0.7980 (mt) cc_final: 0.7551 (mt) REVERT: C 250 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.5529 (ptp) REVERT: C 262 ASP cc_start: 0.6363 (t0) cc_final: 0.6005 (t0) REVERT: C 504 ILE cc_start: 0.8567 (mt) cc_final: 0.8179 (pt) REVERT: 1 865 PHE cc_start: 0.6144 (OUTLIER) cc_final: 0.5846 (m-80) REVERT: 1 888 GLU cc_start: 0.6890 (mp0) cc_final: 0.6604 (mp0) REVERT: 1 1438 MET cc_start: 0.8178 (mmm) cc_final: 0.7903 (mtp) outliers start: 54 outliers final: 41 residues processed: 248 average time/residue: 0.2806 time to fit residues: 112.1864 Evaluate side-chains 230 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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 164 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 294 LEU 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 160 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain C residue 250 MET 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 545 THR Chi-restraints excluded: chain 1 residue 601 LEU Chi-restraints excluded: chain 1 residue 663 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 1136 ASP 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 151 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 159 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 104 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.147115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134049 restraints weight = 105595.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136099 restraints weight = 111341.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136080 restraints weight = 54600.350| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18781 Z= 0.233 Angle : 0.681 22.680 25441 Z= 0.340 Chirality : 0.046 0.170 2815 Planarity : 0.005 0.073 3315 Dihedral : 4.585 18.591 2501 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.10 % Allowed : 14.32 % Favored : 82.58 % 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: 0.59 (0.17), residues: 2285 helix: 1.27 (0.16), residues: 1064 sheet: -1.01 (0.28), residues: 288 loop : -0.02 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 1 671 HIS 0.010 0.002 HIS 11337 PHE 0.027 0.002 PHE C 268 TYR 0.023 0.002 TYR B 503 ARG 0.008 0.001 ARG C 322 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 954) hydrogen bonds : angle 5.27438 ( 2726) metal coordination : bond 0.01554 ( 1) metal coordination : angle 16.88572 ( 3) covalent geometry : bond 0.00536 (18780) covalent geometry : angle 0.65616 (25438) *********************** 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: 63 poor density : 194 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.7103 (m-10) REVERT: B 127 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7492 (t0) REVERT: B 128 TYR cc_start: 0.7608 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: B 298 TYR cc_start: 0.6207 (t80) cc_final: 0.5381 (t80) REVERT: B 420 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7763 (tt) REVERT: C 262 ASP cc_start: 0.6332 (t0) cc_final: 0.6041 (t0) REVERT: C 304 SER cc_start: 0.8951 (t) cc_final: 0.8709 (m) REVERT: C 504 ILE cc_start: 0.8584 (mt) cc_final: 0.8324 (pt) REVERT: 1 671 TRP cc_start: 0.7251 (m-90) cc_final: 0.6801 (m-90) REVERT: 1 747 MET cc_start: 0.5767 (mtp) cc_final: 0.5533 (mtt) REVERT: 1 783 ASN cc_start: 0.7945 (p0) cc_final: 0.7544 (p0) REVERT: 1 865 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.5985 (m-80) REVERT: 1 866 ASN cc_start: 0.6654 (m-40) cc_final: 0.6406 (m110) REVERT: 1 1027 TYR cc_start: 0.5610 (m-80) cc_final: 0.5357 (m-80) outliers start: 63 outliers final: 49 residues processed: 245 average time/residue: 0.2746 time to fit residues: 108.2138 Evaluate side-chains 236 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 182 time to evaluate : 2.156 ------------------------------------------------------------------------------- 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 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 183 ILE 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 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 271 LYS Chi-restraints excluded: chain C residue 250 MET 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 607 ILE 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 702 LEU 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 539 LEU Chi-restraints excluded: chain 1 residue 545 THR 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 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 1113 ILE Chi-restraints excluded: chain 1 residue 1377 ARG Chi-restraints excluded: chain 1 residue 1440 THR 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 142 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 131 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 chunk 173 optimal weight: 0.4980 chunk 203 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3940 r_free = 0.3940 target = 0.151767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.138695 restraints weight = 98835.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.140927 restraints weight = 101142.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141122 restraints weight = 45843.228| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18781 Z= 0.105 Angle : 0.542 13.557 25441 Z= 0.270 Chirality : 0.041 0.177 2815 Planarity : 0.004 0.072 3315 Dihedral : 4.077 18.399 2501 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.12 % Allowed : 15.60 % Favored : 82.28 % 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: 1.73 (0.16), residues: 1064 sheet: -0.75 (0.29), residues: 291 loop : 0.18 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 134 HIS 0.006 0.001 HIS B 432 PHE 0.024 0.001 PHE 1 485 TYR 0.026 0.001 TYR B 333 ARG 0.006 0.000 ARG 11442 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 954) hydrogen bonds : angle 4.87980 ( 2726) metal coordination : bond 0.00869 ( 1) metal coordination : angle 10.29344 ( 3) covalent geometry : bond 0.00234 (18780) covalent geometry : angle 0.52999 (25438) *********************** 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 244 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.7053 (m-10) REVERT: B 113 LEU cc_start: 0.4622 (mp) cc_final: 0.4117 (mt) REVERT: B 128 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: B 134 LEU cc_start: 0.8246 (mt) cc_final: 0.7911 (mm) REVERT: B 199 VAL cc_start: 0.4186 (OUTLIER) cc_final: 0.3949 (m) REVERT: C 262 ASP cc_start: 0.6220 (t0) cc_final: 0.5901 (t0) REVERT: C 504 ILE cc_start: 0.8476 (mt) cc_final: 0.8130 (pt) REVERT: 1 525 ILE cc_start: 0.8219 (mp) cc_final: 0.7996 (mp) REVERT: 1 671 TRP cc_start: 0.6977 (m-90) cc_final: 0.6677 (m-90) REVERT: 1 865 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5728 (m-10) REVERT: 1 1001 MET cc_start: 0.7816 (mtp) cc_final: 0.7545 (mtm) REVERT: 1 1027 TYR cc_start: 0.5443 (m-80) cc_final: 0.5206 (m-80) outliers start: 43 outliers final: 32 residues processed: 233 average time/residue: 0.2763 time to fit residues: 103.8445 Evaluate side-chains 223 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 PHE 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 199 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain A residue 49 MET 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 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 492 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 692 HIS Chi-restraints excluded: chain C residue 700 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 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 1136 ASP 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 167 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** ** 1 524 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.149455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.138524 restraints weight = 94838.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.139950 restraints weight = 106064.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140045 restraints weight = 55582.977| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18781 Z= 0.155 Angle : 0.582 16.208 25441 Z= 0.289 Chirality : 0.043 0.181 2815 Planarity : 0.005 0.075 3315 Dihedral : 4.135 18.227 2501 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.17 % Allowed : 15.80 % Favored : 82.04 % 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: 1.03 (0.18), residues: 2285 helix: 1.64 (0.16), residues: 1070 sheet: -0.77 (0.28), residues: 301 loop : 0.18 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 134 HIS 0.007 0.001 HIS 11337 PHE 0.020 0.002 PHE 1 485 TYR 0.025 0.002 TYR B 333 ARG 0.005 0.000 ARG 11442 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 954) hydrogen bonds : angle 4.96638 ( 2726) metal coordination : bond 0.01463 ( 1) metal coordination : angle 12.40062 ( 3) covalent geometry : bond 0.00358 (18780) covalent geometry : angle 0.56576 (25438) *********************** 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 232 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.7130 (m-10) REVERT: B 113 LEU cc_start: 0.4429 (mp) cc_final: 0.3880 (mt) REVERT: B 128 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.6525 (m-80) REVERT: B 199 VAL cc_start: 0.4345 (OUTLIER) cc_final: 0.4110 (m) REVERT: C 262 ASP cc_start: 0.6382 (t0) cc_final: 0.6097 (t0) REVERT: C 504 ILE cc_start: 0.8487 (mt) cc_final: 0.8149 (pt) REVERT: 1 525 ILE cc_start: 0.8300 (mp) cc_final: 0.8069 (mp) REVERT: 1 671 TRP cc_start: 0.7208 (m-90) cc_final: 0.6863 (m-90) REVERT: 1 783 ASN cc_start: 0.7864 (p0) cc_final: 0.7442 (p0) REVERT: 1 865 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.5787 (m-80) REVERT: 1 1027 TYR cc_start: 0.5458 (m-80) cc_final: 0.5253 (m-80) REVERT: 1 1420 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6872 (tt0) outliers start: 44 outliers final: 37 residues processed: 223 average time/residue: 0.2718 time to fit residues: 98.3913 Evaluate side-chains 227 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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 166 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain A residue 49 MET 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 289 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 456 THR 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 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 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 1034 ILE Chi-restraints excluded: chain 1 residue 1065 VAL Chi-restraints excluded: chain 1 residue 1136 ASP Chi-restraints excluded: chain 1 residue 1377 ARG Chi-restraints excluded: chain 1 residue 1440 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 9 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 45 optimal weight: 0.1980 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.151946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.138076 restraints weight = 126388.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140359 restraints weight = 106086.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140937 restraints weight = 65169.284| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18781 Z= 0.105 Angle : 0.530 11.634 25441 Z= 0.263 Chirality : 0.041 0.187 2815 Planarity : 0.004 0.070 3315 Dihedral : 3.900 17.801 2501 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.02 % Allowed : 15.99 % Favored : 81.99 % 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: 1.33 (0.18), residues: 2285 helix: 1.90 (0.16), residues: 1058 sheet: -0.55 (0.28), residues: 297 loop : 0.30 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 134 HIS 0.006 0.001 HIS 11337 PHE 0.022 0.001 PHE 1 485 TYR 0.024 0.001 TYR B 333 ARG 0.005 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03170 ( 954) hydrogen bonds : angle 4.77756 ( 2726) metal coordination : bond 0.01053 ( 1) metal coordination : angle 9.15921 ( 3) covalent geometry : bond 0.00232 (18780) covalent geometry : angle 0.52053 (25438) ********************** 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 248 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.7073 (m-10) REVERT: B 113 LEU cc_start: 0.4547 (mp) cc_final: 0.4032 (mt) REVERT: B 128 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: B 134 LEU cc_start: 0.8299 (mt) cc_final: 0.8044 (mm) REVERT: B 199 VAL cc_start: 0.4206 (OUTLIER) cc_final: 0.3963 (m) REVERT: B 447 GLU cc_start: 0.6912 (mp0) cc_final: 0.6709 (mp0) REVERT: C 262 ASP cc_start: 0.6223 (t0) cc_final: 0.5928 (t0) REVERT: C 504 ILE cc_start: 0.8416 (mt) cc_final: 0.8076 (pt) REVERT: 1 525 ILE cc_start: 0.8227 (mp) cc_final: 0.8006 (mp) REVERT: 1 671 TRP cc_start: 0.7006 (m-90) cc_final: 0.6760 (m-90) REVERT: 1 865 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.5674 (m-10) REVERT: 1 1001 MET cc_start: 0.7768 (mtp) cc_final: 0.7519 (mtm) REVERT: 1 1027 TYR cc_start: 0.5388 (m-80) cc_final: 0.5172 (m-80) REVERT: 1 1420 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6953 (tt0) outliers start: 41 outliers final: 32 residues processed: 238 average time/residue: 0.2850 time to fit residues: 108.4053 Evaluate side-chains 234 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 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 199 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain A residue 49 MET 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 323 MET 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 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 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 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 37 optimal weight: 0.8980 chunk 217 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 109 optimal weight: 0.0470 chunk 55 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 205 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.151447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.139687 restraints weight = 107856.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141504 restraints weight = 106653.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.141510 restraints weight = 59064.663| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3764 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18781 Z= 0.112 Angle : 0.534 11.600 25441 Z= 0.267 Chirality : 0.042 0.186 2815 Planarity : 0.004 0.069 3315 Dihedral : 3.888 17.350 2501 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.87 % Allowed : 16.19 % 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: 1.36 (0.18), residues: 2285 helix: 1.93 (0.16), residues: 1058 sheet: -0.54 (0.29), residues: 297 loop : 0.32 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 439 HIS 0.007 0.001 HIS 11337 PHE 0.021 0.001 PHE 1 485 TYR 0.024 0.001 TYR B 333 ARG 0.004 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 954) hydrogen bonds : angle 4.75764 ( 2726) metal coordination : bond 0.01176 ( 1) metal coordination : angle 9.23586 ( 3) covalent geometry : bond 0.00255 (18780) covalent geometry : angle 0.52499 (25438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5781.99 seconds wall clock time: 102 minutes 49.02 seconds (6169.02 seconds total)