Starting phenix.real_space_refine on Sat Sep 28 15:53:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/09_2024/7opl_13020.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/09_2024/7opl_13020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/09_2024/7opl_13020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/09_2024/7opl_13020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/09_2024/7opl_13020.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7opl_13020/09_2024/7opl_13020.cif" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 3 6.06 5 S 105 5.16 5 C 12633 2.51 5 N 3352 2.21 5 O 3646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 19743 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8641 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1014} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3451 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 26, 'TRANS': 412} Chain: "C" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3261 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 16, 'TRANS': 372} Chain breaks: 2 Chain: "D" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 20, 'TRANS': 413} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" 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 7229 SG CYS A1283 112.373 17.705 58.207 1.00135.57 S ATOM 7249 SG CYS A1286 111.889 15.123 60.842 1.00147.72 S ATOM 7435 SG CYS A1310 113.695 18.494 61.673 1.00149.57 S ATOM 7471 SG CYS A1315 115.418 15.846 59.618 1.00171.25 S ATOM 7749 SG CYS A1348 83.298 50.604 69.806 1.00 90.83 S ATOM 7787 SG CYS A1353 80.639 47.930 70.287 1.00 93.60 S ATOM 7937 SG CYS A1371 80.342 50.706 67.461 1.00 91.47 S ATOM 7955 SG CYS A1374 79.873 51.104 71.398 1.00 94.18 S ATOM 13140 SG CYS C 121 125.948 135.610 55.829 1.00275.08 S ATOM 13146 SG CYS C 122 122.661 136.917 54.444 1.00275.04 S ATOM 13185 SG CYS C 128 125.718 137.241 52.329 1.00274.28 S ATOM 13207 SG CYS C 131 124.419 133.886 52.725 1.00274.93 S ATOM 18208 SG CYS D 367 118.684 61.213 83.318 1.00 94.23 S ATOM 18336 SG CYS D 384 117.254 67.057 87.000 1.00100.01 S ATOM 18652 SG CYS D 424 122.851 64.361 86.683 1.00114.38 S ATOM 17537 SG CYS D 287 117.830 61.835 89.046 1.00111.07 S Time building chain proxies: 11.21, per 1000 atoms: 0.57 Number of scatterers: 19743 At special positions: 0 Unit cell: (160.308, 153.738, 118.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 Fe 4 26.01 S 105 16.00 O 3646 8.00 N 3352 7.00 C 12633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 601 " pdb="FE3 SF4 D 601 " - pdb=" SG CYS D 424 " pdb="FE1 SF4 D 601 " - pdb=" SG CYS D 367 " pdb="FE2 SF4 D 601 " - pdb=" SG CYS D 384 " pdb="FE4 SF4 D 601 " - pdb=" SG CYS D 287 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1283 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1315 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1286 " pdb="ZN ZN A1501 " - pdb=" SG CYS A1310 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1353 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1374 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1348 " pdb="ZN ZN A1502 " - pdb=" SG CYS A1371 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 128 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 131 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 121 " Number of angles added : 18 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 20 sheets defined 47.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 409 through 425 removed outlier: 4.475A pdb=" N ALA A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 614 through 630 Processing helix chain 'A' and resid 642 through 655 Processing helix chain 'A' and resid 658 through 663 removed outlier: 3.559A pdb=" N ILE A 662 " --> pdb=" O TRP A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 701 Processing helix chain 'A' and resid 707 through 715 Processing helix chain 'A' and resid 727 through 732 removed outlier: 3.813A pdb=" N MET A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 760 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 775 through 782 Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.676A pdb=" N ARG A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 909 through 931 Processing helix chain 'A' and resid 935 through 961 removed outlier: 4.218A pdb=" N TYR A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY A 958 " --> pdb=" O ASN A 954 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 960 " --> pdb=" O MET A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 994 Processing helix chain 'A' and resid 1014 through 1033 Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1085 through 1100 Processing helix chain 'A' and resid 1104 through 1125 Processing helix chain 'A' and resid 1129 through 1134 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.533A pdb=" N TYR A1146 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1165 Processing helix chain 'A' and resid 1187 through 1192 removed outlier: 3.632A pdb=" N ALA A1192 " --> pdb=" O SER A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1201 Processing helix chain 'A' and resid 1207 through 1215 Processing helix chain 'A' and resid 1216 through 1225 removed outlier: 4.297A pdb=" N ILE A1223 " --> pdb=" O VAL A1219 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1240 Processing helix chain 'A' and resid 1242 through 1249 Processing helix chain 'A' and resid 1268 through 1273 Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 4.017A pdb=" N ASP A1302 " --> pdb=" O SER A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1309 removed outlier: 3.508A pdb=" N ARG A1309 " --> pdb=" O SER A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1318 through 1321 Processing helix chain 'A' and resid 1322 through 1343 Processing helix chain 'A' and resid 1384 through 1400 Processing helix chain 'A' and resid 1400 through 1405 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1423 through 1442 removed outlier: 3.899A pdb=" N ALA A1437 " --> pdb=" O LEU A1433 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE A1440 " --> pdb=" O THR A1436 " (cutoff:3.500A) Processing helix chain 'A' and resid 1451 through 1456 Processing helix chain 'B' and resid 212 through 236 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 357 through 371 Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 397 through 413 Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 475 through 484 removed outlier: 4.026A pdb=" N GLU B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 505 Processing helix chain 'B' and resid 521 through 529 Processing helix chain 'C' and resid 5 through 7 No H-bonds generated for 'chain 'C' and resid 5 through 7' Processing helix chain 'C' and resid 8 through 20 removed outlier: 3.878A pdb=" N LYS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 32 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 62 through 74 removed outlier: 3.596A pdb=" N MET C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 94 removed outlier: 5.530A pdb=" N ASN C 92 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 128 through 131 Processing helix chain 'C' and resid 132 through 149 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 209 through 227 removed outlier: 4.323A pdb=" N LYS C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 3.887A pdb=" N LYS C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 264 through 283 Processing helix chain 'C' and resid 291 through 302 removed outlier: 3.600A pdb=" N MET C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 4.151A pdb=" N SER C 310 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 Processing helix chain 'C' and resid 381 through 386 Processing helix chain 'C' and resid 388 through 412 Processing helix chain 'D' and resid 39 through 63 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 88 through 111 removed outlier: 3.549A pdb=" N GLU D 92 " --> pdb=" O ASN D 88 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 113 through 135 Processing helix chain 'D' and resid 136 through 147 removed outlier: 3.511A pdb=" N ILE D 140 " --> pdb=" O PRO D 136 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 170 removed outlier: 5.053A pdb=" N GLN D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 196 Processing helix chain 'D' and resid 210 through 241 Proline residue: D 238 - end of helix Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 275 through 284 removed outlier: 3.512A pdb=" N PHE D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 316 Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.739A pdb=" N LYS D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 354 removed outlier: 4.728A pdb=" N TYR D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 373 Processing helix chain 'D' and resid 384 through 389 Processing helix chain 'D' and resid 390 through 401 Processing helix chain 'D' and resid 404 through 417 Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 443 through 455 Processing helix chain 'E' and resid 22 through 26 removed outlier: 3.870A pdb=" N VAL E 26 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 49 removed outlier: 3.502A pdb=" N LEU E 39 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER E 40 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 519 through 520 removed outlier: 8.786A pdb=" N ALA A 520 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET A 379 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 363 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 380 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 359 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE A 360 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALA A 348 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE A 362 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP A 366 " --> pdb=" O HIS A 342 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N HIS A 342 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 341 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 434 through 436 removed outlier: 3.519A pdb=" N VAL A 435 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU A 451 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 475 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 394 through 396 removed outlier: 7.124A pdb=" N LYS A 395 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 581 through 583 removed outlier: 3.867A pdb=" N SER A 581 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A 583 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER A 567 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU A 537 " --> pdb=" O SER A 567 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 585 through 586 removed outlier: 3.697A pdb=" N VAL A 586 " --> pdb=" O GLU A 610 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 850 through 852 removed outlier: 4.030A pdb=" N TYR A1000 " --> pdb=" O MET A1007 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN A1009 " --> pdb=" O VAL A 998 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL A 998 " --> pdb=" O ASN A1009 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 850 through 852 removed outlier: 5.355A pdb=" N PHE A1044 " --> pdb=" O VAL A1060 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A1060 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER A1046 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1050 " --> pdb=" O LYS A1054 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA A1057 " --> pdb=" O GLU A1073 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU A1073 " --> pdb=" O ALA A1057 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A1061 " --> pdb=" O VAL A1069 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1135 through 1138 Processing sheet with id=AA9, first strand: chain 'A' and resid 1279 through 1282 removed outlier: 3.520A pdb=" N TYR A1292 " --> pdb=" O PHE A1279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1356 through 1357 Processing sheet with id=AB2, first strand: chain 'A' and resid 1448 through 1450 Processing sheet with id=AB3, first strand: chain 'B' and resid 170 through 174 removed outlier: 5.922A pdb=" N VAL B 170 " --> pdb=" O ARG B 597 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ARG B 597 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 172 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA B 592 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR B 570 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N CYS B 346 " --> pdb=" O THR B 570 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 572 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 574 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET B 341 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE B 376 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU B 343 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE B 378 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA B 345 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 420 " --> pdb=" O GLN B 454 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 194 through 195 removed outlier: 6.116A pdb=" N ILE B 468 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE B 539 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY B 470 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 547 " --> pdb=" O ASN B 558 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.610A pdb=" N GLY B 255 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 58 removed outlier: 4.667A pdb=" N TYR C 57 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE C 45 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU C 44 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 77 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C 103 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 54 through 58 removed outlier: 4.667A pdb=" N TYR C 57 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N PHE C 45 " --> pdb=" O TYR C 57 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU C 44 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS C 77 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 317 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 109 through 111 removed outlier: 4.050A pdb=" N ILE C 110 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 165 " --> pdb=" O ILE C 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.708A pdb=" N TYR D 184 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 209 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 14 through 19 removed outlier: 4.169A pdb=" N VAL E 14 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE E 71 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY E 105 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG E 73 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR E 103 " --> pdb=" O ARG E 73 " (cutoff:3.500A) 899 hydrogen bonds defined for protein. 2574 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: 7.19 Time building geometry restraints manager: 6.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 8369 1.43 - 1.64: 11656 1.64 - 1.86: 146 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 20183 Sorted by residual: bond pdb=" N ILE D 371 " pdb=" CA ILE D 371 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 9.04e+00 bond pdb=" N LEU D 372 " pdb=" CA LEU D 372 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.33e-02 5.65e+03 8.55e+00 bond pdb=" CA SER D 366 " pdb=" CB SER D 366 " ideal model delta sigma weight residual 1.530 1.488 0.042 1.58e-02 4.01e+03 7.23e+00 bond pdb=" N CYS D 367 " pdb=" CA CYS D 367 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.62e+00 bond pdb=" C CYS D 367 " pdb=" O CYS D 367 " ideal model delta sigma weight residual 1.237 1.267 -0.030 1.17e-02 7.31e+03 6.62e+00 ... (remaining 20178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 26309 1.82 - 3.64: 777 3.64 - 5.46: 151 5.46 - 7.28: 31 7.28 - 9.11: 14 Bond angle restraints: 27282 Sorted by residual: angle pdb=" CA PRO C 333 " pdb=" N PRO C 333 " pdb=" CD PRO C 333 " ideal model delta sigma weight residual 112.00 104.35 7.65 1.40e+00 5.10e-01 2.98e+01 angle pdb=" CA PRO C 22 " pdb=" N PRO C 22 " pdb=" CD PRO C 22 " ideal model delta sigma weight residual 112.00 104.58 7.42 1.40e+00 5.10e-01 2.81e+01 angle pdb=" N PRO C 22 " pdb=" CD PRO C 22 " pdb=" CG PRO C 22 " ideal model delta sigma weight residual 103.20 95.83 7.37 1.50e+00 4.44e-01 2.42e+01 angle pdb=" CA SER D 366 " pdb=" C SER D 366 " pdb=" O SER D 366 " ideal model delta sigma weight residual 121.28 115.94 5.34 1.18e+00 7.18e-01 2.05e+01 angle pdb=" N VAL A 607 " pdb=" CA VAL A 607 " pdb=" C VAL A 607 " ideal model delta sigma weight residual 110.05 105.30 4.75 1.09e+00 8.42e-01 1.90e+01 ... (remaining 27277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 11110 18.00 - 35.99: 967 35.99 - 53.99: 165 53.99 - 71.99: 37 71.99 - 89.98: 26 Dihedral angle restraints: 12305 sinusoidal: 5137 harmonic: 7168 Sorted by residual: dihedral pdb=" CA GLU D 356 " pdb=" C GLU D 356 " pdb=" N GLY D 357 " pdb=" CA GLY D 357 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA SER A1444 " pdb=" C SER A1444 " pdb=" N GLY A1445 " pdb=" CA GLY A1445 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ASP A1242 " pdb=" C ASP A1242 " pdb=" N PRO A1243 " pdb=" CA PRO A1243 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 12302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2726 0.082 - 0.165: 266 0.165 - 0.247: 7 0.247 - 0.330: 0 0.330 - 0.412: 1 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CA CYS D 367 " pdb=" N CYS D 367 " pdb=" C CYS D 367 " pdb=" CB CYS D 367 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB THR A1410 " pdb=" CA THR A1410 " pdb=" OG1 THR A1410 " pdb=" CG2 THR A1410 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA PRO B 199 " pdb=" N PRO B 199 " pdb=" C PRO B 199 " pdb=" CB PRO B 199 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2997 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " 0.090 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO C 333 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 534 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO A 535 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 588 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.10e+01 pdb=" N PRO B 589 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.062 5.00e-02 4.00e+02 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 415 2.67 - 3.23: 20239 3.23 - 3.79: 32123 3.79 - 4.34: 42041 4.34 - 4.90: 66502 Nonbonded interactions: 161320 Sorted by model distance: nonbonded pdb=" OH TYR A1383 " pdb=" OE1 GLN A1391 " model vdw 2.116 3.040 nonbonded pdb=" OE1 GLU D 57 " pdb=" NE1 TRP D 119 " model vdw 2.155 3.120 nonbonded pdb=" NE2 GLN B 211 " pdb=" OD1 ASP B 521 " model vdw 2.158 3.120 nonbonded pdb=" O ILE D 166 " pdb=" OG SER D 170 " model vdw 2.162 3.040 nonbonded pdb=" NE2 GLN D 425 " pdb=" O PHE D 439 " model vdw 2.167 3.120 ... (remaining 161315 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 52.340 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.004 0.102 20183 Z= 0.232 Angle : 0.775 9.106 27282 Z= 0.422 Chirality : 0.048 0.412 3000 Planarity : 0.007 0.132 3505 Dihedral : 14.343 89.982 7673 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.51 % 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: -0.84 (0.17), residues: 2420 helix: 0.23 (0.16), residues: 1030 sheet: -0.74 (0.31), residues: 279 loop : -1.19 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A1238 HIS 0.009 0.001 HIS B 278 PHE 0.029 0.002 PHE A 796 TYR 0.023 0.001 TYR A1342 ARG 0.012 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.7369 (tpt) cc_final: 0.6760 (tpp) REVERT: A 731 MET cc_start: 0.9224 (tmm) cc_final: 0.8824 (tmm) REVERT: A 1047 LEU cc_start: 0.8418 (tt) cc_final: 0.8122 (tt) REVERT: A 1052 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7817 (mmtt) REVERT: B 464 ILE cc_start: 0.9151 (mm) cc_final: 0.8924 (mm) REVERT: B 469 PHE cc_start: 0.7237 (m-80) cc_final: 0.6894 (m-80) REVERT: C 45 PHE cc_start: 0.9105 (m-80) cc_final: 0.8857 (m-80) REVERT: C 70 MET cc_start: 0.8343 (mmm) cc_final: 0.7827 (mmm) REVERT: C 112 MET cc_start: 0.8811 (mmp) cc_final: 0.8438 (mmm) REVERT: C 146 LEU cc_start: 0.9761 (mp) cc_final: 0.9531 (pp) REVERT: C 297 MET cc_start: 0.9015 (ppp) cc_final: 0.8708 (ppp) REVERT: C 300 TYR cc_start: 0.6853 (t80) cc_final: 0.5710 (t80) REVERT: D 74 LEU cc_start: 0.9030 (tp) cc_final: 0.8682 (tp) REVERT: E 70 PHE cc_start: 0.8513 (m-80) cc_final: 0.8279 (m-80) outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.3562 time to fit residues: 117.9247 Evaluate side-chains 133 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 40.0000 chunk 183 optimal weight: 40.0000 chunk 101 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 189 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 115 optimal weight: 0.0770 chunk 141 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 overall best weight: 5.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 505 GLN A 713 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 GLN A1391 GLN ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 20183 Z= 0.266 Angle : 0.665 9.481 27282 Z= 0.347 Chirality : 0.045 0.215 3000 Planarity : 0.006 0.104 3505 Dihedral : 5.089 28.463 2657 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 0.36 % Allowed : 4.89 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.73 (0.17), residues: 2420 helix: 0.44 (0.16), residues: 1036 sheet: -1.02 (0.29), residues: 300 loop : -1.18 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 29 HIS 0.007 0.001 HIS B 278 PHE 0.016 0.002 PHE D 447 TYR 0.015 0.002 TYR D 420 ARG 0.005 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 MET cc_start: 0.7722 (tpt) cc_final: 0.7245 (tpp) REVERT: A 428 MET cc_start: 0.9035 (pmm) cc_final: 0.8683 (pmm) REVERT: A 731 MET cc_start: 0.9324 (tmm) cc_final: 0.8782 (tmm) REVERT: A 781 MET cc_start: 0.8394 (tpp) cc_final: 0.8188 (tpp) REVERT: A 989 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: A 1047 LEU cc_start: 0.8506 (tt) cc_final: 0.8274 (tt) REVERT: C 45 PHE cc_start: 0.9153 (m-80) cc_final: 0.8816 (m-80) REVERT: C 112 MET cc_start: 0.8597 (mmp) cc_final: 0.8061 (mmm) REVERT: C 167 CYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6165 (p) REVERT: C 297 MET cc_start: 0.8989 (ppp) cc_final: 0.8759 (ppp) REVERT: C 300 TYR cc_start: 0.6925 (t80) cc_final: 0.5873 (t80) REVERT: D 74 LEU cc_start: 0.8833 (tp) cc_final: 0.8471 (tp) outliers start: 8 outliers final: 2 residues processed: 165 average time/residue: 0.3180 time to fit residues: 82.4554 Evaluate side-chains 120 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 182 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 237 optimal weight: 40.0000 chunk 196 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 176 optimal weight: 30.0000 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN A 946 GLN ** A 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 20183 Z= 0.284 Angle : 0.656 7.826 27282 Z= 0.342 Chirality : 0.044 0.209 3000 Planarity : 0.005 0.109 3505 Dihedral : 5.114 27.549 2657 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.29 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.69 (0.17), residues: 2420 helix: 0.50 (0.16), residues: 1028 sheet: -1.13 (0.29), residues: 288 loop : -1.13 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 29 HIS 0.006 0.001 HIS A 553 PHE 0.015 0.002 PHE D 447 TYR 0.012 0.001 TYR D 309 ARG 0.008 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8994 (pmm) cc_final: 0.8621 (pmm) REVERT: A 731 MET cc_start: 0.9325 (tmm) cc_final: 0.8985 (tmm) REVERT: C 45 PHE cc_start: 0.9295 (m-80) cc_final: 0.8865 (m-80) REVERT: C 112 MET cc_start: 0.8660 (mmp) cc_final: 0.8132 (mmm) REVERT: C 297 MET cc_start: 0.9027 (ppp) cc_final: 0.8806 (ppp) REVERT: C 300 TYR cc_start: 0.6986 (t80) cc_final: 0.5934 (t80) REVERT: D 74 LEU cc_start: 0.8878 (tp) cc_final: 0.8511 (tp) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.3106 time to fit residues: 71.6194 Evaluate side-chains 117 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 209 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20183 Z= 0.240 Angle : 0.632 7.355 27282 Z= 0.329 Chirality : 0.044 0.219 3000 Planarity : 0.005 0.108 3505 Dihedral : 5.032 26.892 2657 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.62 (0.17), residues: 2420 helix: 0.57 (0.16), residues: 1033 sheet: -1.03 (0.30), residues: 280 loop : -1.13 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 29 HIS 0.006 0.001 HIS A 553 PHE 0.015 0.002 PHE D 447 TYR 0.012 0.001 TYR A 964 ARG 0.010 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8968 (pmm) cc_final: 0.8490 (pmm) REVERT: A 519 MET cc_start: 0.8125 (ttp) cc_final: 0.7708 (ttp) REVERT: A 731 MET cc_start: 0.9300 (tmm) cc_final: 0.8884 (tmm) REVERT: A 985 MET cc_start: 0.9138 (tmm) cc_final: 0.8918 (tmm) REVERT: A 1047 LEU cc_start: 0.8667 (tt) cc_final: 0.8301 (tt) REVERT: A 1333 ASP cc_start: 0.8238 (p0) cc_final: 0.8030 (p0) REVERT: C 45 PHE cc_start: 0.9297 (m-80) cc_final: 0.8843 (m-80) REVERT: C 112 MET cc_start: 0.8713 (mmp) cc_final: 0.8191 (mmm) REVERT: C 297 MET cc_start: 0.9198 (ppp) cc_final: 0.8969 (ppp) REVERT: C 300 TYR cc_start: 0.6977 (t80) cc_final: 0.5965 (t80) REVERT: D 74 LEU cc_start: 0.8808 (tp) cc_final: 0.8434 (tp) outliers start: 1 outliers final: 1 residues processed: 149 average time/residue: 0.3174 time to fit residues: 74.3833 Evaluate side-chains 115 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 174 optimal weight: 50.0000 chunk 96 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1136 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 20183 Z= 0.263 Angle : 0.641 7.541 27282 Z= 0.333 Chirality : 0.044 0.216 3000 Planarity : 0.005 0.109 3505 Dihedral : 5.041 26.821 2657 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.63 (0.17), residues: 2420 helix: 0.57 (0.16), residues: 1029 sheet: -1.10 (0.29), residues: 290 loop : -1.13 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 29 HIS 0.007 0.001 HIS B 278 PHE 0.016 0.002 PHE C 108 TYR 0.012 0.001 TYR A 964 ARG 0.011 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8936 (pmm) cc_final: 0.8473 (pmm) REVERT: A 519 MET cc_start: 0.8340 (ttp) cc_final: 0.8054 (ttp) REVERT: A 731 MET cc_start: 0.9343 (tmm) cc_final: 0.8897 (tmm) REVERT: A 1047 LEU cc_start: 0.8217 (tt) cc_final: 0.7988 (tt) REVERT: C 45 PHE cc_start: 0.9314 (m-80) cc_final: 0.8847 (m-80) REVERT: C 70 MET cc_start: 0.8519 (mmm) cc_final: 0.8216 (mmm) REVERT: C 73 MET cc_start: 0.9445 (mmp) cc_final: 0.9235 (mpp) REVERT: C 112 MET cc_start: 0.8723 (mmp) cc_final: 0.8214 (mmm) REVERT: C 300 TYR cc_start: 0.6938 (t80) cc_final: 0.5932 (t80) REVERT: D 74 LEU cc_start: 0.8814 (tp) cc_final: 0.8450 (tp) outliers start: 4 outliers final: 1 residues processed: 150 average time/residue: 0.3305 time to fit residues: 76.9481 Evaluate side-chains 116 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 0.2980 chunk 210 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 234 optimal weight: 40.0000 chunk 194 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 19 optimal weight: 50.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 548 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 20183 Z= 0.247 Angle : 0.642 7.722 27282 Z= 0.333 Chirality : 0.044 0.226 3000 Planarity : 0.005 0.110 3505 Dihedral : 5.041 26.292 2657 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.63 (0.17), residues: 2420 helix: 0.58 (0.16), residues: 1031 sheet: -1.10 (0.29), residues: 290 loop : -1.13 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 29 HIS 0.006 0.001 HIS B 278 PHE 0.015 0.001 PHE D 447 TYR 0.012 0.001 TYR B 546 ARG 0.016 0.001 ARG A1081 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 MET cc_start: 0.8933 (pmm) cc_final: 0.8565 (pmm) REVERT: A 689 MET cc_start: 0.5179 (tpp) cc_final: 0.4912 (tpp) REVERT: A 731 MET cc_start: 0.9355 (tmm) cc_final: 0.8876 (tmm) REVERT: A 1047 LEU cc_start: 0.8258 (tt) cc_final: 0.8007 (tt) REVERT: C 45 PHE cc_start: 0.9318 (m-80) cc_final: 0.8841 (m-80) REVERT: C 73 MET cc_start: 0.9432 (mmp) cc_final: 0.9193 (mpp) REVERT: C 112 MET cc_start: 0.8718 (mmp) cc_final: 0.8217 (mmm) REVERT: C 297 MET cc_start: 0.9205 (ppp) cc_final: 0.8982 (ppp) REVERT: C 300 TYR cc_start: 0.6982 (t80) cc_final: 0.5977 (t80) REVERT: D 74 LEU cc_start: 0.8807 (tp) cc_final: 0.8480 (tp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.3286 time to fit residues: 73.4988 Evaluate side-chains 112 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 233 optimal weight: 0.4980 chunk 145 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 GLN ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 GLN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20183 Z= 0.175 Angle : 0.637 7.925 27282 Z= 0.325 Chirality : 0.045 0.211 3000 Planarity : 0.005 0.110 3505 Dihedral : 4.862 24.871 2657 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.46 (0.17), residues: 2420 helix: 0.74 (0.16), residues: 1019 sheet: -0.95 (0.31), residues: 279 loop : -1.07 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 29 HIS 0.004 0.001 HIS A 744 PHE 0.020 0.001 PHE C 47 TYR 0.011 0.001 TYR A 957 ARG 0.013 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 519 MET cc_start: 0.8332 (ttt) cc_final: 0.8015 (ttp) REVERT: A 731 MET cc_start: 0.9332 (tmm) cc_final: 0.8829 (tmm) REVERT: A 1047 LEU cc_start: 0.8132 (tt) cc_final: 0.7905 (tt) REVERT: A 1052 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8332 (mptt) REVERT: C 45 PHE cc_start: 0.9293 (m-80) cc_final: 0.8827 (m-80) REVERT: C 73 MET cc_start: 0.9393 (mmp) cc_final: 0.9157 (mpp) REVERT: C 112 MET cc_start: 0.8675 (mmp) cc_final: 0.8193 (mmm) REVERT: C 297 MET cc_start: 0.9223 (ppp) cc_final: 0.9007 (ppp) REVERT: C 300 TYR cc_start: 0.6973 (t80) cc_final: 0.5994 (t80) REVERT: D 74 LEU cc_start: 0.8716 (tp) cc_final: 0.8298 (tp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3174 time to fit residues: 78.8665 Evaluate side-chains 124 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 148 optimal weight: 9.9990 chunk 158 optimal weight: 40.0000 chunk 115 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN D 251 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 20183 Z= 0.221 Angle : 0.635 9.488 27282 Z= 0.327 Chirality : 0.044 0.212 3000 Planarity : 0.005 0.112 3505 Dihedral : 4.872 25.911 2657 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.75 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.46 (0.17), residues: 2420 helix: 0.72 (0.16), residues: 1030 sheet: -1.02 (0.30), residues: 280 loop : -1.04 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 294 HIS 0.005 0.001 HIS B 278 PHE 0.016 0.001 PHE C 47 TYR 0.020 0.001 TYR A 344 ARG 0.011 0.001 ARG A1081 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9341 (tmm) cc_final: 0.8858 (tmm) REVERT: A 1047 LEU cc_start: 0.8214 (tt) cc_final: 0.7985 (tt) REVERT: C 45 PHE cc_start: 0.9319 (m-80) cc_final: 0.8949 (m-80) REVERT: C 73 MET cc_start: 0.9422 (mmp) cc_final: 0.9156 (mpp) REVERT: C 112 MET cc_start: 0.8706 (mmp) cc_final: 0.8224 (mmm) REVERT: C 300 TYR cc_start: 0.7163 (t80) cc_final: 0.6122 (t80) REVERT: D 74 LEU cc_start: 0.8778 (tp) cc_final: 0.8359 (tp) REVERT: E 22 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8190 (tm-30) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.3058 time to fit residues: 72.1413 Evaluate side-chains 112 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 7.9990 chunk 203 optimal weight: 9.9990 chunk 217 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 170 optimal weight: 0.0000 chunk 66 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 overall best weight: 3.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 788 ASN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 20183 Z= 0.213 Angle : 0.655 11.161 27282 Z= 0.334 Chirality : 0.045 0.264 3000 Planarity : 0.005 0.112 3505 Dihedral : 4.884 25.049 2657 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.92 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.46 (0.17), residues: 2420 helix: 0.72 (0.16), residues: 1029 sheet: -1.03 (0.30), residues: 280 loop : -1.05 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 294 HIS 0.005 0.001 HIS A 553 PHE 0.016 0.001 PHE A 861 TYR 0.022 0.001 TYR B 206 ARG 0.013 0.001 ARG A1081 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9358 (tmm) cc_final: 0.8870 (tmm) REVERT: A 985 MET cc_start: 0.9141 (tmm) cc_final: 0.8854 (tmm) REVERT: C 45 PHE cc_start: 0.9332 (m-80) cc_final: 0.8950 (m-80) REVERT: C 73 MET cc_start: 0.9424 (mmp) cc_final: 0.9145 (mpp) REVERT: C 112 MET cc_start: 0.8706 (mmp) cc_final: 0.8224 (mmm) REVERT: C 297 MET cc_start: 0.9215 (ppp) cc_final: 0.8988 (ppp) REVERT: C 300 TYR cc_start: 0.7208 (t80) cc_final: 0.6196 (t80) REVERT: D 74 LEU cc_start: 0.8771 (tp) cc_final: 0.8343 (tp) REVERT: E 22 GLN cc_start: 0.8382 (tm-30) cc_final: 0.8054 (tm-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2933 time to fit residues: 67.8430 Evaluate side-chains 112 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 7.9990 chunk 140 optimal weight: 30.0000 chunk 109 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 241 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 191 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 152 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1391 GLN ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 20183 Z= 0.282 Angle : 0.689 9.917 27282 Z= 0.355 Chirality : 0.045 0.260 3000 Planarity : 0.005 0.114 3505 Dihedral : 4.987 25.346 2657 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.56 (0.17), residues: 2420 helix: 0.64 (0.16), residues: 1038 sheet: -1.17 (0.30), residues: 286 loop : -1.08 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 294 HIS 0.006 0.001 HIS A 553 PHE 0.016 0.002 PHE C 47 TYR 0.019 0.002 TYR A 344 ARG 0.013 0.001 ARG A 916 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4840 Ramachandran restraints generated. 2420 Oldfield, 0 Emsley, 2420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9358 (tmm) cc_final: 0.8855 (tmm) REVERT: A 1047 LEU cc_start: 0.8229 (tt) cc_final: 0.7983 (tt) REVERT: A 1333 ASP cc_start: 0.8082 (p0) cc_final: 0.7881 (p0) REVERT: C 45 PHE cc_start: 0.9359 (m-80) cc_final: 0.8983 (m-80) REVERT: C 73 MET cc_start: 0.9413 (mmp) cc_final: 0.9075 (mpp) REVERT: C 112 MET cc_start: 0.8747 (mmp) cc_final: 0.8247 (mmm) REVERT: C 297 MET cc_start: 0.9231 (ppp) cc_final: 0.9016 (ppp) REVERT: C 300 TYR cc_start: 0.7296 (t80) cc_final: 0.6328 (t80) REVERT: D 74 LEU cc_start: 0.8833 (tp) cc_final: 0.8479 (tp) REVERT: E 22 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8307 (tm-30) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.3005 time to fit residues: 66.7610 Evaluate side-chains 107 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 80 optimal weight: 0.0870 chunk 197 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 35 optimal weight: 0.0980 chunk 168 optimal weight: 30.0000 overall best weight: 4.0364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A1164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** 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 = 0.3330 r_free = 0.3330 target = 0.044551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.030093 restraints weight = 165890.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.030859 restraints weight = 110813.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.031524 restraints weight = 84103.765| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 20183 Z= 0.222 Angle : 0.662 10.020 27282 Z= 0.340 Chirality : 0.045 0.242 3000 Planarity : 0.005 0.114 3505 Dihedral : 4.950 24.846 2657 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.51 % 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: -0.51 (0.17), residues: 2420 helix: 0.68 (0.16), residues: 1033 sheet: -1.14 (0.30), residues: 280 loop : -1.06 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 29 HIS 0.005 0.001 HIS A 553 PHE 0.015 0.001 PHE A 341 TYR 0.029 0.001 TYR D 110 ARG 0.012 0.001 ARG C 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3145.15 seconds wall clock time: 58 minutes 28.74 seconds (3508.74 seconds total)