Starting phenix.real_space_refine on Mon Aug 25 15:39:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c9y_7438/08_2025/6c9y_7438_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c9y_7438/08_2025/6c9y_7438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6c9y_7438/08_2025/6c9y_7438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c9y_7438/08_2025/6c9y_7438.map" model { file = "/net/cci-nas-00/data/ceres_data/6c9y_7438/08_2025/6c9y_7438_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c9y_7438/08_2025/6c9y_7438_neut.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 Zn 2 6.06 5 Mg 1 5.21 5 S 128 5.16 5 C 18120 2.51 5 N 5109 2.21 5 O 5560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28920 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "B" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1708 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 212} Chain breaks: 1 Chain: "C" Number of atoms: 10570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10570 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1280} Chain: "D" Number of atoms: 10434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10434 Classifications: {'peptide': 1350} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 7, 'PTRANS': 55, 'TRANS': 1287} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 3813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3813 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 14, 'TRANS': 453} Chain breaks: 2 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14577 SG CYS D 70 43.842 117.170 79.209 1.00216.28 S ATOM 14591 SG CYS D 72 42.623 118.864 82.061 1.00221.39 S ATOM 14699 SG CYS D 85 42.003 120.398 78.908 1.00200.07 S ATOM 14723 SG CYS D 88 46.657 120.260 80.344 1.00199.43 S ATOM 20387 SG CYS D 814 81.566 96.811 26.121 1.00106.41 S ATOM 20952 SG CYS D 888 81.790 97.295 29.943 1.00106.17 S ATOM 21003 SG CYS D 895 80.453 94.371 28.406 1.00 93.43 S ATOM 21024 SG CYS D 898 84.020 94.017 28.075 1.00 93.84 S Time building chain proxies: 5.09, per 1000 atoms: 0.18 Number of scatterers: 28920 At special positions: 0 Unit cell: (172.396, 193.452, 159.236, 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 2 29.99 S 128 16.00 Mg 1 11.99 O 5560 8.00 N 5109 7.00 C 18120 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: 2.17 Conformation dependent library (CDL) restraints added in 977.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " Number of angles added : 12 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6840 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 46 sheets defined 42.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.539A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.844A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.579A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.557A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.676A pdb=" N ASP B 114 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.709A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.891A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.546A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.657A pdb=" N ARG C 211 " --> pdb=" O THR C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 290 through 294 removed outlier: 4.257A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 3.733A pdb=" N LEU C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.577A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.886A pdb=" N ALA C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.782A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.646A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.601A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 removed outlier: 3.999A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.656A pdb=" N ILE C 524 " --> pdb=" O PRO C 520 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 549 removed outlier: 4.257A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.528A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 614 removed outlier: 3.966A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 614' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 864 removed outlier: 3.766A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 980 removed outlier: 3.692A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 removed outlier: 3.924A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.934A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.503A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 removed outlier: 3.647A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1149 removed outlier: 3.611A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 removed outlier: 3.651A pdb=" N ASN C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C1177 " --> pdb=" O ALA C1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.641A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.927A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.735A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP C1276 " --> pdb=" O GLU C1272 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C1278 " --> pdb=" O GLU C1274 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1291 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 4.128A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.591A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.794A pdb=" N TRP D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.674A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.534A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.974A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.534A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.646A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.800A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.781A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.655A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.713A pdb=" N GLY D 258 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG D 259 " --> pdb=" O ASP D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 259' Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.715A pdb=" N ARG D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.740A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 304 " --> pdb=" O GLN D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.750A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.642A pdb=" N GLU D 386 " --> pdb=" O TYR D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.596A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 417 removed outlier: 4.449A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 removed outlier: 3.657A pdb=" N LEU D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.759A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 593 Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.557A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 605 " --> pdb=" O ILE D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.624A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.539A pdb=" N ALA D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 704 removed outlier: 3.867A pdb=" N ASP D 684 " --> pdb=" O ASN D 680 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 702 " --> pdb=" O MET D 698 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 729 removed outlier: 3.722A pdb=" N ALA D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.702A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 4.269A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.957A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.855A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.742A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.900A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.829A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.642A pdb=" N LEU D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.805A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.900A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.474A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.532A pdb=" N LYS D1286 " --> pdb=" O TYR D1282 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.758A pdb=" N ALA D1315 " --> pdb=" O LYS D1311 " (cutoff:3.500A) Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.767A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER D1324 " --> pdb=" O ILE D1320 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.547A pdb=" N VAL D1337 " --> pdb=" O THR D1333 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY D1339 " --> pdb=" O ALA D1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.927A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1373 removed outlier: 4.294A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.584A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 32 removed outlier: 4.204A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.875A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 77 removed outlier: 4.061A pdb=" N GLN E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 4.042A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 136 removed outlier: 3.596A pdb=" N VAL F 130 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 152 removed outlier: 3.620A pdb=" N LEU F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 234 removed outlier: 3.529A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR F 228 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.823A pdb=" N GLU F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER F 253 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU F 254 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE F 256 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 290 removed outlier: 3.612A pdb=" N ASP F 267 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 332 removed outlier: 3.696A pdb=" N HIS F 331 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 332 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 351 removed outlier: 3.708A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN F 342 " --> pdb=" O HIS F 338 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN F 345 " --> pdb=" O LEU F 341 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 382 removed outlier: 3.623A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ASN F 362 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 Processing helix chain 'F' and resid 400 through 419 removed outlier: 3.516A pdb=" N LYS F 414 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 415 " --> pdb=" O GLY F 411 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.693A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.656A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 438 " --> pdb=" O TRP F 434 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP F 445 " --> pdb=" O ARG F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.513A pdb=" N ILE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN F 472 " --> pdb=" O ARG F 468 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU F 473 " --> pdb=" O GLN F 469 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 487 removed outlier: 3.845A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 501 removed outlier: 3.940A pdb=" N LYS F 496 " --> pdb=" O ASP F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 Processing helix chain 'F' and resid 530 through 550 removed outlier: 3.568A pdb=" N THR F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP F 546 " --> pdb=" O ALA F 542 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL F 547 " --> pdb=" O ALA F 543 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY F 550 " --> pdb=" O ASP F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 563 removed outlier: 3.512A pdb=" N MET F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 562 " --> pdb=" O VAL F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 581 removed outlier: 3.675A pdb=" N VAL F 576 " --> pdb=" O THR F 572 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 598 removed outlier: 3.960A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS F 597 " --> pdb=" O LYS F 593 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 598 " --> pdb=" O ALA F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 609 removed outlier: 3.891A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER F 609 " --> pdb=" O GLU F 605 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.564A pdb=" N LYS A 25 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N THR A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL A 192 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 removed outlier: 3.907A pdb=" N VAL A 98 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.859A pdb=" N LYS A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 140 " --> pdb=" O LYS A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.632A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 17 removed outlier: 3.597A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 27 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B 25 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 196 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG B 191 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 60 removed outlier: 4.857A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.684A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.571A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.855A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.633A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU C 100 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU C 102 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 104 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.615A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.578A pdb=" N ARG C 452 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS C 150 " --> pdb=" O ARG C 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.728A pdb=" N GLU C 240 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.084A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.254A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.705A pdb=" N TYR C 301 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.056A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.879A pdb=" N HIS C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC4, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.913A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 removed outlier: 4.039A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 4.776A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET C1232 " --> pdb=" O GLN C 798 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN C 798 " --> pdb=" O MET C1232 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1066 through 1068 Processing sheet with id=AD1, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.409A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.032A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.754A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1250 through 1251 removed outlier: 3.834A pdb=" N SER C1250 " --> pdb=" O LEU C1259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1268 through 1269 removed outlier: 3.944A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1335 through 1337 removed outlier: 3.544A pdb=" N ALA D 23 " --> pdb=" O ASN C1336 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.718A pdb=" N SER D 34 " --> pdb=" O MET D 102 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS D 104 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AE1, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AE2, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.054A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 705 through 707 removed outlier: 4.287A pdb=" N THR D 705 " --> pdb=" O GLN D 716 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE5, first strand: chain 'D' and resid 960 through 961 removed outlier: 3.604A pdb=" N SER D 961 " --> pdb=" O GLU D 981 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 981 " --> pdb=" O SER D 961 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE7, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 6.119A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1034 through 1038 Processing sheet with id=AE9, first strand: chain 'D' and resid 1187 through 1190 removed outlier: 3.695A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1277 through 1279 1080 hydrogen bonds defined for protein. 3024 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: 5.99 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8227 1.33 - 1.46: 5070 1.46 - 1.58: 15812 1.58 - 1.70: 4 1.70 - 1.82: 225 Bond restraints: 29338 Sorted by residual: bond pdb=" C ALA D 426 " pdb=" N PRO D 427 " ideal model delta sigma weight residual 1.334 1.426 -0.092 2.34e-02 1.83e+03 1.53e+01 bond pdb=" C TYR C 742 " pdb=" N PRO C 743 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C MET F 489 " pdb=" N PRO F 490 " ideal model delta sigma weight residual 1.334 1.415 -0.081 2.34e-02 1.83e+03 1.19e+01 bond pdb=" C THR C 896 " pdb=" N PRO C 897 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 1.00e+01 bond pdb=" CA ASP C1160 " pdb=" C ASP C1160 " ideal model delta sigma weight residual 1.529 1.571 -0.042 1.40e-02 5.10e+03 8.98e+00 ... (remaining 29333 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 37924 3.37 - 6.75: 1430 6.75 - 10.12: 196 10.12 - 13.50: 44 13.50 - 16.87: 7 Bond angle restraints: 39601 Sorted by residual: angle pdb=" C LEU A 28 " pdb=" N GLU A 29 " pdb=" CA GLU A 29 " ideal model delta sigma weight residual 119.78 130.84 -11.06 1.24e+00 6.50e-01 7.96e+01 angle pdb=" C GLU D1343 " pdb=" N LEU D1344 " pdb=" CA LEU D1344 " ideal model delta sigma weight residual 121.54 138.34 -16.80 1.91e+00 2.74e-01 7.73e+01 angle pdb=" N HIS A 160 " pdb=" CA HIS A 160 " pdb=" C HIS A 160 " ideal model delta sigma weight residual 114.62 105.85 8.77 1.14e+00 7.69e-01 5.92e+01 angle pdb=" C ASP C1160 " pdb=" N LEU C1161 " pdb=" CA LEU C1161 " ideal model delta sigma weight residual 121.70 134.58 -12.88 1.80e+00 3.09e-01 5.12e+01 angle pdb=" N GLY C 168 " pdb=" CA GLY C 168 " pdb=" C GLY C 168 " ideal model delta sigma weight residual 113.18 96.31 16.87 2.37e+00 1.78e-01 5.07e+01 ... (remaining 39596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 16293 17.45 - 34.89: 1539 34.89 - 52.34: 255 52.34 - 69.79: 35 69.79 - 87.23: 15 Dihedral angle restraints: 18137 sinusoidal: 7527 harmonic: 10610 Sorted by residual: dihedral pdb=" CA THR F 569 " pdb=" C THR F 569 " pdb=" N ASP F 570 " pdb=" CA ASP F 570 " ideal model delta harmonic sigma weight residual -180.00 -107.53 -72.47 0 5.00e+00 4.00e-02 2.10e+02 dihedral pdb=" CA ILE C 198 " pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta harmonic sigma weight residual -180.00 -123.42 -56.58 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA ALA C 109 " pdb=" C ALA C 109 " pdb=" N PRO C 110 " pdb=" CA PRO C 110 " ideal model delta harmonic sigma weight residual 180.00 141.12 38.88 0 5.00e+00 4.00e-02 6.05e+01 ... (remaining 18134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 4246 0.147 - 0.293: 258 0.293 - 0.440: 13 0.440 - 0.587: 1 0.587 - 0.734: 1 Chirality restraints: 4519 Sorted by residual: chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -1.90 -0.73 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CB ILE C1079 " pdb=" CA ILE C1079 " pdb=" CG1 ILE C1079 " pdb=" CG2 ILE C1079 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 4516 not shown) Planarity restraints: 5193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 150 " -0.012 2.00e-02 2.50e+03 4.71e-02 3.33e+01 pdb=" CG HIS C 150 " 0.081 2.00e-02 2.50e+03 pdb=" ND1 HIS C 150 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 HIS C 150 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 HIS C 150 " 0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS C 150 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 438 " 0.072 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO D 439 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO D 439 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 439 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 589 " -0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C GLN F 589 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN F 589 " -0.025 2.00e-02 2.50e+03 pdb=" N ILE F 590 " -0.023 2.00e-02 2.50e+03 ... (remaining 5190 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 385 2.63 - 3.20: 24878 3.20 - 3.77: 41092 3.77 - 4.33: 55822 4.33 - 4.90: 90807 Nonbonded interactions: 212984 Sorted by model distance: nonbonded pdb=" NH1 ARG C 74 " pdb=" OE2 GLU C 121 " model vdw 2.064 3.120 nonbonded pdb=" OD2 ASP D 462 " pdb="MG MG D2001 " model vdw 2.077 2.170 nonbonded pdb=" NZ LYS C 299 " pdb=" O ASP C 300 " model vdw 2.115 3.120 nonbonded pdb=" NH2 ARG A 33 " pdb=" OD2 ASP A 197 " model vdw 2.132 3.120 nonbonded pdb=" OG SER C 93 " pdb=" OE1 GLU C 126 " model vdw 2.133 3.040 ... (remaining 212979 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 160 or resid 168 through 233)) selection = (chain 'B' and resid 7 through 233) } 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: 1.000 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 24.870 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.371 29346 Z= 0.381 Angle : 1.561 24.999 39613 Z= 0.879 Chirality : 0.078 0.734 4519 Planarity : 0.008 0.111 5193 Dihedral : 13.655 87.233 11297 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 1.53 % Allowed : 7.81 % Favored : 90.66 % Rotamer: Outliers : 5.32 % Allowed : 10.48 % Favored : 84.20 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 2.08 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.11), residues: 3663 helix: -3.11 (0.10), residues: 1268 sheet: -1.59 (0.23), residues: 393 loop : -2.62 (0.12), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG C 821 TYR 0.050 0.005 TYR C 605 PHE 0.049 0.004 PHE C 505 TRP 0.035 0.004 TRP C 997 HIS 0.069 0.003 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00777 (29338) covalent geometry : angle 1.53030 (39601) hydrogen bonds : bond 0.29993 ( 1076) hydrogen bonds : angle 9.05103 ( 3024) metal coordination : bond 0.20308 ( 8) metal coordination : angle 17.80093 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 590 time to evaluate : 0.806 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 THR cc_start: 0.6892 (t) cc_final: 0.5584 (p) REVERT: B 59 VAL cc_start: 0.7768 (t) cc_final: 0.7487 (p) REVERT: B 203 ILE cc_start: 0.2784 (mm) cc_final: 0.2101 (mt) REVERT: C 231 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7290 (pm20) REVERT: C 239 MET cc_start: -0.4549 (ttt) cc_final: -0.4954 (tmm) REVERT: C 436 ARG cc_start: 0.0292 (tpt90) cc_final: -0.0344 (tpt-90) REVERT: C 733 VAL cc_start: -0.0405 (t) cc_final: -0.0685 (t) REVERT: C 764 CYS cc_start: -0.0502 (OUTLIER) cc_final: -0.1882 (p) REVERT: C 773 LEU cc_start: 0.0177 (mt) cc_final: -0.0173 (mt) REVERT: C 895 LEU cc_start: 0.4150 (OUTLIER) cc_final: 0.3513 (pp) REVERT: C 1210 ILE cc_start: 0.2848 (OUTLIER) cc_final: 0.2455 (mt) REVERT: C 1274 GLU cc_start: 0.1076 (mp0) cc_final: 0.0250 (mp0) REVERT: D 1123 ARG cc_start: 0.3004 (mtt90) cc_final: 0.2603 (ptp90) REVERT: D 1221 LEU cc_start: 0.2047 (OUTLIER) cc_final: 0.1216 (tp) REVERT: D 1251 LYS cc_start: -0.0216 (OUTLIER) cc_final: -0.1528 (ttmt) REVERT: D 1261 LEU cc_start: 0.1860 (OUTLIER) cc_final: 0.1582 (pt) REVERT: D 1263 LYS cc_start: 0.5654 (mmtt) cc_final: 0.3858 (tppt) REVERT: F 114 GLU cc_start: 0.2701 (OUTLIER) cc_final: 0.2369 (tp30) REVERT: F 261 LEU cc_start: -0.2493 (OUTLIER) cc_final: -0.3231 (mt) REVERT: F 288 MET cc_start: -0.0615 (ttp) cc_final: -0.2159 (mmt) REVERT: F 345 GLN cc_start: 0.6471 (mt0) cc_final: 0.6018 (pm20) REVERT: F 607 LEU cc_start: 0.7716 (mp) cc_final: 0.7512 (tp) outliers start: 167 outliers final: 31 residues processed: 725 average time/residue: 0.1968 time to fit residues: 215.3067 Evaluate side-chains 349 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 310 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0570 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 93 GLN B 41 ASN B 66 HIS B 132 HIS C 330 HIS C 510 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 GLN ** C1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1220 GLN C1288 GLN C1324 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 594 GLN D1010 GLN D1350 ASN E 29 GLN F 147 GLN ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.137909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.114748 restraints weight = 103666.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.116898 restraints weight = 64943.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.117188 restraints weight = 43997.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.117449 restraints weight = 42282.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.117823 restraints weight = 38292.885| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1868 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29346 Z= 0.173 Angle : 0.805 11.796 39613 Z= 0.418 Chirality : 0.048 0.282 4519 Planarity : 0.006 0.079 5193 Dihedral : 5.918 43.075 4039 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.51 % Favored : 94.29 % Rotamer: Outliers : 0.13 % Allowed : 4.91 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 2.08 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.12), residues: 3663 helix: -0.98 (0.13), residues: 1364 sheet: -0.81 (0.24), residues: 383 loop : -2.10 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 425 TYR 0.026 0.002 TYR B 177 PHE 0.023 0.002 PHE C 80 TRP 0.025 0.001 TRP F 433 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00363 (29338) covalent geometry : angle 0.79890 (39601) hydrogen bonds : bond 0.05510 ( 1076) hydrogen bonds : angle 5.69747 ( 3024) metal coordination : bond 0.00961 ( 8) metal coordination : angle 5.60502 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 359 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash REVERT: B 59 VAL cc_start: 0.7267 (t) cc_final: 0.6952 (p) REVERT: C 239 MET cc_start: -0.2907 (ttt) cc_final: -0.3425 (ttp) REVERT: C 436 ARG cc_start: 0.0186 (tpt90) cc_final: -0.0101 (tpt-90) REVERT: C 527 LYS cc_start: 0.0165 (pttt) cc_final: -0.0608 (tppp) REVERT: C 741 MET cc_start: 0.0127 (tpp) cc_final: -0.0505 (tpp) REVERT: C 881 ASP cc_start: 0.5685 (t0) cc_final: 0.5394 (t0) REVERT: C 1066 MET cc_start: -0.3494 (tpp) cc_final: -0.3697 (tpp) REVERT: D 644 MET cc_start: -0.0684 (ptm) cc_final: -0.0893 (ptm) REVERT: D 697 MET cc_start: 0.5834 (ptm) cc_final: 0.5463 (ptm) REVERT: D 990 ARG cc_start: 0.7582 (ttm170) cc_final: 0.6946 (tpt170) REVERT: D 1210 ILE cc_start: 0.7377 (mt) cc_final: 0.7077 (mp) REVERT: D 1260 MET cc_start: 0.1571 (mmp) cc_final: 0.0602 (tmm) REVERT: F 288 MET cc_start: -0.0388 (ttp) cc_final: -0.2360 (mmt) REVERT: F 345 GLN cc_start: 0.5953 (mt0) cc_final: 0.5632 (pm20) REVERT: F 433 TRP cc_start: 0.2596 (t60) cc_final: 0.1719 (m-10) REVERT: F 435 ILE cc_start: 0.8309 (mt) cc_final: 0.8094 (mm) REVERT: F 545 HIS cc_start: 0.6588 (t-90) cc_final: 0.6267 (t70) outliers start: 4 outliers final: 1 residues processed: 361 average time/residue: 0.1788 time to fit residues: 99.1303 Evaluate side-chains 249 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 347 optimal weight: 0.9980 chunk 181 optimal weight: 0.2980 chunk 190 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 334 optimal weight: 9.9990 chunk 354 optimal weight: 0.3980 chunk 353 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 66 HIS B 132 HIS C 83 GLN ** C 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 767 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN C1146 GLN C1257 GLN D 11 GLN D 113 HIS D 157 GLN D 450 HIS D 594 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.138932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.115886 restraints weight = 105211.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.118457 restraints weight = 71963.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.118294 restraints weight = 48044.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.118794 restraints weight = 44643.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.118921 restraints weight = 39185.067| |-----------------------------------------------------------------------------| r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1833 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29346 Z= 0.135 Angle : 0.688 10.766 39613 Z= 0.353 Chirality : 0.045 0.271 4519 Planarity : 0.005 0.079 5193 Dihedral : 5.387 37.513 4039 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.27 % Favored : 94.59 % Rotamer: Outliers : 0.03 % Allowed : 3.82 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 0.69 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.13), residues: 3663 helix: -0.29 (0.13), residues: 1372 sheet: -0.33 (0.25), residues: 376 loop : -1.80 (0.13), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1174 TYR 0.016 0.001 TYR D1186 PHE 0.034 0.001 PHE C 506 TRP 0.040 0.002 TRP D 868 HIS 0.008 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00282 (29338) covalent geometry : angle 0.68185 (39601) hydrogen bonds : bond 0.04758 ( 1076) hydrogen bonds : angle 5.16771 ( 3024) metal coordination : bond 0.00909 ( 8) metal coordination : angle 5.16622 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.925 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: 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 15 ASP cc_start: 0.7672 (m-30) cc_final: 0.7377 (m-30) REVERT: A 205 MET cc_start: -0.0687 (ttt) cc_final: -0.1070 (ttt) REVERT: C 641 GLU cc_start: 0.4737 (tp30) cc_final: 0.4372 (tp30) REVERT: C 741 MET cc_start: 0.0412 (tpp) cc_final: -0.0297 (tpp) REVERT: C 881 ASP cc_start: 0.5503 (t0) cc_final: 0.5215 (t0) REVERT: C 1066 MET cc_start: -0.3542 (tpp) cc_final: -0.4249 (tpp) REVERT: D 338 PHE cc_start: 0.7297 (t80) cc_final: 0.6837 (t80) REVERT: D 990 ARG cc_start: 0.7478 (ttm170) cc_final: 0.6822 (tpt170) REVERT: D 1210 ILE cc_start: 0.7095 (mt) cc_final: 0.6796 (mp) REVERT: F 288 MET cc_start: -0.0342 (ttp) cc_final: -0.2328 (mmt) REVERT: F 422 ARG cc_start: 0.5370 (mtp-110) cc_final: 0.5133 (ptp-170) REVERT: F 433 TRP cc_start: 0.2653 (t60) cc_final: 0.1837 (m-10) REVERT: F 435 ILE cc_start: 0.8375 (mt) cc_final: 0.8159 (mm) REVERT: F 458 GLU cc_start: 0.4599 (pt0) cc_final: 0.3736 (tp30) REVERT: F 572 THR cc_start: 0.5211 (p) cc_final: 0.4931 (p) outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.1912 time to fit residues: 94.9008 Evaluate side-chains 244 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 331 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 273 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 358 optimal weight: 6.9990 chunk 334 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 265 optimal weight: 7.9990 chunk 122 optimal weight: 0.2980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 66 HIS B 84 ASN B 132 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.140365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.118231 restraints weight = 108234.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.120912 restraints weight = 68700.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.122660 restraints weight = 44156.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.122665 restraints weight = 38647.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.122679 restraints weight = 31976.739| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2039 moved from start: 0.5927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 29346 Z= 0.138 Angle : 0.660 8.508 39613 Z= 0.340 Chirality : 0.045 0.427 4519 Planarity : 0.005 0.094 5193 Dihedral : 5.184 38.317 4039 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.19 % Favored : 94.70 % Rotamer: Outliers : 0.03 % Allowed : 3.76 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 0.69 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.13), residues: 3663 helix: -0.06 (0.13), residues: 1372 sheet: -0.15 (0.26), residues: 362 loop : -1.66 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 91 TYR 0.019 0.001 TYR C 301 PHE 0.026 0.002 PHE C 136 TRP 0.020 0.002 TRP D 868 HIS 0.010 0.001 HIS D 865 Details of bonding type rmsd covalent geometry : bond 0.00285 (29338) covalent geometry : angle 0.65737 (39601) hydrogen bonds : bond 0.03953 ( 1076) hydrogen bonds : angle 4.88587 ( 3024) metal coordination : bond 0.00409 ( 8) metal coordination : angle 3.69897 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 0.724 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: 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 205 MET cc_start: -0.0401 (ttt) cc_final: -0.3158 (mtt) REVERT: C 459 MET cc_start: 0.2113 (tmm) cc_final: 0.0723 (ptm) REVERT: C 741 MET cc_start: 0.0352 (tpp) cc_final: -0.1165 (mmm) REVERT: C 805 MET cc_start: 0.3290 (pmm) cc_final: 0.2249 (ppp) REVERT: C 1030 GLU cc_start: 0.6830 (pp20) cc_final: 0.6014 (mm-30) REVERT: C 1066 MET cc_start: -0.3268 (tpp) cc_final: -0.4101 (tpp) REVERT: D 294 ASN cc_start: 0.7150 (m-40) cc_final: 0.6549 (t0) REVERT: D 338 PHE cc_start: 0.6866 (t80) cc_final: 0.6638 (t80) REVERT: D 372 MET cc_start: 0.0418 (mmt) cc_final: -0.0330 (mmt) REVERT: D 625 MET cc_start: -0.0155 (ptm) cc_final: -0.1004 (ptp) REVERT: D 644 MET cc_start: 0.1017 (ptt) cc_final: 0.0666 (ptt) REVERT: D 990 ARG cc_start: 0.7524 (ttm170) cc_final: 0.6938 (tpt170) REVERT: D 1210 ILE cc_start: 0.6717 (mt) cc_final: 0.6470 (mp) REVERT: D 1370 MET cc_start: 0.2677 (tpp) cc_final: 0.2036 (mmt) REVERT: F 288 MET cc_start: -0.0018 (ttp) cc_final: -0.2139 (mmt) REVERT: F 422 ARG cc_start: 0.5611 (mtp-110) cc_final: 0.5353 (ptt180) REVERT: F 433 TRP cc_start: 0.2595 (t60) cc_final: 0.1818 (m-10) REVERT: F 458 GLU cc_start: 0.4528 (pt0) cc_final: 0.3599 (tp30) REVERT: F 474 MET cc_start: 0.4206 (ppp) cc_final: 0.3814 (ppp) REVERT: F 507 MET cc_start: -0.3956 (ttm) cc_final: -0.4232 (ttt) REVERT: F 583 THR cc_start: 0.5274 (t) cc_final: 0.4888 (m) outliers start: 1 outliers final: 0 residues processed: 300 average time/residue: 0.1700 time to fit residues: 81.8603 Evaluate side-chains 238 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 15 optimal weight: 6.9990 chunk 346 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 57 optimal weight: 0.0030 chunk 357 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 262 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 overall best weight: 2.6154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 132 HIS C 760 ASN C1146 GLN C1257 GLN D 80 HIS D 435 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 HIS D 593 ASN D 700 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.141930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.122049 restraints weight = 112475.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.123993 restraints weight = 73409.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.124894 restraints weight = 48994.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.125825 restraints weight = 39630.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.125811 restraints weight = 35754.789| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2612 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29346 Z= 0.170 Angle : 0.734 9.903 39613 Z= 0.379 Chirality : 0.046 0.262 4519 Planarity : 0.006 0.070 5193 Dihedral : 5.424 33.650 4039 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.01 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.13), residues: 3663 helix: -0.25 (0.13), residues: 1373 sheet: -0.30 (0.26), residues: 369 loop : -1.72 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 158 TYR 0.036 0.002 TYR D1241 PHE 0.028 0.002 PHE D 377 TRP 0.030 0.002 TRP D 868 HIS 0.008 0.001 HIS C1070 Details of bonding type rmsd covalent geometry : bond 0.00368 (29338) covalent geometry : angle 0.73164 (39601) hydrogen bonds : bond 0.04205 ( 1076) hydrogen bonds : angle 5.19080 ( 3024) metal coordination : bond 0.00607 ( 8) metal coordination : angle 3.55370 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.117 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.0053 (ttt) cc_final: -0.2259 (mtt) REVERT: C 92 TYR cc_start: 0.3865 (t80) cc_final: 0.3577 (t80) REVERT: C 628 HIS cc_start: 0.5920 (p-80) cc_final: 0.5623 (p-80) REVERT: C 741 MET cc_start: 0.0840 (tpp) cc_final: -0.1009 (mmm) REVERT: C 805 MET cc_start: 0.3449 (pmm) cc_final: 0.1111 (tmm) REVERT: C 899 GLU cc_start: 0.5708 (pt0) cc_final: 0.4611 (mp0) REVERT: C 1034 ARG cc_start: 0.8044 (ptm-80) cc_final: 0.7809 (ptm-80) REVERT: C 1243 MET cc_start: 0.0055 (tpt) cc_final: -0.0428 (tpt) REVERT: D 294 ASN cc_start: 0.7158 (m-40) cc_final: 0.6801 (t0) REVERT: D 372 MET cc_start: 0.0564 (mmt) cc_final: 0.0127 (mmt) REVERT: D 625 MET cc_start: 0.1120 (ptm) cc_final: -0.0111 (ptp) REVERT: D 658 GLU cc_start: 0.7199 (tt0) cc_final: 0.6843 (mt-10) REVERT: D 837 ASP cc_start: 0.6861 (m-30) cc_final: 0.6611 (m-30) REVERT: D 990 ARG cc_start: 0.7978 (ttm170) cc_final: 0.7266 (tpt170) REVERT: F 273 MET cc_start: -0.5397 (mtm) cc_final: -0.5932 (mtm) REVERT: F 288 MET cc_start: 0.0269 (ttp) cc_final: -0.1953 (mmt) REVERT: F 365 MET cc_start: -0.2841 (mtp) cc_final: -0.3141 (tpt) REVERT: F 422 ARG cc_start: 0.5782 (mtp-110) cc_final: 0.5577 (ptp-170) REVERT: F 507 MET cc_start: -0.3645 (ttm) cc_final: -0.3921 (ttt) REVERT: F 583 THR cc_start: 0.5446 (t) cc_final: 0.5067 (m) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1803 time to fit residues: 86.6873 Evaluate side-chains 244 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 348 optimal weight: 5.9990 chunk 364 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 204 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 327 optimal weight: 30.0000 chunk 24 optimal weight: 0.5980 chunk 302 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 66 HIS ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN C1257 GLN D 294 ASN D 465 GLN D 593 ASN ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.142457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.122117 restraints weight = 111902.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.124569 restraints weight = 70803.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.125336 restraints weight = 45835.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.126661 restraints weight = 37673.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.126505 restraints weight = 34315.210| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2533 moved from start: 0.7488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 29346 Z= 0.120 Angle : 0.636 9.478 39613 Z= 0.326 Chirality : 0.044 0.190 4519 Planarity : 0.005 0.087 5193 Dihedral : 5.050 33.102 4039 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.05 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 0.69 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.13), residues: 3663 helix: 0.06 (0.13), residues: 1382 sheet: -0.24 (0.26), residues: 396 loop : -1.51 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 780 TYR 0.019 0.001 TYR D1241 PHE 0.027 0.001 PHE D 620 TRP 0.032 0.002 TRP C 807 HIS 0.008 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00263 (29338) covalent geometry : angle 0.63484 (39601) hydrogen bonds : bond 0.03634 ( 1076) hydrogen bonds : angle 4.85615 ( 3024) metal coordination : bond 0.00349 ( 8) metal coordination : angle 2.49001 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.911 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: symmetry clash REVERT: A 205 MET cc_start: 0.0756 (ttt) cc_final: -0.1017 (mtt) REVERT: C 92 TYR cc_start: 0.3227 (t80) cc_final: 0.2990 (t80) REVERT: C 409 LEU cc_start: 0.5979 (mp) cc_final: 0.4714 (mp) REVERT: C 459 MET cc_start: 0.1762 (tmm) cc_final: -0.1022 (ptp) REVERT: C 486 THR cc_start: 0.5328 (m) cc_final: 0.4367 (m) REVERT: C 741 MET cc_start: 0.0551 (tpp) cc_final: -0.1338 (mmm) REVERT: C 768 MET cc_start: -0.2395 (mtp) cc_final: -0.3534 (tpt) REVERT: C 805 MET cc_start: 0.3321 (pmm) cc_final: 0.1096 (tmm) REVERT: C 899 GLU cc_start: 0.5770 (pt0) cc_final: 0.4665 (mp0) REVERT: C 1030 GLU cc_start: 0.6765 (pp20) cc_final: 0.5806 (mp0) REVERT: C 1066 MET cc_start: -0.1833 (tpp) cc_final: -0.2581 (tpp) REVERT: D 137 ARG cc_start: 0.5809 (ttt90) cc_final: 0.5203 (ptm-80) REVERT: D 161 THR cc_start: 0.7644 (m) cc_final: 0.7297 (m) REVERT: D 372 MET cc_start: 0.0163 (mmt) cc_final: -0.0287 (mmt) REVERT: D 625 MET cc_start: 0.0216 (ptm) cc_final: -0.0308 (ptm) REVERT: D 658 GLU cc_start: 0.7110 (tt0) cc_final: 0.6750 (mt-10) REVERT: D 837 ASP cc_start: 0.6970 (m-30) cc_final: 0.6606 (p0) REVERT: D 1241 TYR cc_start: 0.2739 (m-80) cc_final: 0.1112 (m-80) REVERT: F 273 MET cc_start: -0.5193 (mtm) cc_final: -0.5875 (mtm) REVERT: F 288 MET cc_start: 0.0258 (ttp) cc_final: -0.1933 (mmt) REVERT: F 422 ARG cc_start: 0.5675 (mtp-110) cc_final: 0.5453 (ptp-170) REVERT: F 433 TRP cc_start: 0.2401 (t60) cc_final: 0.1606 (m-10) REVERT: F 507 MET cc_start: -0.3855 (ttm) cc_final: -0.4104 (ttt) REVERT: F 583 THR cc_start: 0.5415 (t) cc_final: 0.5025 (m) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1675 time to fit residues: 76.5951 Evaluate side-chains 234 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 113 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 317 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 5 optimal weight: 0.1980 chunk 76 optimal weight: 10.0000 chunk 312 optimal weight: 0.0060 chunk 302 optimal weight: 7.9990 chunk 297 optimal weight: 8.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 66 HIS ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 618 GLN C 684 ASN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.142908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.123385 restraints weight = 113596.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.125436 restraints weight = 71198.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.126113 restraints weight = 50171.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.127205 restraints weight = 39139.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.127137 restraints weight = 36022.982| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2650 moved from start: 0.7836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29346 Z= 0.114 Angle : 0.627 7.891 39613 Z= 0.321 Chirality : 0.043 0.188 4519 Planarity : 0.005 0.070 5193 Dihedral : 4.983 34.689 4039 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.41 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 0.69 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.13), residues: 3663 helix: 0.19 (0.14), residues: 1389 sheet: -0.30 (0.26), residues: 400 loop : -1.49 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1203 TYR 0.019 0.001 TYR F 137 PHE 0.026 0.001 PHE D 620 TRP 0.019 0.001 TRP C 807 HIS 0.005 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00247 (29338) covalent geometry : angle 0.62622 (39601) hydrogen bonds : bond 0.03501 ( 1076) hydrogen bonds : angle 4.81545 ( 3024) metal coordination : bond 0.00291 ( 8) metal coordination : angle 2.10793 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 1.202 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 205 MET cc_start: 0.1211 (ttt) cc_final: -0.0458 (mtt) REVERT: C 459 MET cc_start: 0.1572 (tmm) cc_final: -0.1191 (ptp) REVERT: C 741 MET cc_start: 0.0119 (tpp) cc_final: -0.1877 (mmm) REVERT: C 768 MET cc_start: -0.2321 (mtp) cc_final: -0.3503 (tpt) REVERT: C 805 MET cc_start: 0.3505 (pmm) cc_final: 0.1175 (tmm) REVERT: C 1030 GLU cc_start: 0.6575 (pp20) cc_final: 0.5645 (mp0) REVERT: C 1066 MET cc_start: -0.1539 (tpp) cc_final: -0.2384 (tpp) REVERT: C 1243 MET cc_start: 0.0638 (tpt) cc_final: 0.0021 (tpt) REVERT: D 293 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7344 (ppt170) REVERT: D 372 MET cc_start: 0.0285 (mmt) cc_final: -0.0282 (tpp) REVERT: D 658 GLU cc_start: 0.7125 (tt0) cc_final: 0.6806 (mt-10) REVERT: D 789 LYS cc_start: 0.1016 (pttp) cc_final: 0.0458 (mttm) REVERT: D 837 ASP cc_start: 0.6756 (m-30) cc_final: 0.6518 (p0) REVERT: D 1241 TYR cc_start: 0.3345 (m-80) cc_final: 0.1837 (m-80) REVERT: F 288 MET cc_start: 0.0229 (ttp) cc_final: -0.1928 (mmt) REVERT: F 422 ARG cc_start: 0.5822 (mtp-110) cc_final: 0.5539 (ptp-170) REVERT: F 433 TRP cc_start: 0.2114 (t60) cc_final: 0.1383 (m-10) REVERT: F 583 THR cc_start: 0.5319 (t) cc_final: 0.4995 (m) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.1855 time to fit residues: 83.3396 Evaluate side-chains 234 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 8 optimal weight: 0.0010 chunk 16 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 265 optimal weight: 10.0000 chunk 348 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 269 optimal weight: 7.9990 chunk 282 optimal weight: 40.0000 chunk 77 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS B 66 HIS ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.143278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.123701 restraints weight = 112569.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.125808 restraints weight = 74816.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.126376 restraints weight = 49835.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.126821 restraints weight = 44577.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.126956 restraints weight = 41685.408| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2651 moved from start: 0.8201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29346 Z= 0.112 Angle : 0.624 9.875 39613 Z= 0.318 Chirality : 0.043 0.234 4519 Planarity : 0.005 0.079 5193 Dihedral : 4.910 32.983 4039 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.13), residues: 3663 helix: 0.30 (0.14), residues: 1387 sheet: -0.28 (0.26), residues: 392 loop : -1.40 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 332 TYR 0.016 0.001 TYR F 137 PHE 0.038 0.001 PHE D 620 TRP 0.015 0.001 TRP D 868 HIS 0.007 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00242 (29338) covalent geometry : angle 0.62330 (39601) hydrogen bonds : bond 0.03414 ( 1076) hydrogen bonds : angle 4.76313 ( 3024) metal coordination : bond 0.00514 ( 8) metal coordination : angle 2.16785 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.092 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 13 LEU cc_start: 0.5538 (pt) cc_final: 0.4894 (tt) REVERT: A 205 MET cc_start: 0.1170 (ttt) cc_final: -0.0334 (mtt) REVERT: B 205 MET cc_start: 0.2901 (pmm) cc_final: 0.2389 (pmm) REVERT: B 211 ILE cc_start: 0.1581 (mm) cc_final: 0.1256 (mp) REVERT: C 124 MET cc_start: 0.6343 (mpp) cc_final: 0.4577 (mmp) REVERT: C 459 MET cc_start: 0.1624 (tmm) cc_final: -0.1014 (ptp) REVERT: C 741 MET cc_start: -0.0079 (tpp) cc_final: -0.2087 (mmm) REVERT: C 768 MET cc_start: -0.2030 (mtp) cc_final: -0.3302 (tpt) REVERT: C 804 PHE cc_start: 0.1758 (m-80) cc_final: 0.1525 (m-10) REVERT: C 805 MET cc_start: 0.3344 (pmm) cc_final: 0.2514 (ppp) REVERT: C 1030 GLU cc_start: 0.6845 (pp20) cc_final: 0.5693 (mp0) REVERT: C 1066 MET cc_start: -0.1438 (tpp) cc_final: -0.1979 (tpp) REVERT: C 1073 LYS cc_start: 0.3870 (ttmt) cc_final: 0.3635 (mmtt) REVERT: C 1230 MET cc_start: 0.3849 (pmm) cc_final: 0.3457 (pmm) REVERT: C 1243 MET cc_start: 0.1368 (tpt) cc_final: 0.0582 (tpt) REVERT: D 137 ARG cc_start: 0.5871 (ttt90) cc_final: 0.5505 (ptm-80) REVERT: D 293 ARG cc_start: 0.7626 (mmt180) cc_final: 0.7384 (ppt170) REVERT: D 372 MET cc_start: 0.0504 (mmt) cc_final: -0.0075 (tpp) REVERT: D 466 MET cc_start: 0.1998 (ppp) cc_final: 0.1675 (ppp) REVERT: D 625 MET cc_start: 0.0193 (ptm) cc_final: -0.0418 (mtp) REVERT: D 644 MET cc_start: -0.0418 (ptt) cc_final: -0.0771 (ptm) REVERT: D 658 GLU cc_start: 0.7130 (tt0) cc_final: 0.6849 (mt-10) REVERT: D 799 ARG cc_start: 0.5671 (mtm180) cc_final: 0.5452 (mmt-90) REVERT: D 822 MET cc_start: -0.1981 (ppp) cc_final: -0.3962 (mmm) REVERT: D 1241 TYR cc_start: 0.3303 (m-80) cc_final: 0.1943 (m-80) REVERT: D 1370 MET cc_start: 0.3227 (tpp) cc_final: 0.2509 (ppp) REVERT: F 276 MET cc_start: 0.0584 (mmm) cc_final: -0.0379 (mtt) REVERT: F 288 MET cc_start: 0.0773 (ttp) cc_final: -0.1409 (mmt) REVERT: F 433 TRP cc_start: 0.2110 (t60) cc_final: 0.1336 (m-10) REVERT: F 508 GLU cc_start: 0.3119 (mm-30) cc_final: 0.1848 (mp0) REVERT: F 583 THR cc_start: 0.5465 (t) cc_final: 0.5130 (m) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.2001 time to fit residues: 91.7339 Evaluate side-chains 239 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 291 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 331 optimal weight: 30.0000 chunk 46 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 268 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 143 optimal weight: 0.0570 overall best weight: 4.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN B 41 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN C 69 GLN ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 437 ASN C 462 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN C1061 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 593 ASN ** D 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 690 ASN D 700 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D1195 GLN D1218 HIS D1244 GLN D1252 HIS E 7 GLN ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.145497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.128173 restraints weight = 123452.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.129933 restraints weight = 85956.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.131545 restraints weight = 58470.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.131957 restraints weight = 44161.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.132117 restraints weight = 38727.338| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3723 moved from start: 1.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 29346 Z= 0.277 Angle : 1.058 19.067 39613 Z= 0.550 Chirality : 0.058 0.414 4519 Planarity : 0.009 0.156 5193 Dihedral : 7.021 40.982 4039 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.67 % Favored : 92.22 % Rotamer: Outliers : 0.10 % Allowed : 1.62 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.12), residues: 3663 helix: -1.00 (0.13), residues: 1385 sheet: -1.12 (0.26), residues: 356 loop : -2.04 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.001 ARG A 91 TYR 0.043 0.004 TYR C 73 PHE 0.037 0.004 PHE C 804 TRP 0.039 0.004 TRP C 183 HIS 0.016 0.003 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00613 (29338) covalent geometry : angle 1.04926 (39601) hydrogen bonds : bond 0.05820 ( 1076) hydrogen bonds : angle 6.45963 ( 3024) metal coordination : bond 0.01505 ( 8) metal coordination : angle 8.02533 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 352 time to evaluate : 1.168 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.3537 (ttt) cc_final: 0.2278 (mtt) REVERT: B 135 ASP cc_start: 0.7164 (t0) cc_final: 0.6715 (t0) REVERT: C 741 MET cc_start: 0.1265 (tpp) cc_final: 0.0394 (tpp) REVERT: C 805 MET cc_start: 0.3780 (pmm) cc_final: 0.2263 (tmm) REVERT: C 899 GLU cc_start: 0.5674 (pt0) cc_final: 0.4515 (mp0) REVERT: C 1119 MET cc_start: 0.5275 (tpp) cc_final: 0.5006 (tpt) REVERT: C 1230 MET cc_start: 0.6389 (pmm) cc_final: 0.5283 (pmm) REVERT: D 137 ARG cc_start: 0.5924 (ttt90) cc_final: 0.5528 (ptm-80) REVERT: D 330 MET cc_start: 0.4694 (mpp) cc_final: 0.4234 (tpp) REVERT: D 658 GLU cc_start: 0.7675 (tt0) cc_final: 0.7454 (mt-10) REVERT: D 1370 MET cc_start: 0.3590 (tpp) cc_final: 0.3233 (ppp) REVERT: F 413 MET cc_start: 0.1527 (ptt) cc_final: 0.1297 (ptt) REVERT: F 433 TRP cc_start: 0.3033 (t60) cc_final: 0.2008 (m-10) REVERT: F 466 ILE cc_start: 0.6533 (mt) cc_final: 0.6319 (tt) REVERT: F 583 THR cc_start: 0.5761 (t) cc_final: 0.5388 (m) outliers start: 3 outliers final: 0 residues processed: 355 average time/residue: 0.2007 time to fit residues: 113.4939 Evaluate side-chains 285 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 348 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 191 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 162 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 HIS B 37 HIS B 66 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS D 80 HIS ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 419 HIS ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 594 GLN D 690 ASN D 700 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN D1244 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1252 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.146878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.127883 restraints weight = 118998.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.130554 restraints weight = 76701.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.131644 restraints weight = 54533.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.133116 restraints weight = 37096.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.133216 restraints weight = 29343.875| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3451 moved from start: 1.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 29346 Z= 0.144 Angle : 0.746 11.648 39613 Z= 0.382 Chirality : 0.046 0.306 4519 Planarity : 0.005 0.060 5193 Dihedral : 5.846 33.002 4039 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.71 % Favored : 94.19 % Rotamer: Outliers : 0.03 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 0.69 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.13), residues: 3663 helix: -0.51 (0.13), residues: 1400 sheet: -1.15 (0.26), residues: 339 loop : -1.76 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 182 TYR 0.030 0.002 TYR D1241 PHE 0.031 0.002 PHE D 620 TRP 0.072 0.003 TRP C1276 HIS 0.007 0.001 HIS C 673 Details of bonding type rmsd covalent geometry : bond 0.00325 (29338) covalent geometry : angle 0.74078 (39601) hydrogen bonds : bond 0.04124 ( 1076) hydrogen bonds : angle 5.43317 ( 3024) metal coordination : bond 0.00806 ( 8) metal coordination : angle 4.91662 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7326 Ramachandran restraints generated. 3663 Oldfield, 0 Emsley, 3663 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.091 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: symmetry clash REVERT: A 205 MET cc_start: 0.3910 (ttt) cc_final: 0.3214 (mtp) REVERT: C 668 ILE cc_start: 0.4458 (mt) cc_final: 0.3175 (tp) REVERT: C 741 MET cc_start: 0.0954 (tpp) cc_final: -0.1077 (mmm) REVERT: C 773 LEU cc_start: 0.1956 (mt) cc_final: 0.1341 (mt) REVERT: C 805 MET cc_start: 0.3489 (pmm) cc_final: 0.2064 (ttt) REVERT: C 899 GLU cc_start: 0.5498 (pt0) cc_final: 0.4835 (mp0) REVERT: C 1034 ARG cc_start: 0.7305 (tpm170) cc_final: 0.7013 (ptp90) REVERT: C 1057 LYS cc_start: 0.4014 (tptp) cc_final: 0.3269 (pptt) REVERT: C 1073 LYS cc_start: 0.4612 (ttmt) cc_final: 0.4289 (mmtt) REVERT: C 1119 MET cc_start: 0.5049 (tpp) cc_final: 0.4673 (tpt) REVERT: C 1230 MET cc_start: 0.5240 (pmm) cc_final: 0.3947 (pmm) REVERT: C 1243 MET cc_start: 0.3050 (tpt) cc_final: 0.2648 (tpp) REVERT: D 137 ARG cc_start: 0.6170 (ttt90) cc_final: 0.5603 (ptm-80) REVERT: D 372 MET cc_start: 0.0038 (mmt) cc_final: -0.0332 (mmt) REVERT: D 381 ILE cc_start: 0.5350 (mp) cc_final: 0.4734 (mm) REVERT: D 382 TYR cc_start: 0.5414 (m-10) cc_final: 0.5101 (m-10) REVERT: D 424 ASN cc_start: 0.5830 (m110) cc_final: 0.5461 (m-40) REVERT: D 747 MET cc_start: 0.2732 (mmp) cc_final: 0.2400 (mmp) REVERT: D 1198 VAL cc_start: 0.3470 (p) cc_final: 0.3221 (m) REVERT: F 433 TRP cc_start: 0.2661 (t60) cc_final: 0.1873 (m-10) REVERT: F 583 THR cc_start: 0.5665 (t) cc_final: 0.5202 (m) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.1780 time to fit residues: 91.3375 Evaluate side-chains 268 residues out of total 3153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 156 optimal weight: 6.9990 chunk 320 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 chunk 230 optimal weight: 0.9990 chunk 339 optimal weight: 20.0000 chunk 1 optimal weight: 0.0570 chunk 237 optimal weight: 0.3980 chunk 99 optimal weight: 40.0000 chunk 71 optimal weight: 8.9990 chunk 336 optimal weight: 0.0010 chunk 27 optimal weight: 0.9990 overall best weight: 0.4908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** C 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 HIS C 686 GLN C 832 HIS ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN C1070 HIS C1090 ASN C1108 ASN ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 594 GLN D 700 ASN ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.147371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.129856 restraints weight = 121975.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.131382 restraints weight = 83568.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.132205 restraints weight = 61191.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.132408 restraints weight = 53830.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.132714 restraints weight = 49156.576| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3362 moved from start: 1.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29346 Z= 0.126 Angle : 0.689 10.932 39613 Z= 0.352 Chirality : 0.045 0.203 4519 Planarity : 0.005 0.078 5193 Dihedral : 5.354 33.007 4039 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.62 % Favored : 94.29 % Rotamer: Outliers : 0.03 % Allowed : 0.13 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.39 % Cis-general : 0.28 % Twisted Proline : 0.69 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.13), residues: 3663 helix: -0.11 (0.14), residues: 1398 sheet: -0.88 (0.27), residues: 351 loop : -1.60 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D 431 TYR 0.018 0.001 TYR C 172 PHE 0.024 0.002 PHE C 506 TRP 0.060 0.002 TRP C1276 HIS 0.009 0.001 HIS C1313 Details of bonding type rmsd covalent geometry : bond 0.00275 (29338) covalent geometry : angle 0.68712 (39601) hydrogen bonds : bond 0.03636 ( 1076) hydrogen bonds : angle 5.06760 ( 3024) metal coordination : bond 0.00410 ( 8) metal coordination : angle 3.29886 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4456.88 seconds wall clock time: 77 minutes 56.13 seconds (4676.13 seconds total)