Starting phenix.real_space_refine on Sat Mar 7 03:25:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfv_71615/03_2026/9pfv_71615.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfv_71615/03_2026/9pfv_71615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pfv_71615/03_2026/9pfv_71615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfv_71615/03_2026/9pfv_71615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pfv_71615/03_2026/9pfv_71615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfv_71615/03_2026/9pfv_71615.map" } resolution = 3.7 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= 0.010 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 125 5.49 5 Mg 1 5.21 5 S 126 5.16 5 C 22446 2.51 5 N 6504 2.21 5 O 7124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36328 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1771 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 218} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2388 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 20, 'TRANS': 303} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 5, 'ASP:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "C" Number of atoms: 10286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 10286 Classifications: {'peptide': 1353} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 64, 'TRANS': 1288} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 14, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 17, 'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 205 Chain: "D" Number of atoms: 10121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1342, 10121 Classifications: {'peptide': 1342} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1278} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 18, 'ASP:plan': 7, 'ASN:plan1': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 186 Chain: "E" Number of atoms: 511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 511 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 3757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3757 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 12, 'TRANS': 477} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 19, 'GLU:plan': 4, 'TRP:plan': 1, 'PHE:plan': 3, 'TYR:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "H" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1340 Classifications: {'DNA': 66} Link IDs: {'rna3p': 65} Chain: "I" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1093 Classifications: {'DNA': 53} Link IDs: {'rna3p': 52} Chain breaks: 1 Chain: "Q" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2474 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 309} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Chain: "R" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2462 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 306} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 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 14910 SG CYS D 71 107.901 109.758 82.647 1.00 87.75 S ATOM 14924 SG CYS D 73 106.767 114.084 83.760 1.00 84.51 S ATOM 20626 SG CYS D 810 100.121 42.945 85.727 1.00 65.06 S ATOM 21156 SG CYS D 884 98.112 46.119 86.321 1.00 54.80 S ATOM 21204 SG CYS D 891 99.051 45.381 82.989 1.00 59.82 S ATOM 21219 SG CYS D 894 96.503 43.247 84.105 1.00 57.19 S Time building chain proxies: 7.89, per 1000 atoms: 0.22 Number of scatterers: 36328 At special positions: 0 Unit cell: (146.88, 194.4, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 126 16.00 P 125 15.00 Mg 1 11.99 O 7124 8.00 N 6504 7.00 C 22446 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: 3.16 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 73 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 71 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 894 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 884 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 810 " Number of angles added : 6 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8214 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 58 sheets defined 42.3% alpha, 11.0% beta 27 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.917A pdb=" N LEU A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 removed outlier: 3.670A pdb=" N VAL A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.778A pdb=" N THR B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER B 52 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.543A pdb=" N LEU B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 211 through 228 removed outlier: 3.744A pdb=" N GLN B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 233 through 245 removed outlier: 4.476A pdb=" N LYS B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 264 through 275 removed outlier: 3.688A pdb=" N LEU B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 274 " --> pdb=" O CYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 removed outlier: 4.241A pdb=" N GLN B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.885A pdb=" N LEU B 301 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 312 removed outlier: 3.648A pdb=" N LEU B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 Processing helix chain 'C' and resid 52 through 61 removed outlier: 3.808A pdb=" N VAL C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 4.108A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLN C 91 " --> pdb=" O GLU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.576A pdb=" N GLU C 225 " --> pdb=" O ASP C 222 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 226 " --> pdb=" O GLY C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 removed outlier: 3.538A pdb=" N LYS C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 285 " --> pdb=" O GLN C 281 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 4.143A pdb=" N GLY C 302 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 355 through 361 Processing helix chain 'C' and resid 366 through 379 Processing helix chain 'C' and resid 386 through 398 removed outlier: 3.554A pdb=" N GLU C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 418 Processing helix chain 'C' and resid 429 through 445 removed outlier: 4.118A pdb=" N ASP C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 463 through 490 removed outlier: 3.793A pdb=" N LEU C 467 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 488 " --> pdb=" O LYS C 484 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER C 489 " --> pdb=" O GLU C 485 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL C 490 " --> pdb=" O ARG C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 516 Processing helix chain 'C' and resid 527 through 535 Processing helix chain 'C' and resid 548 through 552 removed outlier: 3.539A pdb=" N ALA C 551 " --> pdb=" O ARG C 548 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 548 through 552' Processing helix chain 'C' and resid 559 through 563 removed outlier: 3.660A pdb=" N TYR C 563 " --> pdb=" O PRO C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 667 removed outlier: 3.895A pdb=" N VAL C 667 " --> pdb=" O PRO C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.652A pdb=" N LEU C 674 " --> pdb=" O VAL C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 693 removed outlier: 4.117A pdb=" N MET C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 removed outlier: 4.098A pdb=" N ALA C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 831 Processing helix chain 'C' and resid 864 through 868 Processing helix chain 'C' and resid 902 through 913 Processing helix chain 'C' and resid 948 through 982 Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1012 through 1018 removed outlier: 3.613A pdb=" N TRP C1016 " --> pdb=" O GLY C1013 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C1018 " --> pdb=" O TRP C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1055 removed outlier: 4.311A pdb=" N SER C1031 " --> pdb=" O GLY C1027 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C1032 " --> pdb=" O GLU C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1117 through 1121 removed outlier: 3.521A pdb=" N GLY C1120 " --> pdb=" O ASN C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1151 removed outlier: 3.546A pdb=" N LEU C1142 " --> pdb=" O ALA C1138 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY C1143 " --> pdb=" O CYS C1139 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C1144 " --> pdb=" O ALA C1140 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C1149 " --> pdb=" O GLN C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1152 through 1154 No H-bonds generated for 'chain 'C' and resid 1152 through 1154' Processing helix chain 'C' and resid 1160 through 1170 Processing helix chain 'C' and resid 1179 through 1189 removed outlier: 3.842A pdb=" N GLU C1185 " --> pdb=" O GLU C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1205 through 1217 Processing helix chain 'C' and resid 1275 through 1279 Processing helix chain 'C' and resid 1285 through 1296 Processing helix chain 'C' and resid 1298 through 1306 Processing helix chain 'C' and resid 1314 through 1325 removed outlier: 3.710A pdb=" N TYR C1319 " --> pdb=" O ARG C1315 " (cutoff:3.500A) Processing helix chain 'C' and resid 1334 through 1346 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 71 through 75 removed outlier: 4.039A pdb=" N GLY D 74 " --> pdb=" O CYS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 114 through 120 removed outlier: 3.537A pdb=" N LEU D 118 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER D 120 " --> pdb=" O TRP D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 162 through 173 Processing helix chain 'D' and resid 182 through 193 removed outlier: 3.553A pdb=" N ALA D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 193 " --> pdb=" O ASN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.738A pdb=" N LYS D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 233 " --> pdb=" O PHE D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 239 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.910A pdb=" N ASP D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 310 Processing helix chain 'D' and resid 330 through 335 removed outlier: 3.648A pdb=" N LYS D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY D 335 " --> pdb=" O ASP D 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 330 through 335' Processing helix chain 'D' and resid 338 through 344 Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'D' and resid 379 through 390 removed outlier: 4.069A pdb=" N ASP D 388 " --> pdb=" O TYR D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 409 through 418 removed outlier: 3.799A pdb=" N ILE D 413 " --> pdb=" O GLN D 409 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 436 removed outlier: 3.772A pdb=" N ILE D 436 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 460 removed outlier: 4.488A pdb=" N ALA D 458 " --> pdb=" O LEU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 487 through 491 Processing helix chain 'D' and resid 506 through 516 removed outlier: 3.699A pdb=" N LEU D 510 " --> pdb=" O GLN D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 541 Processing helix chain 'D' and resid 571 through 579 removed outlier: 3.516A pdb=" N ALA D 579 " --> pdb=" O MET D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.536A pdb=" N LEU D 591 " --> pdb=" O GLY D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 635 removed outlier: 3.782A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.585A pdb=" N ILE D 644 " --> pdb=" O LYS D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 666 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.197A pdb=" N TRP D 686 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA D 687 " --> pdb=" O VAL D 683 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET D 703 " --> pdb=" O ALA D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 724 Processing helix chain 'D' and resid 729 through 738 Processing helix chain 'D' and resid 764 through 800 removed outlier: 3.828A pdb=" N HIS D 773 " --> pdb=" O PHE D 769 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY D 774 " --> pdb=" O ASN D 770 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY D 778 " --> pdb=" O GLY D 774 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 779 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR D 786 " --> pdb=" O THR D 782 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA D 787 " --> pdb=" O ALA D 783 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN D 788 " --> pdb=" O LEU D 784 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 836 Processing helix chain 'D' and resid 861 through 871 removed outlier: 3.657A pdb=" N ALA D 867 " --> pdb=" O ASN D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 921 Processing helix chain 'D' and resid 1128 through 1138 Processing helix chain 'D' and resid 1212 through 1220 Processing helix chain 'D' and resid 1221 through 1241 removed outlier: 4.030A pdb=" N VAL D1236 " --> pdb=" O GLU D1232 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR D1237 " --> pdb=" O ILE D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1245 through 1257 removed outlier: 4.332A pdb=" N ILE D1249 " --> pdb=" O ASN D1245 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D1257 " --> pdb=" O VAL D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1277 through 1292 removed outlier: 3.744A pdb=" N ARG D1291 " --> pdb=" O LYS D1287 " (cutoff:3.500A) Processing helix chain 'D' and resid 1304 through 1309 Processing helix chain 'D' and resid 1315 through 1322 removed outlier: 3.769A pdb=" N GLN D1322 " --> pdb=" O ALA D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1335 Processing helix chain 'D' and resid 1342 through 1349 Processing helix chain 'D' and resid 1356 through 1378 removed outlier: 3.524A pdb=" N TYR D1360 " --> pdb=" O GLY D1356 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLN D1378 " --> pdb=" O GLN D1374 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 removed outlier: 4.326A pdb=" N CYS E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.568A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 44 through 54 removed outlier: 3.842A pdb=" N LEU E 50 " --> pdb=" O PRO E 46 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 64 removed outlier: 4.488A pdb=" N GLY E 62 " --> pdb=" O ASP E 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 125 removed outlier: 3.843A pdb=" N LEU F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 152 removed outlier: 4.326A pdb=" N ILE F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA F 136 " --> pdb=" O GLU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 removed outlier: 3.968A pdb=" N VAL F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 189 Processing helix chain 'F' and resid 244 through 260 removed outlier: 3.684A pdb=" N SER F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU F 257 " --> pdb=" O ALA F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 275 removed outlier: 3.618A pdb=" N ASP F 266 " --> pdb=" O ARG F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 299 removed outlier: 3.891A pdb=" N ARG F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY F 288 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR F 299 " --> pdb=" O GLN F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 336 removed outlier: 3.546A pdb=" N GLN F 313 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA F 316 " --> pdb=" O GLU F 312 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 331 " --> pdb=" O ARG F 327 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER F 334 " --> pdb=" O ARG F 330 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY F 336 " --> pdb=" O ALA F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 348 removed outlier: 3.511A pdb=" N LEU F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS F 344 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 357 Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 369 through 392 removed outlier: 3.949A pdb=" N GLN F 375 " --> pdb=" O GLU F 371 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER F 376 " --> pdb=" O ASN F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 423 removed outlier: 3.696A pdb=" N ALA F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN F 423 " --> pdb=" O MET F 419 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 431 removed outlier: 4.169A pdb=" N VAL F 427 " --> pdb=" O ASN F 423 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 428 " --> pdb=" O LEU F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 456 Processing helix chain 'F' and resid 457 through 459 No H-bonds generated for 'chain 'F' and resid 457 through 459' Processing helix chain 'F' and resid 466 through 486 removed outlier: 4.073A pdb=" N TYR F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP F 473 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP F 474 " --> pdb=" O TYR F 470 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA F 478 " --> pdb=" O TRP F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 512 removed outlier: 3.956A pdb=" N THR F 499 " --> pdb=" O HIS F 495 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS F 512 " --> pdb=" O ARG F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 527 removed outlier: 4.961A pdb=" N GLU F 525 " --> pdb=" O GLU F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 537 Processing helix chain 'F' and resid 570 through 589 removed outlier: 3.694A pdb=" N ALA F 589 " --> pdb=" O THR F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 592 through 603 removed outlier: 3.918A pdb=" N LEU F 599 " --> pdb=" O GLU F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 621 Processing helix chain 'F' and resid 626 through 639 Processing helix chain 'F' and resid 644 through 649 removed outlier: 4.020A pdb=" N SER F 649 " --> pdb=" O ARG F 645 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 20 removed outlier: 4.188A pdb=" N ALA Q 6 " --> pdb=" O ARG Q 2 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR Q 7 " --> pdb=" O HIS Q 3 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA Q 20 " --> pdb=" O LEU Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 32 removed outlier: 3.600A pdb=" N ALA Q 30 " --> pdb=" O ASP Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 78 through 96 removed outlier: 4.353A pdb=" N ALA Q 84 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU Q 85 " --> pdb=" O GLU Q 81 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG Q 86 " --> pdb=" O LEU Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 113 removed outlier: 3.635A pdb=" N LEU Q 107 " --> pdb=" O SER Q 103 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU Q 108 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA Q 109 " --> pdb=" O TYR Q 105 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS Q 110 " --> pdb=" O ALA Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 124 removed outlier: 4.451A pdb=" N ARG Q 121 " --> pdb=" O GLY Q 117 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG Q 122 " --> pdb=" O SER Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 133 Processing helix chain 'Q' and resid 147 through 159 Processing helix chain 'Q' and resid 209 through 211 No H-bonds generated for 'chain 'Q' and resid 209 through 211' Processing helix chain 'Q' and resid 228 through 234 Processing helix chain 'Q' and resid 255 through 261 removed outlier: 3.691A pdb=" N ARG Q 261 " --> pdb=" O GLU Q 257 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 295 removed outlier: 4.085A pdb=" N TRP Q 292 " --> pdb=" O ARG Q 288 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS Q 293 " --> pdb=" O GLU Q 289 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 311 removed outlier: 3.587A pdb=" N LYS Q 310 " --> pdb=" O PRO Q 306 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP Q 311 " --> pdb=" O GLN Q 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 306 through 311' Processing helix chain 'Q' and resid 312 through 325 removed outlier: 4.134A pdb=" N GLU Q 316 " --> pdb=" O MET Q 312 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 18 removed outlier: 4.256A pdb=" N LEU R 10 " --> pdb=" O ALA R 6 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP R 11 " --> pdb=" O THR R 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.014A pdb=" N MET R 28 " --> pdb=" O THR R 24 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 50 removed outlier: 3.859A pdb=" N GLU R 40 " --> pdb=" O ARG R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 95 removed outlier: 3.749A pdb=" N LEU R 82 " --> pdb=" O THR R 78 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA R 83 " --> pdb=" O ALA R 79 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU R 85 " --> pdb=" O GLU R 81 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA R 88 " --> pdb=" O ALA R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 114 Processing helix chain 'R' and resid 116 through 123 Processing helix chain 'R' and resid 123 through 132 removed outlier: 3.981A pdb=" N VAL R 127 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU R 128 " --> pdb=" O ALA R 124 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN R 132 " --> pdb=" O GLU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 161 Processing helix chain 'R' and resid 207 through 211 Processing helix chain 'R' and resid 228 through 236 removed outlier: 3.889A pdb=" N SER R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 261 Processing helix chain 'R' and resid 286 through 296 removed outlier: 4.223A pdb=" N THR R 296 " --> pdb=" O TRP R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 325 removed outlier: 3.919A pdb=" N MET R 312 " --> pdb=" O VAL R 308 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET R 313 " --> pdb=" O LEU R 309 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL R 314 " --> pdb=" O LYS R 310 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN R 315 " --> pdb=" O ASP R 311 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG R 318 " --> pdb=" O VAL R 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 107 removed outlier: 7.410A pdb=" N ARG A 143 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ILE A 64 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU A 145 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE A 62 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N THR A 147 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 58 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 151 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 7.011A pdb=" N VAL A 113 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 removed outlier: 3.872A pdb=" N VAL A 155 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 179 through 181 removed outlier: 7.051A pdb=" N GLU A 205 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.588A pdb=" N GLU B 18 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 28 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 101 through 106 removed outlier: 7.935A pdb=" N ARG B 143 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE B 64 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU B 145 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 62 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR B 147 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY B 151 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 56 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 113 through 114 removed outlier: 3.522A pdb=" N VAL B 113 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 154 through 155 removed outlier: 3.600A pdb=" N VAL B 155 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.748A pdb=" N LYS C 13 " --> pdb=" O ALA C1197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 63 through 64 removed outlier: 4.977A pdb=" N LEU C 72 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE C 107 " --> pdb=" O LEU C 72 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TYR C 74 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG C 105 " --> pdb=" O TYR C 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB4, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB5, first strand: chain 'C' and resid 459 through 462 removed outlier: 6.410A pdb=" N SER C 153 " --> pdb=" O SER C 539 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 160 through 164 Processing sheet with id=AB7, first strand: chain 'C' and resid 191 through 193 removed outlier: 3.559A pdb=" N ASP C 191 " --> pdb=" O ARG C 203 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 233 through 236 Processing sheet with id=AB9, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AC1, first strand: chain 'C' and resid 261 through 262 Processing sheet with id=AC2, first strand: chain 'C' and resid 588 through 589 Processing sheet with id=AC3, first strand: chain 'C' and resid 588 through 589 Processing sheet with id=AC4, first strand: chain 'C' and resid 624 through 625 Processing sheet with id=AC5, first strand: chain 'C' and resid 723 through 724 removed outlier: 6.946A pdb=" N VAL C 723 " --> pdb=" O ILE C 789 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 754 through 758 removed outlier: 3.731A pdb=" N GLN C 733 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG C 742 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL C 731 " --> pdb=" O ARG C 742 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 763 through 764 Processing sheet with id=AC8, first strand: chain 'C' and resid 795 through 796 Processing sheet with id=AC9, first strand: chain 'C' and resid 1094 through 1098 removed outlier: 6.718A pdb=" N ILE C 822 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE C1097 " --> pdb=" O ILE C 822 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE C 824 " --> pdb=" O ILE C1097 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR C1240 " --> pdb=" O PHE C 810 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 836 through 845 removed outlier: 4.384A pdb=" N ASP C 936 " --> pdb=" O PHE C1071 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA C1073 " --> pdb=" O ILE C 934 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE C 934 " --> pdb=" O ALA C1073 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 848 through 849 removed outlier: 3.896A pdb=" N THR C 849 " --> pdb=" O GLY C 852 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 855 through 856 Processing sheet with id=AD4, first strand: chain 'C' and resid 888 through 890 removed outlier: 6.744A pdb=" N LEU C 924 " --> pdb=" O LEU C 889 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1000 through 1001 removed outlier: 4.163A pdb=" N GLY C1000 " --> pdb=" O ALA C 990 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1258 through 1260 Processing sheet with id=AD7, first strand: chain 'C' and resid 1258 through 1260 removed outlier: 7.838A pdb=" N ILE D 449 " --> pdb=" O ARG D 354 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL D 356 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU D 451 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL D 358 " --> pdb=" O LEU D 451 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1352 through 1354 removed outlier: 3.669A pdb=" N GLU C1354 " --> pdb=" O GLN D 20 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLN D 20 " --> pdb=" O GLU C1354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 104 through 107 Processing sheet with id=AE1, first strand: chain 'D' and resid 160 through 161 removed outlier: 3.580A pdb=" N LEU D 161 " --> pdb=" O TYR D 145 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 263 through 264 Processing sheet with id=AE3, first strand: chain 'D' and resid 368 through 371 removed outlier: 6.333A pdb=" N CYS D 368 " --> pdb=" O LYS D 442 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 444 " --> pdb=" O CYS D 368 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU D 370 " --> pdb=" O ILE D 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 528 through 529 removed outlier: 3.892A pdb=" N ARG D 553 " --> pdb=" O PHE D 529 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 556 through 557 Processing sheet with id=AE6, first strand: chain 'D' and resid 805 through 807 Processing sheet with id=AE7, first strand: chain 'D' and resid 816 through 818 Processing sheet with id=AE8, first strand: chain 'D' and resid 821 through 823 removed outlier: 7.666A pdb=" N VAL D 821 " --> pdb=" O LEU D 828 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 828 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 952 through 956 Processing sheet with id=AF1, first strand: chain 'D' and resid 959 through 961 Processing sheet with id=AF2, first strand: chain 'D' and resid 995 through 996 removed outlier: 4.131A pdb=" N ARG D 995 " --> pdb=" O ASP D1012 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP D1012 " --> pdb=" O ARG D 995 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 1017 through 1021 removed outlier: 4.312A pdb=" N ALA D1113 " --> pdb=" O ILE D1020 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1089 through 1091 removed outlier: 3.859A pdb=" N ALA D1069 " --> pdb=" O GLU D1031 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D1026 " --> pdb=" O VAL D1106 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1039 through 1043 Processing sheet with id=AF6, first strand: chain 'D' and resid 1183 through 1184 Processing sheet with id=AF7, first strand: chain 'D' and resid 1275 through 1276 removed outlier: 6.902A pdb=" N VAL D1297 " --> pdb=" O LEU D1263 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 134 through 136 removed outlier: 7.434A pdb=" N THR Q 135 " --> pdb=" O PHE R 187 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 134 through 136 removed outlier: 7.434A pdb=" N THR Q 135 " --> pdb=" O PHE R 187 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU R 196 " --> pdb=" O PRO R 182 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU R 186 " --> pdb=" O TYR R 192 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR R 192 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA R 195 " --> pdb=" O ARG R 204 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 204 through 207 removed outlier: 3.626A pdb=" N GLY Q 184 " --> pdb=" O VAL Q 194 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU Q 196 " --> pdb=" O PRO Q 182 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 269 through 272 removed outlier: 7.991A pdb=" N VAL Q 248 " --> pdb=" O VAL Q 304 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL Q 304 " --> pdb=" O VAL Q 248 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 54 through 56 Processing sheet with id=AG4, first strand: chain 'R' and resid 271 through 272 removed outlier: 3.567A pdb=" N THR R 271 " --> pdb=" O LEU R 279 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL R 278 " --> pdb=" O ILE R 251 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA R 305 " --> pdb=" O VAL R 248 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG R 250 " --> pdb=" O ILE R 303 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE R 303 " --> pdb=" O ARG R 250 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 3807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 9.59 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11449 1.34 - 1.46: 5611 1.46 - 1.58: 19630 1.58 - 1.70: 245 1.70 - 1.82: 229 Bond restraints: 37164 Sorted by residual: bond pdb=" C3' DA H 74 " pdb=" O3' DA H 74 " ideal model delta sigma weight residual 1.422 1.466 -0.044 3.00e-02 1.11e+03 2.12e+00 bond pdb=" CB GLN F 446 " pdb=" CG GLN F 446 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" CG1 ILE R 158 " pdb=" CD1 ILE R 158 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.48e+00 bond pdb=" C3' DC I 54 " pdb=" O3' DC I 54 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CG1 ILE A 62 " pdb=" CD1 ILE A 62 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+00 ... (remaining 37159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 50373 2.45 - 4.91: 424 4.91 - 7.36: 39 7.36 - 9.81: 3 9.81 - 12.27: 3 Bond angle restraints: 50842 Sorted by residual: angle pdb=" N ILE A 229 " pdb=" CA ILE A 229 " pdb=" C ILE A 229 " ideal model delta sigma weight residual 112.96 109.22 3.74 1.00e+00 1.00e+00 1.40e+01 angle pdb=" CA LEU C 294 " pdb=" CB LEU C 294 " pdb=" CG LEU C 294 " ideal model delta sigma weight residual 116.30 128.57 -12.27 3.50e+00 8.16e-02 1.23e+01 angle pdb=" CA LEU D 155 " pdb=" CB LEU D 155 " pdb=" CG LEU D 155 " ideal model delta sigma weight residual 116.30 127.85 -11.55 3.50e+00 8.16e-02 1.09e+01 angle pdb=" CA TRP D 34 " pdb=" CB TRP D 34 " pdb=" CG TRP D 34 " ideal model delta sigma weight residual 113.60 119.77 -6.17 1.90e+00 2.77e-01 1.06e+01 angle pdb=" C SER D 33 " pdb=" N TRP D 34 " pdb=" CA TRP D 34 " ideal model delta sigma weight residual 122.83 117.89 4.94 1.54e+00 4.22e-01 1.03e+01 ... (remaining 50837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 21504 35.39 - 70.78: 770 70.78 - 106.17: 49 106.17 - 141.56: 4 141.56 - 176.95: 4 Dihedral angle restraints: 22331 sinusoidal: 9594 harmonic: 12737 Sorted by residual: dihedral pdb=" CG ARG C 942 " pdb=" CD ARG C 942 " pdb=" NE ARG C 942 " pdb=" CZ ARG C 942 " ideal model delta sinusoidal sigma weight residual -90.00 -13.80 -76.20 2 1.50e+01 4.44e-03 2.01e+01 dihedral pdb=" CA ASP C1108 " pdb=" C ASP C1108 " pdb=" N GLY C1109 " pdb=" CA GLY C1109 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA LYS C 504 " pdb=" C LYS C 504 " pdb=" N PRO C 505 " pdb=" CA PRO C 505 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 22328 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4539 0.045 - 0.090: 993 0.090 - 0.135: 296 0.135 - 0.180: 14 0.180 - 0.226: 5 Chirality restraints: 5847 Sorted by residual: chirality pdb=" CG LEU F 580 " pdb=" CB LEU F 580 " pdb=" CD1 LEU F 580 " pdb=" CD2 LEU F 580 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL D 835 " pdb=" CA VAL D 835 " pdb=" CG1 VAL D 835 " pdb=" CG2 VAL D 835 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CB THR C1110 " pdb=" CA THR C1110 " pdb=" OG1 THR C1110 " pdb=" CG2 THR C1110 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 5844 not shown) Planarity restraints: 6237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 34 " -0.029 2.00e-02 2.50e+03 2.44e-02 1.48e+01 pdb=" CG TRP D 34 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP D 34 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP D 34 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 34 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 34 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 34 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 34 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 34 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 34 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG D 235 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO D 236 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 236 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 236 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C1060 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO C1061 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C1061 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C1061 " 0.031 5.00e-02 4.00e+02 ... (remaining 6234 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 271 2.57 - 3.15: 28847 3.15 - 3.73: 56070 3.73 - 4.32: 71079 4.32 - 4.90: 118244 Nonbonded interactions: 274511 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D2001 " model vdw 1.985 2.170 nonbonded pdb=" O LEU D 72 " pdb="ZN ZN D2002 " model vdw 2.033 2.230 nonbonded pdb=" OD2 ASP D 462 " pdb="MG MG D2001 " model vdw 2.087 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D2001 " model vdw 2.164 2.170 nonbonded pdb=" OG1 THR D 395 " pdb=" OD1 ASN F 579 " model vdw 2.188 3.040 ... (remaining 274506 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 'L' selection = chain 'Y' } ncs_group { reference = (chain 'Q' and ((resid 4 through 6 and (name N or name CA or name C or name O or \ name CB )) or resid 7 through 92 or (resid 93 through 94 and (name N or name CA \ or name C or name O or name CB )) or resid 95 through 161 or (resid 162 through \ 163 and (name N or name CA or name C or name O or name CB )) or resid 164 throu \ gh 226 or (resid 227 and (name N or name CA or name C or name O or name CB )) or \ resid 228 through 245 or (resid 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 327)) selection = (chain 'R' and (resid 4 through 62 or (resid 63 and (name N or name CA or name C \ or name O or name CB )) or resid 64 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 103 or (resid 104 and \ (name N or name CA or name C or name O or name CB )) or resid 105 through 115 or \ (resid 116 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 7 through 124 or (resid 125 and (name N or name CA or name C or name O or name C \ B )) or resid 126 through 138 or (resid 139 through 140 and (name N or name CA o \ r name C or name O or name CB )) or resid 141 through 175 or (resid 176 and (nam \ e N or name CA or name C or name O or name CB )) or resid 177 through 223 or (re \ sid 224 and (name N or name CA or name C or name O or name CB )) or resid 225 th \ rough 310 or (resid 311 and (name N or name CA or name C or name O or name CB )) \ or resid 312 through 315 or (resid 316 and (name N or name CA or name C or name \ O or name CB )) or resid 317 through 327)) } 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: 3.540 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: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 43.240 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 : 0.003 0.047 37170 Z= 0.122 Angle : 0.562 12.266 50848 Z= 0.289 Chirality : 0.041 0.226 5847 Planarity : 0.004 0.061 6237 Dihedral : 17.130 176.954 14117 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.03 % Allowed : 0.44 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -1.14 (0.13), residues: 4437 helix: 0.65 (0.13), residues: 1675 sheet: -0.91 (0.25), residues: 466 loop : -1.85 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 847 TYR 0.018 0.001 TYR Q 105 PHE 0.015 0.001 PHE C 236 TRP 0.067 0.001 TRP D 34 HIS 0.004 0.001 HIS C 156 Details of bonding type rmsd covalent geometry : bond 0.00274 (37164) covalent geometry : angle 0.55650 (50842) hydrogen bonds : bond 0.15658 ( 1434) hydrogen bonds : angle 5.97791 ( 3947) metal coordination : bond 0.01428 ( 6) metal coordination : angle 7.53092 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 972 time to evaluate : 1.300 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: B 17 ILE cc_start: 0.8856 (pt) cc_final: 0.8528 (pt) REVERT: B 18 GLU cc_start: 0.7882 (pp20) cc_final: 0.7212 (pp20) REVERT: B 70 GLU cc_start: 0.8122 (pp20) cc_final: 0.7914 (pp20) REVERT: B 87 ASN cc_start: 0.8878 (m110) cc_final: 0.8526 (m110) REVERT: B 89 LYS cc_start: 0.9244 (ptmm) cc_final: 0.8941 (ptpt) REVERT: B 224 GLN cc_start: 0.8777 (tt0) cc_final: 0.8496 (tt0) REVERT: B 225 ASP cc_start: 0.8381 (t0) cc_final: 0.8053 (t0) REVERT: B 226 GLN cc_start: 0.8731 (tp40) cc_final: 0.8371 (tp-100) REVERT: C 20 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7016 (mm-30) REVERT: C 36 GLU cc_start: 0.7210 (tp30) cc_final: 0.6731 (tp30) REVERT: C 148 GLU cc_start: 0.8012 (pt0) cc_final: 0.7734 (pt0) REVERT: C 167 LYS cc_start: 0.8809 (mmpt) cc_final: 0.8400 (mmmt) REVERT: C 169 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8374 (mttm) REVERT: C 205 ASP cc_start: 0.8476 (t0) cc_final: 0.8190 (t0) REVERT: C 355 MET cc_start: 0.7463 (ttp) cc_final: 0.7229 (ttp) REVERT: C 392 MET cc_start: 0.8715 (tmm) cc_final: 0.8425 (tmm) REVERT: C 512 GLU cc_start: 0.7970 (tp30) cc_final: 0.7612 (tp30) REVERT: C 613 TYR cc_start: 0.8724 (m-10) cc_final: 0.8193 (m-10) REVERT: C 701 GLN cc_start: 0.8317 (tt0) cc_final: 0.8102 (tt0) REVERT: C 703 ASP cc_start: 0.8163 (t70) cc_final: 0.7657 (t0) REVERT: C 778 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8286 (mmtm) REVERT: C 843 GLU cc_start: 0.7577 (tt0) cc_final: 0.7087 (tt0) REVERT: C 958 GLU cc_start: 0.7955 (tp30) cc_final: 0.7680 (tp30) REVERT: C 1044 ASP cc_start: 0.8213 (m-30) cc_final: 0.7594 (m-30) REVERT: C 1067 MET cc_start: 0.8357 (ptt) cc_final: 0.8055 (ptp) REVERT: C 1103 MET cc_start: 0.9251 (mmm) cc_final: 0.7882 (mmm) REVERT: C 1189 ASN cc_start: 0.8843 (m-40) cc_final: 0.8524 (m-40) REVERT: C 1299 TYR cc_start: 0.8928 (m-80) cc_final: 0.8483 (m-80) REVERT: D 216 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8320 (tm-30) REVERT: D 239 MET cc_start: 0.8736 (mtm) cc_final: 0.8504 (mtm) REVERT: D 679 TYR cc_start: 0.6805 (t80) cc_final: 0.6599 (t80) REVERT: D 796 LEU cc_start: 0.9513 (mm) cc_final: 0.9278 (mm) REVERT: D 1184 PHE cc_start: 0.8012 (m-10) cc_final: 0.7434 (m-10) REVERT: D 1361 LEU cc_start: 0.8969 (tp) cc_final: 0.8745 (tp) REVERT: E 11 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7900 (tm-30) REVERT: E 12 LYS cc_start: 0.7924 (tppp) cc_final: 0.7277 (tptm) REVERT: F 121 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8165 (ttp-170) REVERT: F 248 MET cc_start: 0.7826 (mtm) cc_final: 0.7618 (mtm) REVERT: F 425 ARG cc_start: 0.7088 (ttm-80) cc_final: 0.6800 (ttm-80) REVERT: F 452 LEU cc_start: 0.8301 (mm) cc_final: 0.8084 (mm) REVERT: F 543 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6924 (tm-30) REVERT: F 619 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8492 (tm-30) REVERT: F 637 LYS cc_start: 0.8436 (mtpp) cc_final: 0.7987 (tttm) REVERT: Q 100 ARG cc_start: 0.6853 (ttp-110) cc_final: 0.6216 (mmp-170) REVERT: Q 211 MET cc_start: 0.0646 (mtm) cc_final: -0.1183 (tpp) outliers start: 1 outliers final: 1 residues processed: 973 average time/residue: 0.2461 time to fit residues: 379.2225 Evaluate side-chains 800 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 799 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 942 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 432 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 684 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1251 HIS D 863 ASN D1365 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.206297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.141440 restraints weight = 47251.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.137737 restraints weight = 29375.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.137567 restraints weight = 23973.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.138366 restraints weight = 19813.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.139659 restraints weight = 15747.039| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 37170 Z= 0.165 Angle : 0.607 10.587 50848 Z= 0.312 Chirality : 0.042 0.174 5847 Planarity : 0.004 0.061 6237 Dihedral : 15.948 174.368 6168 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 2.32 % Allowed : 11.29 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -1.09 (0.13), residues: 4437 helix: 0.67 (0.13), residues: 1705 sheet: -0.95 (0.25), residues: 472 loop : -1.82 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 847 TYR 0.013 0.001 TYR C 403 PHE 0.014 0.001 PHE C1131 TRP 0.033 0.001 TRP D 34 HIS 0.007 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00383 (37164) covalent geometry : angle 0.60179 (50842) hydrogen bonds : bond 0.04179 ( 1434) hydrogen bonds : angle 4.72045 ( 3947) metal coordination : bond 0.01277 ( 6) metal coordination : angle 7.14803 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 848 time to evaluate : 0.832 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: A 18 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 26 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8476 (mmmt) REVERT: A 228 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8205 (mm-40) REVERT: B 63 GLN cc_start: 0.8645 (mm110) cc_final: 0.8407 (mm-40) REVERT: B 70 GLU cc_start: 0.7984 (pp20) cc_final: 0.7756 (pp20) REVERT: B 87 ASN cc_start: 0.8859 (m110) cc_final: 0.8519 (m110) REVERT: B 89 LYS cc_start: 0.9242 (ptmm) cc_final: 0.8966 (ptpt) REVERT: B 224 GLN cc_start: 0.8857 (tt0) cc_final: 0.8651 (tt0) REVERT: B 226 GLN cc_start: 0.8929 (tp40) cc_final: 0.8615 (tp-100) REVERT: C 26 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8222 (t0) REVERT: C 36 GLU cc_start: 0.7291 (tp30) cc_final: 0.6809 (tp30) REVERT: C 139 LYS cc_start: 0.8679 (mttm) cc_final: 0.8388 (mttp) REVERT: C 148 GLU cc_start: 0.7945 (pt0) cc_final: 0.7686 (pt0) REVERT: C 167 LYS cc_start: 0.8663 (mmpt) cc_final: 0.8310 (mmmt) REVERT: C 355 MET cc_start: 0.7440 (ttp) cc_final: 0.7167 (ttp) REVERT: C 382 GLU cc_start: 0.5037 (mt-10) cc_final: 0.4729 (mt-10) REVERT: C 487 MET cc_start: 0.7488 (tmm) cc_final: 0.7284 (tmm) REVERT: C 613 TYR cc_start: 0.8653 (m-10) cc_final: 0.8214 (m-10) REVERT: C 701 GLN cc_start: 0.8389 (tt0) cc_final: 0.8118 (tt0) REVERT: C 843 GLU cc_start: 0.7547 (tt0) cc_final: 0.7114 (tt0) REVERT: C 1067 MET cc_start: 0.8352 (ptt) cc_final: 0.7984 (ptp) REVERT: C 1189 ASN cc_start: 0.8878 (m-40) cc_final: 0.8509 (m-40) REVERT: D 216 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8329 (tm-30) REVERT: D 406 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7099 (tm-30) REVERT: D 431 LEU cc_start: 0.8766 (mm) cc_final: 0.8466 (mm) REVERT: D 445 GLU cc_start: 0.7785 (mp0) cc_final: 0.7430 (mp0) REVERT: D 679 TYR cc_start: 0.6825 (t80) cc_final: 0.6584 (t80) REVERT: D 734 LYS cc_start: 0.8995 (tttm) cc_final: 0.8790 (tttp) REVERT: D 796 LEU cc_start: 0.9561 (mm) cc_final: 0.9243 (mm) REVERT: D 1184 PHE cc_start: 0.7869 (m-10) cc_final: 0.7604 (m-10) REVERT: D 1199 TYR cc_start: 0.7969 (t80) cc_final: 0.7693 (t80) REVERT: D 1361 LEU cc_start: 0.9049 (tp) cc_final: 0.8630 (tp) REVERT: E 11 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7881 (tm-30) REVERT: E 12 LYS cc_start: 0.8070 (tppp) cc_final: 0.7200 (tptm) REVERT: F 118 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7542 (ttm) REVERT: F 121 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7957 (ttp-170) REVERT: F 474 TRP cc_start: 0.7064 (OUTLIER) cc_final: 0.5400 (m-90) REVERT: F 502 LYS cc_start: 0.9179 (ttmm) cc_final: 0.8945 (ptmm) REVERT: F 535 ARG cc_start: 0.8328 (mtp180) cc_final: 0.7988 (mtp180) REVERT: F 543 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6666 (tm-30) REVERT: F 637 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7903 (tttm) REVERT: Q 100 ARG cc_start: 0.7401 (ttp-110) cc_final: 0.6535 (mmp-170) REVERT: Q 211 MET cc_start: 0.0260 (mtm) cc_final: -0.1406 (tpp) REVERT: R 86 ARG cc_start: 0.8314 (tmm160) cc_final: 0.7842 (tmm160) REVERT: R 167 ARG cc_start: 0.5794 (ptp90) cc_final: 0.5593 (ptp90) outliers start: 80 outliers final: 57 residues processed: 874 average time/residue: 0.2319 time to fit residues: 324.0297 Evaluate side-chains 856 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 796 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 26 ASN Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 831 ASP Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1333 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 750 ILE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 868 ILE Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain D residue 1195 HIS Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 536 LYS Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 607 MET Chi-restraints excluded: chain F residue 640 HIS Chi-restraints excluded: chain R residue 52 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 107 optimal weight: 0.9990 chunk 438 optimal weight: 7.9990 chunk 435 optimal weight: 0.0040 chunk 16 optimal weight: 0.3980 chunk 378 optimal weight: 0.5980 chunk 212 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 307 optimal weight: 0.6980 chunk 179 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.213654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.148849 restraints weight = 46601.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.146600 restraints weight = 29261.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.146655 restraints weight = 19908.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.147135 restraints weight = 17744.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.149211 restraints weight = 14259.776| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37170 Z= 0.114 Angle : 0.572 12.582 50848 Z= 0.292 Chirality : 0.041 0.163 5847 Planarity : 0.004 0.053 6237 Dihedral : 15.916 175.787 6164 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.41 % Allowed : 14.45 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -1.03 (0.13), residues: 4437 helix: 0.74 (0.13), residues: 1708 sheet: -0.89 (0.26), residues: 453 loop : -1.81 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 488 TYR 0.011 0.001 TYR C 403 PHE 0.039 0.001 PHE D 18 TRP 0.019 0.001 TRP D 34 HIS 0.010 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00258 (37164) covalent geometry : angle 0.56991 (50842) hydrogen bonds : bond 0.03537 ( 1434) hydrogen bonds : angle 4.50600 ( 3947) metal coordination : bond 0.00989 ( 6) metal coordination : angle 4.85991 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 833 time to evaluate : 1.369 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 26 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8447 (mmmt) REVERT: A 28 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7495 (ttm-80) REVERT: B 16 GLN cc_start: 0.8105 (pp30) cc_final: 0.7866 (pp30) REVERT: B 87 ASN cc_start: 0.8881 (m110) cc_final: 0.8514 (m110) REVERT: B 89 LYS cc_start: 0.9191 (ptmm) cc_final: 0.8926 (ptpt) REVERT: B 224 GLN cc_start: 0.8847 (tt0) cc_final: 0.8593 (tt0) REVERT: B 226 GLN cc_start: 0.8929 (tp40) cc_final: 0.8512 (tp-100) REVERT: C 36 GLU cc_start: 0.7256 (tp30) cc_final: 0.6762 (tp30) REVERT: C 139 LYS cc_start: 0.8674 (mttm) cc_final: 0.8429 (mttp) REVERT: C 148 GLU cc_start: 0.7935 (pt0) cc_final: 0.7708 (pt0) REVERT: C 205 ASP cc_start: 0.8629 (t0) cc_final: 0.8291 (t0) REVERT: C 355 MET cc_start: 0.7329 (ttp) cc_final: 0.7101 (ttp) REVERT: C 382 GLU cc_start: 0.5249 (mt-10) cc_final: 0.5019 (mt-10) REVERT: C 404 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.6518 (t0) REVERT: C 487 MET cc_start: 0.7546 (tmm) cc_final: 0.7310 (tmm) REVERT: C 613 TYR cc_start: 0.8657 (m-10) cc_final: 0.8306 (m-80) REVERT: C 701 GLN cc_start: 0.8409 (tt0) cc_final: 0.8131 (tt0) REVERT: C 843 GLU cc_start: 0.7585 (tt0) cc_final: 0.7159 (tt0) REVERT: C 1067 MET cc_start: 0.8370 (ptt) cc_final: 0.8003 (ptp) REVERT: C 1103 MET cc_start: 0.8850 (mmt) cc_final: 0.8177 (mmm) REVERT: C 1189 ASN cc_start: 0.8864 (m-40) cc_final: 0.8511 (m-40) REVERT: C 1299 TYR cc_start: 0.8814 (m-80) cc_final: 0.8439 (m-80) REVERT: D 189 ASN cc_start: 0.8599 (t0) cc_final: 0.8376 (t0) REVERT: D 216 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8258 (tm-30) REVERT: D 406 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7165 (tm-30) REVERT: D 431 LEU cc_start: 0.8786 (mm) cc_final: 0.8424 (mm) REVERT: D 734 LYS cc_start: 0.8950 (tttm) cc_final: 0.8736 (tttp) REVERT: D 796 LEU cc_start: 0.9488 (mm) cc_final: 0.9142 (mm) REVERT: E 11 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7866 (tm-30) REVERT: E 12 LYS cc_start: 0.8057 (tppp) cc_final: 0.7369 (tptm) REVERT: F 118 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7496 (ttm) REVERT: F 121 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7952 (ttp-170) REVERT: F 148 MET cc_start: 0.6547 (mmm) cc_final: 0.6143 (mmm) REVERT: F 248 MET cc_start: 0.7764 (mtm) cc_final: 0.7457 (mtm) REVERT: F 452 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8161 (mm) REVERT: F 474 TRP cc_start: 0.6913 (OUTLIER) cc_final: 0.5329 (m-90) REVERT: F 488 ARG cc_start: 0.7053 (mmm160) cc_final: 0.6697 (tpt170) REVERT: F 502 LYS cc_start: 0.9097 (ttmm) cc_final: 0.8701 (tttp) REVERT: F 535 ARG cc_start: 0.8322 (mtp180) cc_final: 0.8061 (mtp85) REVERT: F 543 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6803 (tm-30) REVERT: F 577 GLN cc_start: 0.8427 (tp40) cc_final: 0.8191 (mm-40) REVERT: F 597 ARG cc_start: 0.6479 (ptt90) cc_final: 0.6249 (ptt90) REVERT: F 637 LYS cc_start: 0.8350 (mtpp) cc_final: 0.7852 (tttm) REVERT: Q 100 ARG cc_start: 0.7410 (ttp-110) cc_final: 0.6546 (mmp-170) REVERT: Q 121 ARG cc_start: 0.8448 (ptp90) cc_final: 0.7989 (ptp90) REVERT: Q 211 MET cc_start: 0.0277 (mtm) cc_final: -0.1099 (mmm) REVERT: R 86 ARG cc_start: 0.8349 (tmm160) cc_final: 0.7945 (tmm160) outliers start: 83 outliers final: 56 residues processed: 861 average time/residue: 0.2301 time to fit residues: 318.2765 Evaluate side-chains 841 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 781 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 831 ASP Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 750 ILE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1195 HIS Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1259 LYS Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 607 MET Chi-restraints excluded: chain F residue 640 HIS Chi-restraints excluded: chain Q residue 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 44 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 49 optimal weight: 40.0000 chunk 266 optimal weight: 2.9990 chunk 451 optimal weight: 8.9990 chunk 111 optimal weight: 0.0170 chunk 205 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 63 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1365 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.212754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.145992 restraints weight = 46366.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.144635 restraints weight = 24758.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.145252 restraints weight = 18543.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.145774 restraints weight = 16968.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.145996 restraints weight = 14138.913| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37170 Z= 0.126 Angle : 0.572 14.363 50848 Z= 0.290 Chirality : 0.041 0.176 5847 Planarity : 0.004 0.054 6237 Dihedral : 15.903 175.947 6164 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.90 % Allowed : 16.88 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.98 (0.13), residues: 4437 helix: 0.79 (0.13), residues: 1708 sheet: -0.87 (0.26), residues: 447 loop : -1.80 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 4 TYR 0.012 0.001 TYR C 403 PHE 0.025 0.001 PHE D 18 TRP 0.021 0.001 TRP D 34 HIS 0.008 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00293 (37164) covalent geometry : angle 0.56935 (50842) hydrogen bonds : bond 0.03406 ( 1434) hydrogen bonds : angle 4.38692 ( 3947) metal coordination : bond 0.00906 ( 6) metal coordination : angle 5.26589 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 935 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 835 time to evaluate : 1.191 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 16 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 18 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 26 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8446 (mmmt) REVERT: A 28 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7731 (ttm-80) REVERT: B 16 GLN cc_start: 0.8132 (pp30) cc_final: 0.7787 (pp30) REVERT: B 87 ASN cc_start: 0.8901 (m110) cc_final: 0.8543 (m110) REVERT: B 89 LYS cc_start: 0.9209 (ptmm) cc_final: 0.8959 (ptpt) REVERT: B 224 GLN cc_start: 0.8845 (tt0) cc_final: 0.8606 (tt0) REVERT: B 226 GLN cc_start: 0.8924 (tp40) cc_final: 0.8499 (tp-100) REVERT: C 36 GLU cc_start: 0.7305 (tp30) cc_final: 0.6781 (tp30) REVERT: C 139 LYS cc_start: 0.8724 (mttm) cc_final: 0.8237 (mttp) REVERT: C 205 ASP cc_start: 0.8685 (t0) cc_final: 0.8294 (t0) REVERT: C 355 MET cc_start: 0.7444 (ttp) cc_final: 0.7201 (ttp) REVERT: C 382 GLU cc_start: 0.5239 (mt-10) cc_final: 0.4983 (mt-10) REVERT: C 404 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.6490 (t0) REVERT: C 487 MET cc_start: 0.7546 (tmm) cc_final: 0.7289 (tmm) REVERT: C 613 TYR cc_start: 0.8665 (m-10) cc_final: 0.8320 (m-80) REVERT: C 701 GLN cc_start: 0.8445 (tt0) cc_final: 0.8181 (tt0) REVERT: C 843 GLU cc_start: 0.7579 (tt0) cc_final: 0.7201 (tt0) REVERT: C 1097 ILE cc_start: 0.8853 (mm) cc_final: 0.8386 (mt) REVERT: C 1103 MET cc_start: 0.8818 (mmt) cc_final: 0.8176 (mmm) REVERT: C 1110 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8816 (p) REVERT: C 1189 ASN cc_start: 0.8861 (m-40) cc_final: 0.8507 (m-40) REVERT: C 1299 TYR cc_start: 0.8796 (m-80) cc_final: 0.8459 (m-80) REVERT: D 189 ASN cc_start: 0.8635 (t0) cc_final: 0.8410 (t0) REVERT: D 216 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8261 (tm-30) REVERT: D 398 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8322 (tp40) REVERT: D 406 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7210 (tm-30) REVERT: D 431 LEU cc_start: 0.8739 (mm) cc_final: 0.8385 (mm) REVERT: D 703 MET cc_start: 0.7675 (ppp) cc_final: 0.7278 (ppp) REVERT: D 734 LYS cc_start: 0.8940 (tttm) cc_final: 0.8704 (tttp) REVERT: D 796 LEU cc_start: 0.9479 (mm) cc_final: 0.9152 (mm) REVERT: D 807 GLU cc_start: 0.7519 (tt0) cc_final: 0.7236 (tt0) REVERT: D 877 LYS cc_start: 0.8392 (tttp) cc_final: 0.7863 (ttmm) REVERT: E 11 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 12 LYS cc_start: 0.8117 (tppp) cc_final: 0.7387 (tptm) REVERT: F 118 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7592 (ttm) REVERT: F 121 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7927 (ttp-170) REVERT: F 248 MET cc_start: 0.8001 (mtm) cc_final: 0.7744 (mtm) REVERT: F 452 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8157 (mm) REVERT: F 474 TRP cc_start: 0.6962 (OUTLIER) cc_final: 0.5335 (m-90) REVERT: F 488 ARG cc_start: 0.7132 (mmm160) cc_final: 0.6861 (tpt170) REVERT: F 502 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8716 (tttp) REVERT: F 535 ARG cc_start: 0.8413 (mtp180) cc_final: 0.8134 (mtp180) REVERT: F 543 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6794 (tm-30) REVERT: F 637 LYS cc_start: 0.8428 (mtpp) cc_final: 0.7891 (tttm) REVERT: Q 100 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.6346 (mmp80) REVERT: Q 211 MET cc_start: 0.0633 (mtm) cc_final: -0.0824 (mmm) REVERT: R 86 ARG cc_start: 0.8304 (tmm160) cc_final: 0.7912 (tmm160) outliers start: 100 outliers final: 74 residues processed: 870 average time/residue: 0.2302 time to fit residues: 322.9588 Evaluate side-chains 862 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 783 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 831 ASP Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1309 SER Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 750 ILE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 868 ILE Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1195 HIS Chi-restraints excluded: chain D residue 1222 VAL Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1259 LYS Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 607 MET Chi-restraints excluded: chain F residue 640 HIS Chi-restraints excluded: chain Q residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 366 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 387 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 12 optimal weight: 0.0270 chunk 423 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 155 optimal weight: 0.0670 chunk 91 optimal weight: 4.9990 chunk 304 optimal weight: 2.9990 chunk 425 optimal weight: 7.9990 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 GLN ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1365 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 579 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.202716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.132944 restraints weight = 47396.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.134019 restraints weight = 24392.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.134849 restraints weight = 16134.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135337 restraints weight = 13442.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135341 restraints weight = 12032.847| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 37170 Z= 0.254 Angle : 0.683 14.328 50848 Z= 0.348 Chirality : 0.044 0.176 5847 Planarity : 0.005 0.052 6237 Dihedral : 16.017 176.201 6164 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.90 % Allowed : 17.84 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -1.24 (0.13), residues: 4437 helix: 0.58 (0.13), residues: 1703 sheet: -1.12 (0.25), residues: 446 loop : -1.91 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 4 TYR 0.019 0.002 TYR B 218 PHE 0.021 0.002 PHE D 18 TRP 0.026 0.001 TRP D 34 HIS 0.009 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00593 (37164) covalent geometry : angle 0.67547 (50842) hydrogen bonds : bond 0.04389 ( 1434) hydrogen bonds : angle 4.66936 ( 3947) metal coordination : bond 0.01583 ( 6) metal coordination : angle 9.36788 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 813 time to evaluate : 1.420 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 14 LYS cc_start: 0.8328 (tmtt) cc_final: 0.8077 (tmmt) REVERT: A 18 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 123 ASP cc_start: 0.8613 (t0) cc_final: 0.8400 (t0) REVERT: B 16 GLN cc_start: 0.8237 (pp30) cc_final: 0.7838 (pp30) REVERT: B 44 ASN cc_start: 0.9150 (t0) cc_final: 0.8840 (t0) REVERT: B 87 ASN cc_start: 0.9107 (m110) cc_final: 0.8757 (m110) REVERT: B 89 LYS cc_start: 0.9285 (ptmm) cc_final: 0.9082 (ptpt) REVERT: B 123 ASP cc_start: 0.8199 (t0) cc_final: 0.7946 (t0) REVERT: C 167 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8654 (mmmt) REVERT: C 404 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7466 (t0) REVERT: C 487 MET cc_start: 0.7657 (tmm) cc_final: 0.7297 (tmm) REVERT: C 613 TYR cc_start: 0.8773 (m-80) cc_final: 0.8381 (m-80) REVERT: C 701 GLN cc_start: 0.8631 (tt0) cc_final: 0.8323 (tt0) REVERT: C 843 GLU cc_start: 0.7663 (tt0) cc_final: 0.7153 (tt0) REVERT: C 982 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7404 (mmtt) REVERT: C 1069 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8421 (mtpp) REVERT: C 1097 ILE cc_start: 0.9224 (mm) cc_final: 0.8931 (mm) REVERT: C 1106 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8909 (tt) REVERT: C 1189 ASN cc_start: 0.8992 (m-40) cc_final: 0.8634 (m-40) REVERT: C 1206 MET cc_start: 0.7845 (mmm) cc_final: 0.7501 (mmp) REVERT: C 1292 LEU cc_start: 0.9525 (mt) cc_final: 0.9181 (mt) REVERT: D 216 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8400 (tm-30) REVERT: D 398 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8514 (tp40) REVERT: D 406 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7340 (tm-30) REVERT: D 703 MET cc_start: 0.7865 (ppp) cc_final: 0.7299 (ppp) REVERT: D 796 LEU cc_start: 0.9601 (mm) cc_final: 0.9221 (mm) REVERT: D 860 ILE cc_start: 0.9210 (mt) cc_final: 0.8991 (mm) REVERT: D 877 LYS cc_start: 0.8576 (tttp) cc_final: 0.8320 (ttmm) REVERT: D 1190 LYS cc_start: 0.8543 (tptp) cc_final: 0.7913 (ptpt) REVERT: E 11 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8009 (tm-30) REVERT: E 12 LYS cc_start: 0.8110 (tppp) cc_final: 0.7363 (tptm) REVERT: F 121 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7982 (ttp-170) REVERT: F 248 MET cc_start: 0.8110 (mtm) cc_final: 0.7780 (mtm) REVERT: F 452 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8311 (mm) REVERT: F 474 TRP cc_start: 0.7286 (OUTLIER) cc_final: 0.5594 (m-90) REVERT: F 502 LYS cc_start: 0.9223 (ttmm) cc_final: 0.9007 (ptmm) REVERT: F 535 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8191 (mtp180) REVERT: F 543 GLU cc_start: 0.7539 (tm-30) cc_final: 0.6696 (tm-30) REVERT: Q 100 ARG cc_start: 0.7169 (ttp-110) cc_final: 0.6498 (mmp-170) REVERT: Q 211 MET cc_start: 0.1207 (mtm) cc_final: -0.0466 (mmm) REVERT: R 86 ARG cc_start: 0.8237 (tmm160) cc_final: 0.7861 (tmm160) outliers start: 169 outliers final: 124 residues processed: 890 average time/residue: 0.2391 time to fit residues: 341.6264 Evaluate side-chains 909 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 780 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 663 SER Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 854 GLU Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 982 LYS Chi-restraints excluded: chain C residue 1060 LEU Chi-restraints excluded: chain C residue 1106 LEU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1255 ASP Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1309 SER Chi-restraints excluded: chain C residue 1328 THR Chi-restraints excluded: chain C residue 1343 GLU Chi-restraints excluded: chain D residue 34 TRP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 673 ILE Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 750 ILE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 868 ILE Chi-restraints excluded: chain D residue 878 VAL Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain D residue 1195 HIS Chi-restraints excluded: chain D residue 1222 VAL Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1298 THR Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1311 GLN Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain D residue 1337 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 536 LYS Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 607 MET Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain Q residue 249 LEU Chi-restraints excluded: chain R residue 21 GLU Chi-restraints excluded: chain R residue 25 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 244 optimal weight: 0.5980 chunk 257 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 287 optimal weight: 0.1980 chunk 233 optimal weight: 0.4980 chunk 314 optimal weight: 0.7980 chunk 379 optimal weight: 10.0000 chunk 403 optimal weight: 9.9990 chunk 352 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 191 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1141 ASN D 311 ASN ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1365 GLN F 579 ASN F 611 HIS ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.210295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.138249 restraints weight = 47355.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.141752 restraints weight = 23593.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.142622 restraints weight = 13382.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.143236 restraints weight = 11522.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.143141 restraints weight = 10408.541| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37170 Z= 0.122 Angle : 0.593 15.160 50848 Z= 0.299 Chirality : 0.041 0.174 5847 Planarity : 0.004 0.051 6237 Dihedral : 15.986 176.905 6164 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.45 % Allowed : 20.16 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -1.06 (0.13), residues: 4437 helix: 0.72 (0.13), residues: 1706 sheet: -0.96 (0.26), residues: 440 loop : -1.82 (0.13), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 2 TYR 0.015 0.001 TYR A 154 PHE 0.017 0.001 PHE D 18 TRP 0.022 0.001 TRP D 34 HIS 0.006 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00282 (37164) covalent geometry : angle 0.59009 (50842) hydrogen bonds : bond 0.03419 ( 1434) hydrogen bonds : angle 4.41304 ( 3947) metal coordination : bond 0.00820 ( 6) metal coordination : angle 5.84982 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 812 time to evaluate : 1.324 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 14 LYS cc_start: 0.8421 (tmtt) cc_final: 0.8146 (tmmt) REVERT: A 28 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7686 (ttm-80) REVERT: A 119 GLU cc_start: 0.8378 (tp30) cc_final: 0.8114 (tp30) REVERT: A 123 ASP cc_start: 0.8566 (t0) cc_final: 0.8348 (t0) REVERT: A 187 GLU cc_start: 0.8179 (pm20) cc_final: 0.7849 (pm20) REVERT: B 16 GLN cc_start: 0.8174 (pp30) cc_final: 0.7800 (pp30) REVERT: B 70 GLU cc_start: 0.8086 (pp20) cc_final: 0.7704 (pp20) REVERT: B 87 ASN cc_start: 0.9073 (m110) cc_final: 0.8675 (m110) REVERT: B 123 ASP cc_start: 0.8270 (t0) cc_final: 0.7809 (t0) REVERT: B 133 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8051 (pp) REVERT: B 145 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 226 GLN cc_start: 0.8909 (tp40) cc_final: 0.8434 (tp-100) REVERT: C 148 GLU cc_start: 0.8358 (pt0) cc_final: 0.7966 (pt0) REVERT: C 205 ASP cc_start: 0.8754 (t0) cc_final: 0.8286 (t0) REVERT: C 379 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7143 (mmm-85) REVERT: C 382 GLU cc_start: 0.5307 (mt-10) cc_final: 0.4943 (mt-10) REVERT: C 404 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.6778 (t0) REVERT: C 426 ARG cc_start: 0.8063 (mmt180) cc_final: 0.7631 (mmt180) REVERT: C 487 MET cc_start: 0.7617 (tmm) cc_final: 0.7414 (tmm) REVERT: C 613 TYR cc_start: 0.8759 (m-80) cc_final: 0.8357 (m-80) REVERT: C 701 GLN cc_start: 0.8534 (tt0) cc_final: 0.8250 (tt0) REVERT: C 843 GLU cc_start: 0.7641 (tt0) cc_final: 0.7344 (tt0) REVERT: C 1097 ILE cc_start: 0.8953 (mm) cc_final: 0.8530 (mt) REVERT: C 1189 ASN cc_start: 0.8965 (m-40) cc_final: 0.8622 (m-40) REVERT: D 216 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8274 (tm-30) REVERT: D 398 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8453 (tp40) REVERT: D 406 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7397 (tm-30) REVERT: D 431 LEU cc_start: 0.8817 (mm) cc_final: 0.8437 (mm) REVERT: D 703 MET cc_start: 0.7824 (ppp) cc_final: 0.7294 (ppp) REVERT: D 734 LYS cc_start: 0.8948 (tttm) cc_final: 0.8562 (tttp) REVERT: D 796 LEU cc_start: 0.9555 (mm) cc_final: 0.9204 (mm) REVERT: D 877 LYS cc_start: 0.8554 (tttp) cc_final: 0.8316 (ttmm) REVERT: D 1184 PHE cc_start: 0.7789 (m-10) cc_final: 0.7354 (m-10) REVERT: D 1190 LYS cc_start: 0.8568 (tptp) cc_final: 0.7867 (pttm) REVERT: D 1341 GLU cc_start: 0.7609 (mp0) cc_final: 0.7198 (mp0) REVERT: E 11 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7936 (tm-30) REVERT: E 12 LYS cc_start: 0.8088 (tppp) cc_final: 0.7349 (tptm) REVERT: F 121 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7919 (ttp-170) REVERT: F 248 MET cc_start: 0.8107 (mtm) cc_final: 0.7786 (mtm) REVERT: F 452 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8144 (mm) REVERT: F 474 TRP cc_start: 0.6998 (OUTLIER) cc_final: 0.5561 (m-90) REVERT: F 535 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8271 (mtp180) REVERT: F 543 GLU cc_start: 0.7521 (tm-30) cc_final: 0.6805 (tm-30) REVERT: Q 100 ARG cc_start: 0.6953 (ttp-110) cc_final: 0.6290 (mmp80) REVERT: Q 211 MET cc_start: 0.1008 (mtm) cc_final: -0.0585 (mmm) REVERT: R 86 ARG cc_start: 0.8109 (tmm160) cc_final: 0.7742 (tmm160) outliers start: 119 outliers final: 83 residues processed: 866 average time/residue: 0.2327 time to fit residues: 325.5030 Evaluate side-chains 878 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 791 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 831 ASP Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1309 SER Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 664 TYR Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 750 ILE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 868 ILE Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain D residue 1195 HIS Chi-restraints excluded: chain D residue 1222 VAL Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 607 MET Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 640 HIS Chi-restraints excluded: chain R residue 21 GLU Chi-restraints excluded: chain R residue 53 MET Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 313 optimal weight: 4.9990 chunk 49 optimal weight: 40.0000 chunk 188 optimal weight: 0.5980 chunk 339 optimal weight: 30.0000 chunk 195 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 311 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 128 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN D 460 ASN D 917 GLN D1365 GLN R 52 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.207988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.135397 restraints weight = 47328.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.138584 restraints weight = 23359.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.140023 restraints weight = 13448.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.140412 restraints weight = 11018.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.140352 restraints weight = 10199.704| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 37170 Z= 0.170 Angle : 0.619 15.094 50848 Z= 0.312 Chirality : 0.042 0.187 5847 Planarity : 0.004 0.051 6237 Dihedral : 15.983 176.992 6164 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 3.92 % Allowed : 21.03 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -1.11 (0.13), residues: 4437 helix: 0.70 (0.13), residues: 1709 sheet: -1.07 (0.26), residues: 434 loop : -1.86 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 273 TYR 0.012 0.001 TYR C 403 PHE 0.014 0.001 PHE D 18 TRP 0.023 0.001 TRP D 34 HIS 0.008 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00397 (37164) covalent geometry : angle 0.61432 (50842) hydrogen bonds : bond 0.03655 ( 1434) hydrogen bonds : angle 4.44203 ( 3947) metal coordination : bond 0.01050 ( 6) metal coordination : angle 6.94914 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 789 time to evaluate : 1.096 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 14 LYS cc_start: 0.8451 (tmtt) cc_final: 0.8043 (ttpp) REVERT: A 18 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 123 ASP cc_start: 0.8624 (t0) cc_final: 0.8391 (t0) REVERT: B 16 GLN cc_start: 0.8174 (pp30) cc_final: 0.7837 (pp30) REVERT: B 44 ASN cc_start: 0.9134 (t0) cc_final: 0.8694 (t0) REVERT: B 70 GLU cc_start: 0.8128 (pp20) cc_final: 0.7711 (pp20) REVERT: B 87 ASN cc_start: 0.9114 (m110) cc_final: 0.8739 (m110) REVERT: B 123 ASP cc_start: 0.8165 (t0) cc_final: 0.7862 (t0) REVERT: C 148 GLU cc_start: 0.8404 (pt0) cc_final: 0.7973 (pt0) REVERT: C 205 ASP cc_start: 0.8816 (t0) cc_final: 0.8418 (t0) REVERT: C 355 MET cc_start: 0.7614 (ttp) cc_final: 0.7346 (ttp) REVERT: C 404 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7615 (t0) REVERT: C 487 MET cc_start: 0.7648 (tmm) cc_final: 0.7384 (tmm) REVERT: C 613 TYR cc_start: 0.8741 (m-80) cc_final: 0.8304 (m-10) REVERT: C 701 GLN cc_start: 0.8602 (tt0) cc_final: 0.8340 (tt0) REVERT: C 807 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8424 (tt) REVERT: C 843 GLU cc_start: 0.7630 (tt0) cc_final: 0.7312 (tt0) REVERT: C 1097 ILE cc_start: 0.9062 (mm) cc_final: 0.8686 (mt) REVERT: C 1189 ASN cc_start: 0.8971 (m-40) cc_final: 0.8629 (m-40) REVERT: C 1206 MET cc_start: 0.7722 (mmm) cc_final: 0.7398 (mmp) REVERT: C 1292 LEU cc_start: 0.9483 (mt) cc_final: 0.9095 (mt) REVERT: D 216 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D 398 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8481 (tp40) REVERT: D 406 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7314 (tm-30) REVERT: D 431 LEU cc_start: 0.8804 (mm) cc_final: 0.8404 (mm) REVERT: D 703 MET cc_start: 0.7900 (ppp) cc_final: 0.7305 (ppp) REVERT: D 734 LYS cc_start: 0.8961 (tttm) cc_final: 0.8683 (tttp) REVERT: D 796 LEU cc_start: 0.9581 (mm) cc_final: 0.9189 (mm) REVERT: D 807 GLU cc_start: 0.7859 (tt0) cc_final: 0.7487 (tt0) REVERT: D 877 LYS cc_start: 0.8573 (tttp) cc_final: 0.8316 (ttmm) REVERT: D 1184 PHE cc_start: 0.7873 (m-10) cc_final: 0.7425 (m-10) REVERT: D 1190 LYS cc_start: 0.8713 (tptp) cc_final: 0.8060 (pttm) REVERT: D 1247 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8074 (ttpt) REVERT: D 1341 GLU cc_start: 0.7564 (mp0) cc_final: 0.7218 (mp0) REVERT: E 11 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7977 (tm-30) REVERT: E 12 LYS cc_start: 0.8142 (tppp) cc_final: 0.7404 (tptm) REVERT: F 121 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7931 (ttp-170) REVERT: F 248 MET cc_start: 0.8093 (mtm) cc_final: 0.7759 (mtm) REVERT: F 452 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8219 (mm) REVERT: F 474 TRP cc_start: 0.7161 (OUTLIER) cc_final: 0.5637 (m-90) REVERT: F 536 LYS cc_start: 0.8101 (ptpp) cc_final: 0.7890 (pttt) REVERT: F 543 GLU cc_start: 0.7581 (tm-30) cc_final: 0.6842 (tm-30) REVERT: Q 100 ARG cc_start: 0.6956 (ttp-110) cc_final: 0.6285 (mmp80) REVERT: Q 211 MET cc_start: 0.1246 (mtm) cc_final: -0.0358 (mmm) REVERT: R 86 ARG cc_start: 0.8097 (tmm160) cc_final: 0.7712 (tmm160) outliers start: 135 outliers final: 107 residues processed: 854 average time/residue: 0.2355 time to fit residues: 325.0749 Evaluate side-chains 891 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 779 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 831 ASP Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1309 SER Chi-restraints excluded: chain C residue 1343 GLU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 750 ILE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 797 VAL Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 868 ILE Chi-restraints excluded: chain D residue 898 ASP Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain D residue 1195 HIS Chi-restraints excluded: chain D residue 1222 VAL Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1259 LYS Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1311 GLN Chi-restraints excluded: chain D residue 1337 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 416 LYS Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 607 MET Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 21 GLU Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 13 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 291 optimal weight: 0.0870 chunk 448 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 420 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 453 optimal weight: 8.9990 chunk 357 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 128 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN ** D 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 917 GLN D1365 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.207474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.137249 restraints weight = 47274.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.139643 restraints weight = 22872.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.140571 restraints weight = 13550.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.140981 restraints weight = 12396.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.141117 restraints weight = 10918.175| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 37170 Z= 0.128 Angle : 0.603 15.543 50848 Z= 0.302 Chirality : 0.041 0.198 5847 Planarity : 0.004 0.054 6237 Dihedral : 15.964 177.191 6164 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.89 % Allowed : 21.47 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -1.03 (0.13), residues: 4437 helix: 0.79 (0.13), residues: 1700 sheet: -1.01 (0.26), residues: 432 loop : -1.81 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 2 TYR 0.011 0.001 TYR C 403 PHE 0.013 0.001 PHE D 18 TRP 0.021 0.001 TRP D 34 HIS 0.007 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00300 (37164) covalent geometry : angle 0.59951 (50842) hydrogen bonds : bond 0.03339 ( 1434) hydrogen bonds : angle 4.35144 ( 3947) metal coordination : bond 0.00866 ( 6) metal coordination : angle 5.75694 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 809 time to evaluate : 1.298 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 14 LYS cc_start: 0.8352 (tmtt) cc_final: 0.7986 (ttpp) REVERT: A 18 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7407 (tm-30) REVERT: A 123 ASP cc_start: 0.8628 (t0) cc_final: 0.8422 (t0) REVERT: B 16 GLN cc_start: 0.8196 (pp30) cc_final: 0.7854 (pp30) REVERT: B 70 GLU cc_start: 0.8110 (pp20) cc_final: 0.7684 (pp20) REVERT: B 87 ASN cc_start: 0.9063 (m110) cc_final: 0.8671 (m110) REVERT: B 123 ASP cc_start: 0.8103 (t0) cc_final: 0.7812 (t0) REVERT: B 145 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7548 (tm-30) REVERT: C 148 GLU cc_start: 0.8363 (pt0) cc_final: 0.8015 (pt0) REVERT: C 198 ASP cc_start: 0.8018 (m-30) cc_final: 0.6981 (t70) REVERT: C 205 ASP cc_start: 0.8743 (t0) cc_final: 0.8362 (t0) REVERT: C 355 MET cc_start: 0.7580 (ttp) cc_final: 0.7362 (ttp) REVERT: C 404 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7581 (t0) REVERT: C 429 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7193 (mtm110) REVERT: C 487 MET cc_start: 0.7592 (tmm) cc_final: 0.7362 (tmm) REVERT: C 613 TYR cc_start: 0.8728 (m-80) cc_final: 0.8259 (m-10) REVERT: C 701 GLN cc_start: 0.8577 (tt0) cc_final: 0.8273 (tt0) REVERT: C 732 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7768 (mm-30) REVERT: C 807 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8411 (tt) REVERT: C 843 GLU cc_start: 0.7610 (tt0) cc_final: 0.7314 (tt0) REVERT: C 1097 ILE cc_start: 0.9003 (mm) cc_final: 0.8521 (mt) REVERT: C 1103 MET cc_start: 0.8779 (mmt) cc_final: 0.7945 (mmm) REVERT: C 1189 ASN cc_start: 0.8951 (m-40) cc_final: 0.8618 (m-40) REVERT: C 1206 MET cc_start: 0.7620 (mmm) cc_final: 0.7284 (mmp) REVERT: D 216 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8305 (tm-30) REVERT: D 398 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8446 (tp40) REVERT: D 406 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7321 (tm-30) REVERT: D 431 LEU cc_start: 0.8766 (mm) cc_final: 0.8365 (mm) REVERT: D 703 MET cc_start: 0.7937 (ppp) cc_final: 0.7383 (ppp) REVERT: D 734 LYS cc_start: 0.8935 (tttm) cc_final: 0.8690 (tttp) REVERT: D 796 LEU cc_start: 0.9537 (mm) cc_final: 0.9171 (mm) REVERT: D 807 GLU cc_start: 0.7782 (tt0) cc_final: 0.7389 (tt0) REVERT: D 1184 PHE cc_start: 0.7734 (m-10) cc_final: 0.7334 (m-10) REVERT: D 1190 LYS cc_start: 0.8710 (tptp) cc_final: 0.8105 (pttm) REVERT: D 1247 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8136 (ttpt) REVERT: D 1341 GLU cc_start: 0.7586 (mp0) cc_final: 0.7202 (mp0) REVERT: E 11 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7966 (tm-30) REVERT: E 12 LYS cc_start: 0.8131 (tppp) cc_final: 0.7386 (tptm) REVERT: F 121 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7933 (ttp-170) REVERT: F 148 MET cc_start: 0.6485 (mmm) cc_final: 0.6056 (mmm) REVERT: F 248 MET cc_start: 0.8026 (mtm) cc_final: 0.7737 (mtm) REVERT: F 452 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8215 (mm) REVERT: F 474 TRP cc_start: 0.7051 (OUTLIER) cc_final: 0.5608 (m-90) REVERT: F 543 GLU cc_start: 0.7590 (tm-30) cc_final: 0.6873 (tm-30) REVERT: F 620 PHE cc_start: 0.7648 (m-10) cc_final: 0.7335 (m-10) REVERT: Q 2 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7979 (ttp80) REVERT: Q 100 ARG cc_start: 0.7023 (ttp-110) cc_final: 0.6304 (mmp80) REVERT: Q 211 MET cc_start: 0.0743 (mtm) cc_final: -0.0752 (mmm) REVERT: Q 288 ARG cc_start: 0.7613 (ttp-110) cc_final: 0.7351 (ttp-110) REVERT: R 86 ARG cc_start: 0.8166 (tmm160) cc_final: 0.7740 (tmm160) outliers start: 134 outliers final: 106 residues processed: 870 average time/residue: 0.2342 time to fit residues: 329.6741 Evaluate side-chains 901 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 790 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 831 ASP Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1309 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 750 ILE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 868 ILE Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain D residue 1195 HIS Chi-restraints excluded: chain D residue 1222 VAL Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 607 MET Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 640 HIS Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 21 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 226 optimal weight: 0.9980 chunk 231 optimal weight: 0.2980 chunk 378 optimal weight: 0.3980 chunk 391 optimal weight: 0.0370 chunk 355 optimal weight: 2.9990 chunk 427 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 370 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 404 optimal weight: 8.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN B 128 ASN C 165 HIS ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1365 GLN E 60 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.211317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.137062 restraints weight = 47243.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.141972 restraints weight = 23737.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.142712 restraints weight = 13512.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.143763 restraints weight = 10960.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.144154 restraints weight = 9996.721| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37170 Z= 0.117 Angle : 0.603 15.532 50848 Z= 0.301 Chirality : 0.041 0.223 5847 Planarity : 0.004 0.051 6237 Dihedral : 15.929 177.149 6164 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.25 % Allowed : 22.31 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -1.00 (0.13), residues: 4437 helix: 0.81 (0.13), residues: 1706 sheet: -1.04 (0.25), residues: 446 loop : -1.79 (0.13), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 956 TYR 0.021 0.001 TYR C 403 PHE 0.014 0.001 PHE C 285 TRP 0.021 0.001 TRP D 34 HIS 0.009 0.001 HIS E 60 Details of bonding type rmsd covalent geometry : bond 0.00272 (37164) covalent geometry : angle 0.60036 (50842) hydrogen bonds : bond 0.03194 ( 1434) hydrogen bonds : angle 4.29331 ( 3947) metal coordination : bond 0.00847 ( 6) metal coordination : angle 4.93474 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 813 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8259 (tmtt) cc_final: 0.7904 (ttpp) REVERT: A 18 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 187 GLU cc_start: 0.8213 (pm20) cc_final: 0.7988 (pm20) REVERT: B 16 GLN cc_start: 0.8169 (pp30) cc_final: 0.7846 (pp30) REVERT: B 70 GLU cc_start: 0.8084 (pp20) cc_final: 0.7657 (pp20) REVERT: B 87 ASN cc_start: 0.9064 (m110) cc_final: 0.8666 (m110) REVERT: B 123 ASP cc_start: 0.8070 (t0) cc_final: 0.7789 (t0) REVERT: B 145 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7460 (tm-30) REVERT: B 226 GLN cc_start: 0.8909 (tp40) cc_final: 0.8468 (tp-100) REVERT: C 148 GLU cc_start: 0.8340 (pt0) cc_final: 0.8011 (pt0) REVERT: C 198 ASP cc_start: 0.7868 (m-30) cc_final: 0.6842 (t0) REVERT: C 205 ASP cc_start: 0.8696 (t0) cc_final: 0.8306 (t0) REVERT: C 429 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7249 (mtm110) REVERT: C 460 ARG cc_start: 0.8689 (ttp-110) cc_final: 0.8077 (ttt-90) REVERT: C 487 MET cc_start: 0.7552 (tmm) cc_final: 0.7334 (tmm) REVERT: C 613 TYR cc_start: 0.8707 (m-80) cc_final: 0.8299 (m-80) REVERT: C 701 GLN cc_start: 0.8576 (tt0) cc_final: 0.8290 (tt0) REVERT: C 732 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7728 (mm-30) REVERT: C 807 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8398 (tt) REVERT: C 843 GLU cc_start: 0.7616 (tt0) cc_final: 0.7324 (tt0) REVERT: C 1097 ILE cc_start: 0.8931 (mm) cc_final: 0.8520 (mt) REVERT: C 1103 MET cc_start: 0.8776 (mmt) cc_final: 0.7973 (mmm) REVERT: C 1189 ASN cc_start: 0.8938 (m-40) cc_final: 0.8576 (m-40) REVERT: C 1206 MET cc_start: 0.7588 (mmm) cc_final: 0.7256 (mmp) REVERT: D 103 MET cc_start: 0.8659 (ptt) cc_final: 0.8404 (ptt) REVERT: D 216 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8336 (tm-30) REVERT: D 235 ARG cc_start: 0.7306 (mtm110) cc_final: 0.6678 (mtm110) REVERT: D 398 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8408 (tp40) REVERT: D 406 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7291 (tm-30) REVERT: D 431 LEU cc_start: 0.8733 (mm) cc_final: 0.8368 (mm) REVERT: D 686 TRP cc_start: 0.8544 (m100) cc_final: 0.8281 (m100) REVERT: D 703 MET cc_start: 0.7890 (ppp) cc_final: 0.7345 (ppp) REVERT: D 796 LEU cc_start: 0.9511 (mm) cc_final: 0.9172 (mm) REVERT: D 807 GLU cc_start: 0.7729 (tt0) cc_final: 0.7416 (tt0) REVERT: D 1184 PHE cc_start: 0.7802 (m-10) cc_final: 0.7449 (m-10) REVERT: D 1190 LYS cc_start: 0.8691 (tptp) cc_final: 0.8136 (pttm) REVERT: D 1247 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8129 (ttpt) REVERT: D 1341 GLU cc_start: 0.7309 (mp0) cc_final: 0.6938 (mp0) REVERT: E 11 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7948 (tm-30) REVERT: E 12 LYS cc_start: 0.8100 (tppp) cc_final: 0.7344 (tptm) REVERT: F 121 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7937 (ttp-170) REVERT: F 248 MET cc_start: 0.8059 (mtm) cc_final: 0.7764 (mtm) REVERT: F 452 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8166 (mm) REVERT: F 474 TRP cc_start: 0.6974 (OUTLIER) cc_final: 0.5583 (m-90) REVERT: F 535 ARG cc_start: 0.8373 (mtp180) cc_final: 0.8016 (mtp85) REVERT: F 543 GLU cc_start: 0.7597 (tm-30) cc_final: 0.6894 (tm-30) REVERT: F 620 PHE cc_start: 0.7556 (m-10) cc_final: 0.7251 (m-10) REVERT: Q 100 ARG cc_start: 0.6914 (ttp-110) cc_final: 0.6587 (tpp-160) REVERT: Q 211 MET cc_start: 0.0740 (mtm) cc_final: -0.0711 (mmm) REVERT: Q 288 ARG cc_start: 0.7588 (ttp-110) cc_final: 0.7329 (ttp-110) outliers start: 112 outliers final: 95 residues processed: 864 average time/residue: 0.2292 time to fit residues: 318.3741 Evaluate side-chains 902 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 803 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 831 ASP Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1309 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 750 ILE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 863 ASN Chi-restraints excluded: chain D residue 868 ILE Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain D residue 1195 HIS Chi-restraints excluded: chain D residue 1222 VAL Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 607 MET Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 640 HIS Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 21 GLU Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 299 optimal weight: 0.9990 chunk 437 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 345 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 375 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 416 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN B 128 ASN B 224 GLN C 165 HIS ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN D 917 GLN F 579 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.210717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.135841 restraints weight = 47368.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.140852 restraints weight = 23982.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.141766 restraints weight = 13722.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.142390 restraints weight = 10707.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.142797 restraints weight = 9939.913| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37170 Z= 0.133 Angle : 0.618 16.124 50848 Z= 0.309 Chirality : 0.041 0.241 5847 Planarity : 0.004 0.051 6237 Dihedral : 15.923 177.100 6164 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 3.19 % Allowed : 22.54 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.98 (0.13), residues: 4437 helix: 0.83 (0.13), residues: 1699 sheet: -1.01 (0.26), residues: 431 loop : -1.78 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 116 TYR 0.016 0.001 TYR C 403 PHE 0.036 0.001 PHE F 650 TRP 0.024 0.001 TRP D 34 HIS 0.009 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00311 (37164) covalent geometry : angle 0.61526 (50842) hydrogen bonds : bond 0.03288 ( 1434) hydrogen bonds : angle 4.30279 ( 3947) metal coordination : bond 0.00878 ( 6) metal coordination : angle 5.40826 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8874 Ramachandran restraints generated. 4437 Oldfield, 0 Emsley, 4437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 806 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8295 (tmtt) cc_final: 0.7941 (ttpp) REVERT: A 18 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 26 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8611 (mmmt) REVERT: A 28 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7546 (ttm-80) REVERT: A 187 GLU cc_start: 0.8237 (pm20) cc_final: 0.7975 (pm20) REVERT: B 16 GLN cc_start: 0.8196 (pp30) cc_final: 0.7875 (pp30) REVERT: B 70 GLU cc_start: 0.8108 (pp20) cc_final: 0.7698 (pp20) REVERT: B 87 ASN cc_start: 0.9060 (m110) cc_final: 0.8670 (m110) REVERT: B 123 ASP cc_start: 0.8078 (t0) cc_final: 0.7781 (t0) REVERT: B 145 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 226 GLN cc_start: 0.8952 (tp40) cc_final: 0.8532 (tp-100) REVERT: C 148 GLU cc_start: 0.8347 (pt0) cc_final: 0.7999 (pt0) REVERT: C 165 HIS cc_start: 0.7887 (p90) cc_final: 0.7071 (p90) REVERT: C 198 ASP cc_start: 0.7936 (m-30) cc_final: 0.6883 (t70) REVERT: C 205 ASP cc_start: 0.8736 (t0) cc_final: 0.8333 (t0) REVERT: C 355 MET cc_start: 0.7529 (ttp) cc_final: 0.7247 (ttp) REVERT: C 487 MET cc_start: 0.7482 (tmm) cc_final: 0.7228 (tmm) REVERT: C 496 MET cc_start: 0.7538 (tpp) cc_final: 0.7326 (tpp) REVERT: C 613 TYR cc_start: 0.8732 (m-80) cc_final: 0.8299 (m-10) REVERT: C 701 GLN cc_start: 0.8603 (tt0) cc_final: 0.8309 (tt0) REVERT: C 732 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7752 (mm-30) REVERT: C 807 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8374 (tt) REVERT: C 843 GLU cc_start: 0.7639 (tt0) cc_final: 0.7333 (tt0) REVERT: C 1097 ILE cc_start: 0.8983 (mm) cc_final: 0.8543 (mt) REVERT: C 1103 MET cc_start: 0.8830 (mmt) cc_final: 0.8017 (mmm) REVERT: C 1189 ASN cc_start: 0.8961 (m-40) cc_final: 0.8596 (m-40) REVERT: C 1206 MET cc_start: 0.7632 (mmm) cc_final: 0.7319 (mmp) REVERT: D 216 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8344 (tm-30) REVERT: D 398 GLN cc_start: 0.8725 (tp-100) cc_final: 0.8448 (tp40) REVERT: D 406 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7383 (tm-30) REVERT: D 431 LEU cc_start: 0.8778 (mm) cc_final: 0.8380 (mm) REVERT: D 703 MET cc_start: 0.7908 (ppp) cc_final: 0.7336 (ppp) REVERT: D 796 LEU cc_start: 0.9526 (mm) cc_final: 0.9170 (mm) REVERT: D 807 GLU cc_start: 0.7780 (tt0) cc_final: 0.7455 (tt0) REVERT: D 1184 PHE cc_start: 0.7756 (m-10) cc_final: 0.7457 (m-10) REVERT: D 1207 ILE cc_start: 0.8454 (mm) cc_final: 0.8254 (mp) REVERT: D 1247 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8130 (ttpt) REVERT: D 1280 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8542 (mm-30) REVERT: D 1341 GLU cc_start: 0.7416 (mp0) cc_final: 0.7080 (mp0) REVERT: E 11 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7979 (tm-30) REVERT: E 12 LYS cc_start: 0.8108 (tppp) cc_final: 0.7365 (tptm) REVERT: F 121 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7940 (ttp-170) REVERT: F 148 MET cc_start: 0.6338 (mmm) cc_final: 0.5941 (mmm) REVERT: F 248 MET cc_start: 0.8079 (mtm) cc_final: 0.7779 (mtm) REVERT: F 452 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8166 (mm) REVERT: F 474 TRP cc_start: 0.6999 (OUTLIER) cc_final: 0.5577 (m-90) REVERT: F 543 GLU cc_start: 0.7626 (tm-30) cc_final: 0.6893 (tm-30) REVERT: F 620 PHE cc_start: 0.7542 (m-10) cc_final: 0.7242 (m-10) REVERT: Q 100 ARG cc_start: 0.6747 (ttp-110) cc_final: 0.6445 (tpp-160) REVERT: Q 211 MET cc_start: 0.1078 (mtm) cc_final: -0.0500 (mmm) REVERT: Q 288 ARG cc_start: 0.7620 (ttp-110) cc_final: 0.7296 (ttp-110) REVERT: R 86 ARG cc_start: 0.8223 (tmm160) cc_final: 0.7585 (tpp80) outliers start: 110 outliers final: 101 residues processed: 855 average time/residue: 0.2284 time to fit residues: 315.0960 Evaluate side-chains 901 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 796 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 170 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 684 ASN Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 770 CYS Chi-restraints excluded: chain C residue 807 LEU Chi-restraints excluded: chain C residue 831 ASP Chi-restraints excluded: chain C residue 841 GLU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1110 THR Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1194 VAL Chi-restraints excluded: chain C residue 1198 THR Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1269 THR Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1309 SER Chi-restraints excluded: chain C residue 1333 ILE Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 311 ASN Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 368 CYS Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 436 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 587 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 682 VAL Chi-restraints excluded: chain D residue 750 ILE Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 854 VAL Chi-restraints excluded: chain D residue 858 THR Chi-restraints excluded: chain D residue 868 ILE Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain D residue 1195 HIS Chi-restraints excluded: chain D residue 1222 VAL Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain D residue 1337 THR Chi-restraints excluded: chain D residue 1339 THR Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 497 ILE Chi-restraints excluded: chain F residue 553 ASP Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 607 MET Chi-restraints excluded: chain F residue 638 LEU Chi-restraints excluded: chain F residue 640 HIS Chi-restraints excluded: chain Q residue 151 LEU Chi-restraints excluded: chain R residue 21 GLU Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 173 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 292 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 294 optimal weight: 0.4980 chunk 395 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 278 optimal weight: 0.0870 chunk 72 optimal weight: 0.1980 chunk 442 optimal weight: 9.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN B 224 GLN C 26 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.211723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.137355 restraints weight = 47032.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.142078 restraints weight = 23802.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.142885 restraints weight = 14068.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.143957 restraints weight = 11186.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.144447 restraints weight = 10239.033| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37170 Z= 0.117 Angle : 0.623 16.460 50848 Z= 0.311 Chirality : 0.041 0.237 5847 Planarity : 0.004 0.055 6237 Dihedral : 15.914 177.028 6164 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.22 % Allowed : 22.48 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -0.95 (0.13), residues: 4437 helix: 0.84 (0.13), residues: 1699 sheet: -0.98 (0.25), residues: 434 loop : -1.76 (0.13), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 105 TYR 0.015 0.001 TYR C 403 PHE 0.048 0.001 PHE F 650 TRP 0.024 0.001 TRP D 34 HIS 0.010 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00272 (37164) covalent geometry : angle 0.62069 (50842) hydrogen bonds : bond 0.03166 ( 1434) hydrogen bonds : angle 4.27028 ( 3947) metal coordination : bond 0.00846 ( 6) metal coordination : angle 4.72160 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7891.79 seconds wall clock time: 136 minutes 3.54 seconds (8163.54 seconds total)