Starting phenix.real_space_refine on Mon Jul 6 17:25:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pfv_71615/07_2026/9pfv_71615.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pfv_71615/07_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_71615/07_2026/9pfv_71615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pfv_71615/07_2026/9pfv_71615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pfv_71615/07_2026/9pfv_71615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pfv_71615/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 6.21, per 1000 atoms: 0.17 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: 3.19 Conformation dependent library (CDL) restraints added in 1.1 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: 4.35 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: 8.71 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' DT H 53 " pdb=" C2' DT H 53 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DG I 52 " pdb=" C2' DG I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT I 58 " pdb=" C2' DT I 58 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.48e+00 bond pdb=" C3' DG H 40 " pdb=" C2' DG H 40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.00e+00 bond pdb=" C3' DC H 54 " pdb=" C2' DC H 54 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.67e+00 ... (remaining 37159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 50329 2.45 - 4.91: 468 4.91 - 7.36: 39 7.36 - 9.81: 3 9.81 - 12.27: 3 Bond angle restraints: 50842 Sorted by residual: angle pdb=" O4' DC H 37 " pdb=" C4' DC H 37 " pdb=" C3' DC H 37 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.42e+01 angle pdb=" N3 DT H 63 " pdb=" C4 DT H 63 " pdb=" O4 DT H 63 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT I 12 " pdb=" C4 DT I 12 " pdb=" O4 DT I 12 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT I 56 " pdb=" C4 DT I 56 " pdb=" O4 DT I 56 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT H 35 " pdb=" C4 DT H 35 " pdb=" O4 DT H 35 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+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: 4410 0.045 - 0.090: 1106 0.090 - 0.135: 309 0.135 - 0.180: 17 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: 5.380 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: 0.580 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 38.880 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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= 0.220 Angle : 0.592 12.266 50848 Z= 0.364 Chirality : 0.043 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/Z covalent geometry : bond 0.00322 / 0.22 (37164) covalent geometry : angle 0.58666 / 0.36 (50842) hydrogen bonds : bond 0.15658 / 10.57 ( 1434) hydrogen bonds : angle 5.97791 / 4.30 ( 3947) metal coordination : bond 0.01428 / 0.97 ( 6) metal coordination : angle 7.53092 / 3.99 ( 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 : 1.346 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: 0.2239 time to fit residues: 346.4058 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 : 1.254 ------------------------------------------------------------------------------- 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: 40.0000 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: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 311 ASN ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 ASN D1365 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.210814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.147747 restraints weight = 46766.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.146937 restraints weight = 40473.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.147405 restraints weight = 27549.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.146686 restraints weight = 24570.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.147582 restraints weight = 18863.001| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37170 Z= 0.189 Angle : 0.637 10.439 50848 Z= 0.331 Chirality : 0.044 0.242 5847 Planarity : 0.005 0.064 6237 Dihedral : 15.988 171.469 6168 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.47 % Allowed : 11.46 % Favored : 86.07 % 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: -1.16 (0.13), residues: 4437 helix: 0.60 (0.13), residues: 1708 sheet: -0.98 (0.25), residues: 474 loop : -1.86 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 488 TYR 0.013 0.001 TYR D1199 PHE 0.015 0.001 PHE C1131 TRP 0.039 0.001 TRP D 34 HIS 0.009 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (37164) covalent geometry : angle 0.63149 / 0.33 (50842) hydrogen bonds : bond 0.04509 / 3.00 ( 1434) hydrogen bonds : angle 4.87955 / 3.49 ( 3947) metal coordination : bond 0.02032 / 1.15 ( 6) metal coordination : angle 7.42166 / 3.69 ( 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: 85 poor density : 843 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: symmetry clash REVERT: A 26 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8550 (mmmt) REVERT: B 44 ASN cc_start: 0.9087 (t0) cc_final: 0.8611 (t0) REVERT: B 70 GLU cc_start: 0.7959 (pp20) cc_final: 0.7721 (pp20) REVERT: B 87 ASN cc_start: 0.8850 (m110) cc_final: 0.8518 (m110) REVERT: B 89 LYS cc_start: 0.9252 (ptmm) cc_final: 0.8954 (ptpt) REVERT: B 226 GLN cc_start: 0.8935 (tp40) cc_final: 0.8634 (tp-100) REVERT: C 26 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8286 (t0) REVERT: C 36 GLU cc_start: 0.7314 (tp30) cc_final: 0.6845 (tp30) REVERT: C 139 LYS cc_start: 0.8685 (mttm) cc_final: 0.8418 (mttp) REVERT: C 148 GLU cc_start: 0.7947 (pt0) cc_final: 0.7682 (pt0) REVERT: C 167 LYS cc_start: 0.8671 (mmpt) cc_final: 0.8353 (mmmt) REVERT: C 355 MET cc_start: 0.7446 (ttp) cc_final: 0.7216 (ttp) REVERT: C 613 TYR cc_start: 0.8663 (m-10) cc_final: 0.8262 (m-10) REVERT: C 701 GLN cc_start: 0.8407 (tt0) cc_final: 0.8148 (tt0) REVERT: C 843 GLU cc_start: 0.7537 (tt0) cc_final: 0.7128 (tt0) REVERT: C 1067 MET cc_start: 0.8390 (ptt) cc_final: 0.8005 (ptp) REVERT: C 1189 ASN cc_start: 0.8899 (m-40) cc_final: 0.8543 (m-40) REVERT: D 216 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8331 (tm-30) REVERT: D 431 LEU cc_start: 0.8735 (mm) cc_final: 0.8429 (mm) REVERT: D 445 GLU cc_start: 0.7756 (mp0) cc_final: 0.7377 (mp0) REVERT: D 679 TYR cc_start: 0.6829 (t80) cc_final: 0.6610 (t80) REVERT: D 703 MET cc_start: 0.7689 (ppp) cc_final: 0.7200 (ppp) REVERT: D 734 LYS cc_start: 0.9009 (tttm) cc_final: 0.8788 (tttp) REVERT: D 796 LEU cc_start: 0.9582 (mm) cc_final: 0.9255 (mm) REVERT: D 1199 TYR cc_start: 0.7885 (t80) cc_final: 0.7636 (t80) REVERT: D 1361 LEU cc_start: 0.9070 (tp) cc_final: 0.8654 (tp) REVERT: E 11 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7885 (tm-30) REVERT: E 12 LYS cc_start: 0.8093 (tppp) cc_final: 0.7234 (tptm) REVERT: F 118 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7732 (ttm) REVERT: F 121 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7958 (ttp-170) REVERT: F 148 MET cc_start: 0.6570 (mmm) cc_final: 0.5997 (mmm) REVERT: F 474 TRP cc_start: 0.7091 (OUTLIER) cc_final: 0.5373 (m-90) REVERT: F 502 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8869 (ptmm) REVERT: F 543 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6655 (tm-30) REVERT: F 637 LYS cc_start: 0.8270 (mtpp) cc_final: 0.7839 (tttm) REVERT: Q 8 ARG cc_start: 0.7673 (mmt-90) cc_final: 0.7261 (mmt-90) REVERT: Q 100 ARG cc_start: 0.7513 (ttp-110) cc_final: 0.6665 (mmp-170) REVERT: Q 211 MET cc_start: 0.0002 (mtm) cc_final: -0.1508 (tpp) REVERT: R 86 ARG cc_start: 0.8303 (tmm160) cc_final: 0.7920 (tmm160) outliers start: 85 outliers final: 63 residues processed: 874 average time/residue: 0.2170 time to fit residues: 305.2357 Evaluate side-chains 856 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 790 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 183 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 374 ILE 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 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 1257 ILE 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 393 SER 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 789 SER Chi-restraints excluded: chain D residue 817 THR Chi-restraints excluded: chain D residue 1185 LEU 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 123 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 Q residue 249 LEU Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain R residue 53 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 107 optimal weight: 1.9990 chunk 438 optimal weight: 8.9990 chunk 435 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 378 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 307 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1365 GLN E 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.211855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.144628 restraints weight = 46581.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.143586 restraints weight = 24433.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.143796 restraints weight = 18037.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.144497 restraints weight = 16144.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.144773 restraints weight = 13679.241| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37170 Z= 0.139 Angle : 0.593 13.229 50848 Z= 0.308 Chirality : 0.042 0.264 5847 Planarity : 0.004 0.052 6237 Dihedral : 15.994 171.243 6164 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.67 % Allowed : 14.91 % Favored : 82.42 % 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: -1.10 (0.13), residues: 4437 helix: 0.66 (0.13), residues: 1700 sheet: -0.91 (0.25), residues: 460 loop : -1.84 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 488 TYR 0.015 0.001 TYR C 403 PHE 0.012 0.001 PHE C1131 TRP 0.024 0.001 TRP D 34 HIS 0.009 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (37164) covalent geometry : angle 0.58912 / 0.31 (50842) hydrogen bonds : bond 0.04034 / 2.67 ( 1434) hydrogen bonds : angle 4.69111 / 3.35 ( 3947) metal coordination : bond 0.01052 / 0.65 ( 6) metal coordination : angle 5.92782 / 3.03 ( 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 910 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 818 time to evaluate : 0.986 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: 0.8753 (mmmt) cc_final: 0.8465 (mmmt) REVERT: A 28 ARG cc_start: 0.8168 (ttm-80) cc_final: 0.7721 (ttm-80) REVERT: B 87 ASN cc_start: 0.8922 (m110) cc_final: 0.8548 (m110) REVERT: B 89 LYS cc_start: 0.9213 (ptmm) cc_final: 0.8957 (ptpt) REVERT: B 226 GLN cc_start: 0.8914 (tp40) cc_final: 0.8506 (tp-100) REVERT: C 36 GLU cc_start: 0.7271 (tp30) cc_final: 0.6752 (tp30) REVERT: C 139 LYS cc_start: 0.8722 (mttm) cc_final: 0.8410 (mttp) REVERT: C 167 LYS cc_start: 0.8613 (mmpt) cc_final: 0.8364 (mmmt) REVERT: C 355 MET cc_start: 0.7448 (ttp) cc_final: 0.7209 (ttp) REVERT: C 613 TYR cc_start: 0.8680 (m-10) cc_final: 0.8303 (m-10) REVERT: C 701 GLN cc_start: 0.8419 (tt0) cc_final: 0.8139 (tt0) REVERT: C 843 GLU cc_start: 0.7590 (tt0) cc_final: 0.6957 (tt0) REVERT: C 1067 MET cc_start: 0.8380 (ptt) cc_final: 0.7986 (ptp) REVERT: C 1069 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8334 (mtpp) REVERT: C 1103 MET cc_start: 0.8772 (mmt) cc_final: 0.8069 (mmm) REVERT: C 1189 ASN cc_start: 0.8872 (m-40) cc_final: 0.8514 (m-40) REVERT: D 216 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8314 (tm-30) REVERT: D 431 LEU cc_start: 0.8762 (mm) cc_final: 0.8371 (mm) REVERT: D 445 GLU cc_start: 0.7760 (mp0) cc_final: 0.7422 (mp0) REVERT: D 679 TYR cc_start: 0.6852 (t80) cc_final: 0.6596 (t80) REVERT: D 734 LYS cc_start: 0.9026 (tttm) cc_final: 0.8796 (tttp) REVERT: D 796 LEU cc_start: 0.9558 (mm) cc_final: 0.9211 (mm) REVERT: D 860 ILE cc_start: 0.9236 (mt) cc_final: 0.8995 (mm) REVERT: D 1199 TYR cc_start: 0.8023 (t80) cc_final: 0.7810 (t80) REVERT: D 1361 LEU cc_start: 0.8976 (tp) cc_final: 0.8712 (tp) REVERT: E 11 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7901 (tm-30) REVERT: E 12 LYS cc_start: 0.8089 (tppp) cc_final: 0.7394 (tptm) REVERT: F 118 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7530 (ttm) REVERT: F 121 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7945 (ttp-170) REVERT: F 148 MET cc_start: 0.6609 (mmm) cc_final: 0.6361 (mmm) REVERT: F 248 MET cc_start: 0.7866 (mtm) cc_final: 0.7594 (mtm) REVERT: F 452 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8162 (mm) REVERT: F 474 TRP cc_start: 0.6982 (OUTLIER) cc_final: 0.5328 (m-90) REVERT: F 543 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6496 (tm-30) REVERT: F 637 LYS cc_start: 0.8440 (mtpp) cc_final: 0.7958 (tttm) REVERT: Q 100 ARG cc_start: 0.7263 (ttp-110) cc_final: 0.6453 (mmp-170) REVERT: Q 211 MET cc_start: 0.0688 (mtm) cc_final: -0.0865 (mmm) REVERT: R 86 ARG cc_start: 0.8307 (tmm160) cc_final: 0.7966 (tmm160) REVERT: R 167 ARG cc_start: 0.6042 (ptp90) cc_final: 0.5804 (ptp90) outliers start: 92 outliers final: 65 residues processed: 846 average time/residue: 0.2143 time to fit residues: 290.9502 Evaluate side-chains 856 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 788 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 93 VAL Chi-restraints excluded: chain A residue 186 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 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 443 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 663 SER 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 969 GLU Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1257 ILE Chi-restraints excluded: chain C residue 1307 VAL Chi-restraints excluded: chain C residue 1333 ILE Chi-restraints excluded: chain C residue 1344 MET 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 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 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 828 LEU Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1185 LEU 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 F residue 118 MET Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 453 MET Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS 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 R residue 53 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 44 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 49 optimal weight: 40.0000 chunk 266 optimal weight: 0.5980 chunk 451 optimal weight: 30.0000 chunk 111 optimal weight: 0.2980 chunk 205 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 191 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 = 0.4258 r_free = 0.4258 target = 0.213384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.147462 restraints weight = 46664.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.144233 restraints weight = 28277.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.145406 restraints weight = 20983.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.145686 restraints weight = 17182.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.145818 restraints weight = 14058.539| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37170 Z= 0.129 Angle : 0.581 14.286 50848 Z= 0.301 Chirality : 0.042 0.271 5847 Planarity : 0.004 0.061 6237 Dihedral : 16.000 171.672 6164 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.87 % Allowed : 16.83 % Favored : 80.30 % 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: -1.07 (0.13), residues: 4437 helix: 0.70 (0.13), residues: 1707 sheet: -0.90 (0.25), residues: 457 loop : -1.84 (0.13), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 961 TYR 0.015 0.001 TYR C 403 PHE 0.036 0.001 PHE D 18 TRP 0.021 0.001 TRP D 34 HIS 0.008 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (37164) covalent geometry : angle 0.57825 / 0.30 (50842) hydrogen bonds : bond 0.03705 / 2.45 ( 1434) hydrogen bonds : angle 4.55564 / 3.25 ( 3947) metal coordination : bond 0.00908 / 0.55 ( 6) metal coordination : angle 5.51010 / 2.82 ( 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 912 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 813 time to evaluate : 1.280 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 28 ARG cc_start: 0.8174 (ttm-80) cc_final: 0.7732 (ttm-80) REVERT: B 87 ASN cc_start: 0.8892 (m110) cc_final: 0.8529 (m110) REVERT: B 89 LYS cc_start: 0.9213 (ptmm) cc_final: 0.8976 (ptpt) REVERT: B 226 GLN cc_start: 0.8943 (tp40) cc_final: 0.8539 (tp-100) REVERT: C 36 GLU cc_start: 0.7291 (tp30) cc_final: 0.6766 (tp30) REVERT: C 139 LYS cc_start: 0.8682 (mttm) cc_final: 0.8433 (mttp) REVERT: C 205 ASP cc_start: 0.8703 (t0) cc_final: 0.8332 (t0) REVERT: C 355 MET cc_start: 0.7458 (ttp) cc_final: 0.7202 (ttp) REVERT: C 404 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7538 (t70) REVERT: C 487 MET cc_start: 0.7327 (tmm) cc_final: 0.7028 (tmm) REVERT: C 613 TYR cc_start: 0.8673 (m-10) cc_final: 0.8354 (m-80) REVERT: C 701 GLN cc_start: 0.8453 (tt0) cc_final: 0.8171 (tt0) REVERT: C 843 GLU cc_start: 0.7572 (tt0) cc_final: 0.7131 (tt0) REVERT: C 1067 MET cc_start: 0.8376 (ptt) cc_final: 0.7980 (ptp) REVERT: C 1097 ILE cc_start: 0.9064 (mm) cc_final: 0.8637 (mt) REVERT: C 1110 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8720 (p) REVERT: C 1189 ASN cc_start: 0.8886 (m-40) cc_final: 0.8520 (m-40) REVERT: D 216 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8294 (tm-30) REVERT: D 398 GLN cc_start: 0.8607 (tp40) cc_final: 0.8256 (tp40) REVERT: D 431 LEU cc_start: 0.8738 (mm) cc_final: 0.8351 (mm) REVERT: D 445 GLU cc_start: 0.7774 (mp0) cc_final: 0.7452 (mp0) REVERT: D 679 TYR cc_start: 0.6818 (t80) cc_final: 0.6560 (t80) REVERT: D 703 MET cc_start: 0.7671 (ppp) cc_final: 0.7199 (ppp) REVERT: D 734 LYS cc_start: 0.8986 (tttm) cc_final: 0.8765 (tttp) REVERT: D 796 LEU cc_start: 0.9538 (mm) cc_final: 0.9177 (mm) REVERT: D 860 ILE cc_start: 0.9202 (mt) cc_final: 0.8951 (mm) REVERT: D 1184 PHE cc_start: 0.7794 (m-10) cc_final: 0.7345 (m-10) REVERT: D 1341 GLU cc_start: 0.7630 (mp0) cc_final: 0.7302 (mp0) REVERT: D 1361 LEU cc_start: 0.8977 (tp) cc_final: 0.8679 (tp) REVERT: E 11 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7905 (tm-30) REVERT: E 12 LYS cc_start: 0.8089 (tppp) cc_final: 0.7367 (tptm) REVERT: F 118 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7543 (ttm) REVERT: F 121 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7944 (ttp-170) REVERT: F 148 MET cc_start: 0.6814 (mmm) cc_final: 0.6519 (mmm) REVERT: F 248 MET cc_start: 0.7872 (mtm) cc_final: 0.7418 (mtm) REVERT: F 452 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8122 (mm) REVERT: F 474 TRP cc_start: 0.6994 (OUTLIER) cc_final: 0.5379 (m-90) REVERT: F 535 ARG cc_start: 0.8401 (mtp180) cc_final: 0.8119 (mtp85) REVERT: F 543 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6612 (tm-30) REVERT: F 637 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7869 (tttm) REVERT: Q 100 ARG cc_start: 0.7366 (ttp-110) cc_final: 0.6539 (mmp-170) REVERT: Q 211 MET cc_start: 0.0455 (mtm) cc_final: -0.1016 (mmm) REVERT: R 36 ARG cc_start: 0.5562 (tpt90) cc_final: 0.5091 (tpp80) REVERT: R 86 ARG cc_start: 0.8356 (tmm160) cc_final: 0.7990 (tmm160) REVERT: R 167 ARG cc_start: 0.6138 (ptp90) cc_final: 0.5880 (ptp90) outliers start: 99 outliers final: 76 residues processed: 850 average time/residue: 0.2221 time to fit residues: 303.0327 Evaluate side-chains 866 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 785 time to evaluate : 1.284 ------------------------------------------------------------------------------- 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 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 133 LEU 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 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 476 LEU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 532 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 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 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 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 828 LEU 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 1185 LEU 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 1311 GLN Chi-restraints excluded: chain D residue 1312 THR Chi-restraints excluded: chain D residue 1352 LEU 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 498 GLU Chi-restraints excluded: chain F residue 588 LEU Chi-restraints excluded: chain F residue 592 THR 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 Chi-restraints excluded: chain R residue 53 MET Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 366 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 387 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 423 optimal weight: 8.9990 chunk 290 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 304 optimal weight: 7.9990 chunk 425 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 GLN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1355 ASN ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1365 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 611 HIS Q 225 GLN R 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.206519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.138594 restraints weight = 46620.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136096 restraints weight = 24826.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.136653 restraints weight = 18688.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.137132 restraints weight = 16758.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.138255 restraints weight = 13952.107| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 37170 Z= 0.284 Angle : 0.712 15.925 50848 Z= 0.365 Chirality : 0.046 0.274 5847 Planarity : 0.005 0.053 6237 Dihedral : 16.092 172.125 6164 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.82 % Allowed : 17.44 % Favored : 77.75 % 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: -1.34 (0.13), residues: 4437 helix: 0.50 (0.13), residues: 1699 sheet: -1.24 (0.24), residues: 458 loop : -1.96 (0.13), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 120 TYR 0.019 0.002 TYR B 218 PHE 0.028 0.002 PHE D 18 TRP 0.026 0.001 TRP D 34 HIS 0.010 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.28 (37164) covalent geometry : angle 0.70391 / 0.36 (50842) hydrogen bonds : bond 0.04698 / 3.13 ( 1434) hydrogen bonds : angle 4.81931 / 3.42 ( 3947) metal coordination : bond 0.01689 / 1.08 ( 6) metal coordination : angle 9.73166 / 5.16 ( 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 967 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 801 time to evaluate : 1.190 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 16 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 18 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 119 GLU cc_start: 0.8341 (tp30) cc_final: 0.8141 (tp30) REVERT: B 16 GLN cc_start: 0.8294 (pp30) cc_final: 0.7884 (pp30) REVERT: B 44 ASN cc_start: 0.9140 (t0) cc_final: 0.8878 (t0) REVERT: B 87 ASN cc_start: 0.8970 (m110) cc_final: 0.8628 (m110) REVERT: B 89 LYS cc_start: 0.9327 (ptmm) cc_final: 0.9087 (ptpt) REVERT: C 392 MET cc_start: 0.8792 (tmm) cc_final: 0.8371 (tmm) REVERT: C 404 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7581 (t0) REVERT: C 469 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7960 (tm-30) REVERT: C 613 TYR cc_start: 0.8694 (m-80) cc_final: 0.8283 (m-80) REVERT: C 701 GLN cc_start: 0.8579 (tt0) cc_final: 0.8320 (tt0) REVERT: C 821 SER cc_start: 0.8806 (p) cc_final: 0.8545 (m) REVERT: C 843 GLU cc_start: 0.7640 (tt0) cc_final: 0.7103 (tt0) REVERT: C 958 GLU cc_start: 0.7894 (tp30) cc_final: 0.7557 (tp30) REVERT: C 1067 MET cc_start: 0.8509 (ptt) cc_final: 0.8102 (ptp) REVERT: C 1069 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8635 (mtpp) REVERT: C 1097 ILE cc_start: 0.9204 (mm) cc_final: 0.8806 (mt) REVERT: C 1103 MET cc_start: 0.8782 (mmt) cc_final: 0.8041 (mmm) REVERT: C 1189 ASN cc_start: 0.8950 (m-40) cc_final: 0.8624 (m-40) REVERT: C 1206 MET cc_start: 0.7878 (mmm) cc_final: 0.7531 (mmp) REVERT: C 1292 LEU cc_start: 0.9532 (mt) cc_final: 0.9196 (mt) REVERT: D 216 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8395 (tm-30) REVERT: D 287 LEU cc_start: 0.8845 (tt) cc_final: 0.8618 (tt) REVERT: D 398 GLN cc_start: 0.8707 (tp40) cc_final: 0.8370 (tp40) REVERT: D 406 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7300 (tm-30) REVERT: D 445 GLU cc_start: 0.7760 (mp0) cc_final: 0.7514 (mp0) REVERT: D 679 TYR cc_start: 0.6915 (t80) cc_final: 0.6680 (t80) REVERT: D 703 MET cc_start: 0.7867 (ppp) cc_final: 0.7258 (ppp) REVERT: D 734 LYS cc_start: 0.9086 (tttm) cc_final: 0.8814 (tttp) REVERT: D 796 LEU cc_start: 0.9629 (mm) cc_final: 0.9281 (mm) REVERT: D 1184 PHE cc_start: 0.7855 (m-10) cc_final: 0.7331 (m-10) REVERT: D 1341 GLU cc_start: 0.7628 (mp0) cc_final: 0.7255 (mp0) REVERT: E 11 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7992 (tm-30) REVERT: E 12 LYS cc_start: 0.8178 (tppp) cc_final: 0.7445 (tptm) REVERT: F 118 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7743 (ttm) REVERT: F 121 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7975 (ttp-170) REVERT: F 148 MET cc_start: 0.6865 (mmm) cc_final: 0.6401 (mmm) REVERT: F 248 MET cc_start: 0.7832 (mtm) cc_final: 0.7499 (mtm) REVERT: F 452 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8201 (mm) REVERT: F 466 LYS cc_start: 0.5623 (mmtm) cc_final: 0.5417 (mmtm) REVERT: F 474 TRP cc_start: 0.7311 (OUTLIER) cc_final: 0.5599 (m-90) REVERT: F 535 ARG cc_start: 0.8527 (mtp180) cc_final: 0.8255 (mtp85) REVERT: F 543 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6679 (tm-30) REVERT: Q 100 ARG cc_start: 0.7382 (ttp-110) cc_final: 0.6460 (mmp80) REVERT: Q 211 MET cc_start: 0.0879 (mtm) cc_final: -0.0744 (mmm) REVERT: R 36 ARG cc_start: 0.5442 (tpt90) cc_final: 0.5127 (tpp80) REVERT: R 86 ARG cc_start: 0.8371 (tmm160) cc_final: 0.7986 (tmm160) REVERT: R 167 ARG cc_start: 0.6160 (ptp90) cc_final: 0.5910 (ptp90) outliers start: 166 outliers final: 129 residues processed: 870 average time/residue: 0.2240 time to fit residues: 313.2066 Evaluate side-chains 906 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 773 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 A residue 229 ILE 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 170 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 204 ILE 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 415 MET Chi-restraints excluded: chain C residue 454 ASP 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 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 1060 LEU Chi-restraints excluded: chain C residue 1110 THR 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 182 ILE Chi-restraints excluded: chain D residue 232 SER 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 357 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 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 818 LEU Chi-restraints excluded: chain D residue 828 LEU Chi-restraints excluded: chain D residue 835 VAL Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 863 ASN 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 1222 VAL Chi-restraints excluded: chain D residue 1242 VAL Chi-restraints excluded: chain D residue 1271 ILE 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 D residue 1352 LEU 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 118 MET Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 453 MET Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 536 LYS Chi-restraints excluded: chain F residue 551 ILE 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 F residue 640 HIS Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 151 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 Chi-restraints excluded: chain R residue 34 VAL Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain R residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 244 optimal weight: 0.0070 chunk 257 optimal weight: 0.5980 chunk 291 optimal weight: 0.0470 chunk 287 optimal weight: 0.9980 chunk 233 optimal weight: 0.7980 chunk 314 optimal weight: 0.9980 chunk 379 optimal weight: 30.0000 chunk 403 optimal weight: 0.1980 chunk 352 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 GLN F 579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.212333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.145158 restraints weight = 46526.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.144710 restraints weight = 25123.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.145360 restraints weight = 17829.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.146024 restraints weight = 15297.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.146213 restraints weight = 12581.574| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37170 Z= 0.120 Angle : 0.606 15.524 50848 Z= 0.311 Chirality : 0.042 0.277 5847 Planarity : 0.004 0.051 6237 Dihedral : 16.058 172.738 6164 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.25 % Allowed : 20.48 % Favored : 76.27 % 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: -1.14 (0.13), residues: 4437 helix: 0.66 (0.13), residues: 1705 sheet: -1.05 (0.25), residues: 445 loop : -1.87 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 379 TYR 0.016 0.001 TYR A 154 PHE 0.025 0.001 PHE D 18 TRP 0.021 0.001 TRP D 34 HIS 0.008 0.001 HIS D1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (37164) covalent geometry : angle 0.60249 / 0.31 (50842) hydrogen bonds : bond 0.03616 / 2.38 ( 1434) hydrogen bonds : angle 4.49904 / 3.21 ( 3947) metal coordination : bond 0.00909 / 0.52 ( 6) metal coordination : angle 6.08118 / 3.11 ( 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 940 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 828 time to evaluate : 1.120 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 18 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 28 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7728 (ttm-80) REVERT: A 119 GLU cc_start: 0.8323 (tp30) cc_final: 0.8100 (tp30) REVERT: B 16 GLN cc_start: 0.8185 (pp30) cc_final: 0.7853 (pp30) REVERT: B 70 GLU cc_start: 0.8039 (pp20) cc_final: 0.7655 (pp20) REVERT: B 87 ASN cc_start: 0.8891 (m110) cc_final: 0.8521 (m110) REVERT: B 133 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8225 (pp) REVERT: B 226 GLN cc_start: 0.8929 (tp40) cc_final: 0.8519 (tp-100) REVERT: C 167 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8446 (mmmt) REVERT: C 198 ASP cc_start: 0.8154 (m-30) cc_final: 0.7207 (t0) REVERT: C 205 ASP cc_start: 0.8716 (t0) cc_final: 0.8316 (t0) REVERT: C 404 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7581 (t0) REVERT: C 429 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7177 (mtm110) REVERT: C 487 MET cc_start: 0.7365 (tmm) cc_final: 0.7138 (tmm) REVERT: C 613 TYR cc_start: 0.8671 (m-80) cc_final: 0.8296 (m-80) REVERT: C 701 GLN cc_start: 0.8493 (tt0) cc_final: 0.8232 (tt0) REVERT: C 843 GLU cc_start: 0.7609 (tt0) cc_final: 0.7124 (tt0) REVERT: C 1067 MET cc_start: 0.8406 (ptt) cc_final: 0.7986 (ptp) REVERT: C 1097 ILE cc_start: 0.8985 (mm) cc_final: 0.8515 (mt) REVERT: C 1103 MET cc_start: 0.8767 (mmt) cc_final: 0.8044 (mmm) REVERT: C 1189 ASN cc_start: 0.8906 (m-40) cc_final: 0.8592 (m-40) REVERT: C 1299 TYR cc_start: 0.8779 (m-80) cc_final: 0.8562 (m-10) REVERT: D 216 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8332 (tm-30) REVERT: D 398 GLN cc_start: 0.8628 (tp40) cc_final: 0.8255 (tp40) REVERT: D 406 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7241 (tm-30) REVERT: D 431 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8330 (mm) REVERT: D 703 MET cc_start: 0.7817 (ppp) cc_final: 0.7323 (ppp) REVERT: D 734 LYS cc_start: 0.8950 (tttm) cc_final: 0.8716 (tttp) REVERT: D 796 LEU cc_start: 0.9572 (mm) cc_final: 0.9187 (mm) REVERT: D 1184 PHE cc_start: 0.7846 (m-10) cc_final: 0.7368 (m-10) REVERT: D 1247 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.7970 (ttpt) REVERT: D 1341 GLU cc_start: 0.7536 (mp0) cc_final: 0.7118 (mp0) REVERT: E 11 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7900 (tm-30) REVERT: E 12 LYS cc_start: 0.8101 (tppp) cc_final: 0.7337 (tptm) REVERT: F 121 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7940 (ttp-170) REVERT: F 148 MET cc_start: 0.6879 (mmm) cc_final: 0.6507 (mmm) REVERT: F 248 MET cc_start: 0.7975 (mtm) cc_final: 0.7665 (mtm) REVERT: F 452 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8104 (mm) REVERT: F 466 LYS cc_start: 0.5450 (mmtm) cc_final: 0.5235 (mmtm) REVERT: F 474 TRP cc_start: 0.7036 (OUTLIER) cc_final: 0.5587 (m-90) REVERT: F 535 ARG cc_start: 0.8516 (mtp180) cc_final: 0.8162 (mtp180) REVERT: F 543 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6565 (tm-30) REVERT: F 637 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7624 (tttm) REVERT: Q 100 ARG cc_start: 0.7061 (ttp-110) cc_final: 0.6497 (mmp-170) REVERT: Q 211 MET cc_start: 0.0830 (mtm) cc_final: -0.0787 (mmm) REVERT: R 36 ARG cc_start: 0.5164 (tpt90) cc_final: 0.4927 (tpp80) REVERT: R 86 ARG cc_start: 0.8224 (tmm160) cc_final: 0.7851 (tmm160) outliers start: 112 outliers final: 77 residues processed: 875 average time/residue: 0.2190 time to fit residues: 308.2336 Evaluate side-chains 869 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 786 time to evaluate : 1.378 ------------------------------------------------------------------------------- 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 134 CYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 81 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 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 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 674 LEU 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 926 LEU 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 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 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 431 LEU 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 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 828 LEU 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 1242 VAL Chi-restraints excluded: chain D residue 1247 LYS Chi-restraints excluded: chain D residue 1301 VAL Chi-restraints excluded: chain D residue 1311 GLN Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 453 MET Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 536 LYS 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 280 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 241 optimal weight: 0.0010 chunk 313 optimal weight: 4.9990 chunk 49 optimal weight: 40.0000 chunk 188 optimal weight: 0.0570 chunk 339 optimal weight: 30.0000 chunk 195 optimal weight: 4.9990 chunk 167 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 311 optimal weight: 1.9990 overall best weight: 0.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN A 150 ASN A 228 GLN C 26 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.212284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.148440 restraints weight = 46523.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.145593 restraints weight = 26473.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.144833 restraints weight = 21949.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.145725 restraints weight = 20587.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.147096 restraints weight = 16163.567| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1710 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= 0.116 Angle : 0.603 15.666 50848 Z= 0.306 Chirality : 0.042 0.278 5847 Planarity : 0.004 0.057 6237 Dihedral : 16.036 172.456 6164 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.34 % Allowed : 21.67 % Favored : 74.99 % 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: -1.07 (0.13), residues: 4437 helix: 0.73 (0.13), residues: 1705 sheet: -1.04 (0.25), residues: 458 loop : -1.82 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 379 TYR 0.017 0.001 TYR A 154 PHE 0.024 0.001 PHE D 18 TRP 0.021 0.001 TRP D 34 HIS 0.006 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (37164) covalent geometry : angle 0.60066 / 0.31 (50842) hydrogen bonds : bond 0.03391 / 2.21 ( 1434) hydrogen bonds : angle 4.40770 / 3.14 ( 3947) metal coordination : bond 0.00827 / 0.47 ( 6) metal coordination : angle 5.03172 / 2.60 ( 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 919 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 804 time to evaluate : 1.212 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 203 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7426 (mt-10) REVERT: B 16 GLN cc_start: 0.8179 (pp30) cc_final: 0.7844 (pp30) REVERT: B 70 GLU cc_start: 0.8002 (pp20) cc_final: 0.7621 (pp20) REVERT: B 87 ASN cc_start: 0.8875 (m110) cc_final: 0.8509 (m110) REVERT: B 226 GLN cc_start: 0.8922 (tp40) cc_final: 0.8426 (tp-100) REVERT: C 26 ASN cc_start: 0.8586 (OUTLIER) cc_final: 0.8372 (t0) REVERT: C 155 MET cc_start: 0.9023 (ttm) cc_final: 0.8756 (ttp) REVERT: C 167 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8524 (mmmt) REVERT: C 198 ASP cc_start: 0.8110 (m-30) cc_final: 0.7167 (t0) REVERT: C 205 ASP cc_start: 0.8667 (t0) cc_final: 0.8279 (t0) REVERT: C 404 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7610 (t70) REVERT: C 429 ARG cc_start: 0.7504 (mtm-85) cc_final: 0.7198 (mtm110) REVERT: C 487 MET cc_start: 0.7507 (tmm) cc_final: 0.7253 (tmm) REVERT: C 613 TYR cc_start: 0.8612 (m-80) cc_final: 0.8283 (m-80) REVERT: C 701 GLN cc_start: 0.8546 (tt0) cc_final: 0.8258 (tt0) REVERT: C 807 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8230 (tt) REVERT: C 843 GLU cc_start: 0.7584 (tt0) cc_final: 0.7129 (tt0) REVERT: C 1067 MET cc_start: 0.8406 (ptt) cc_final: 0.8014 (ptp) REVERT: C 1097 ILE cc_start: 0.8936 (mm) cc_final: 0.8533 (mt) REVERT: C 1103 MET cc_start: 0.8764 (mmt) cc_final: 0.8018 (mmm) REVERT: C 1189 ASN cc_start: 0.8888 (m-40) cc_final: 0.8537 (m-40) REVERT: C 1206 MET cc_start: 0.7608 (mmm) cc_final: 0.7274 (mmp) REVERT: D 216 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8267 (tm-30) REVERT: D 276 ASN cc_start: 0.8419 (t0) cc_final: 0.7953 (m-40) REVERT: D 398 GLN cc_start: 0.8578 (tp40) cc_final: 0.8241 (tp40) REVERT: D 406 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7282 (tm-30) REVERT: D 431 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8374 (mm) REVERT: D 703 MET cc_start: 0.7818 (ppp) cc_final: 0.7297 (ppp) REVERT: D 734 LYS cc_start: 0.8923 (tttm) cc_final: 0.8699 (tttp) REVERT: D 796 LEU cc_start: 0.9564 (mm) cc_final: 0.9216 (mm) REVERT: D 1184 PHE cc_start: 0.7773 (m-10) cc_final: 0.7382 (m-10) REVERT: D 1247 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8118 (ttpt) REVERT: D 1341 GLU cc_start: 0.7523 (mp0) cc_final: 0.7306 (mp0) REVERT: E 11 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7918 (tm-30) REVERT: E 12 LYS cc_start: 0.8166 (tppp) cc_final: 0.7412 (tptm) REVERT: F 121 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7922 (ttp-170) REVERT: F 148 MET cc_start: 0.6962 (mmm) cc_final: 0.6610 (mmm) REVERT: F 248 MET cc_start: 0.7740 (mtm) cc_final: 0.7498 (mtm) REVERT: F 452 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8216 (mm) REVERT: F 474 TRP cc_start: 0.7017 (OUTLIER) cc_final: 0.5481 (m-90) REVERT: F 535 ARG cc_start: 0.8335 (mtp180) cc_final: 0.7982 (mtp85) REVERT: F 543 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6548 (tm-30) REVERT: F 637 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7531 (tttm) REVERT: Q 100 ARG cc_start: 0.7236 (ttp-110) cc_final: 0.6381 (mmp80) REVERT: Q 211 MET cc_start: 0.0561 (mtm) cc_final: -0.0902 (mmm) REVERT: R 36 ARG cc_start: 0.5334 (tpt90) cc_final: 0.5051 (tpp80) REVERT: R 86 ARG cc_start: 0.8270 (tmm160) cc_final: 0.7820 (tmm160) outliers start: 115 outliers final: 82 residues processed: 859 average time/residue: 0.2191 time to fit residues: 301.9325 Evaluate side-chains 865 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 776 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 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 118 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 158 ASP 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 170 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 210 LEU 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 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 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 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 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 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 431 LEU 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 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 817 THR Chi-restraints excluded: chain D residue 828 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 1143 ASP Chi-restraints excluded: chain D residue 1195 HIS 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 1337 THR 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 453 MET Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 536 LYS 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 280 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 0.0070 chunk 291 optimal weight: 0.0010 chunk 448 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 236 optimal weight: 1.9990 chunk 420 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 453 optimal weight: 8.9990 chunk 357 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS R 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.212670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.145724 restraints weight = 46476.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.145074 restraints weight = 24232.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.146314 restraints weight = 17118.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.146465 restraints weight = 15364.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.146724 restraints weight = 13413.708| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1758 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= 0.116 Angle : 0.602 15.660 50848 Z= 0.306 Chirality : 0.042 0.279 5847 Planarity : 0.004 0.060 6237 Dihedral : 16.024 172.501 6164 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.08 % Allowed : 22.19 % Favored : 74.73 % 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: 0.77 (0.13), residues: 1705 sheet: -0.99 (0.25), residues: 458 loop : -1.81 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 288 TYR 0.011 0.001 TYR C 403 PHE 0.021 0.001 PHE D 18 TRP 0.022 0.001 TRP D 34 HIS 0.011 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (37164) covalent geometry : angle 0.60028 / 0.31 (50842) hydrogen bonds : bond 0.03328 / 2.17 ( 1434) hydrogen bonds : angle 4.38047 / 3.12 ( 3947) metal coordination : bond 0.00801 / 0.46 ( 6) metal coordination : angle 4.75725 / 2.43 ( 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 900 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 794 time to evaluate : 0.917 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 14 LYS cc_start: 0.8249 (tmmt) cc_final: 0.7892 (ttpp) REVERT: A 28 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7700 (ttm-80) REVERT: A 119 GLU cc_start: 0.8328 (tp30) cc_final: 0.8088 (tp30) REVERT: B 16 GLN cc_start: 0.8164 (pp30) cc_final: 0.7857 (pp30) REVERT: B 70 GLU cc_start: 0.8006 (pp20) cc_final: 0.7638 (pp20) REVERT: B 87 ASN cc_start: 0.8859 (m110) cc_final: 0.8471 (m110) REVERT: B 226 GLN cc_start: 0.8895 (tp40) cc_final: 0.8436 (tp-100) REVERT: C 167 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8585 (mmmt) REVERT: C 198 ASP cc_start: 0.8012 (m-30) cc_final: 0.7094 (t0) REVERT: C 205 ASP cc_start: 0.8666 (t0) cc_final: 0.8281 (t0) REVERT: C 404 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7569 (t70) REVERT: C 429 ARG cc_start: 0.7524 (mtm-85) cc_final: 0.7153 (mtm110) REVERT: C 487 MET cc_start: 0.7548 (tmm) cc_final: 0.7324 (tmm) REVERT: C 613 TYR cc_start: 0.8636 (m-80) cc_final: 0.8311 (m-80) REVERT: C 701 GLN cc_start: 0.8554 (tt0) cc_final: 0.8281 (tt0) REVERT: C 807 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8440 (tt) REVERT: C 843 GLU cc_start: 0.7613 (tt0) cc_final: 0.7138 (tt0) REVERT: C 1067 MET cc_start: 0.8413 (ptt) cc_final: 0.8012 (ptp) REVERT: C 1097 ILE cc_start: 0.8924 (mm) cc_final: 0.8619 (mt) REVERT: C 1103 MET cc_start: 0.8787 (mmt) cc_final: 0.8100 (mmm) REVERT: C 1189 ASN cc_start: 0.8901 (m-40) cc_final: 0.8548 (m-40) REVERT: C 1206 MET cc_start: 0.7594 (mmm) cc_final: 0.7281 (mmp) REVERT: D 216 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8330 (tm-30) REVERT: D 276 ASN cc_start: 0.8417 (t0) cc_final: 0.7948 (m-40) REVERT: D 398 GLN cc_start: 0.8644 (tp40) cc_final: 0.8279 (tp40) REVERT: D 406 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7204 (tm-30) REVERT: D 431 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8315 (mm) REVERT: D 703 MET cc_start: 0.7834 (ppp) cc_final: 0.7296 (ppp) REVERT: D 734 LYS cc_start: 0.8930 (tttm) cc_final: 0.8704 (tttp) REVERT: D 796 LEU cc_start: 0.9531 (mm) cc_final: 0.9196 (mm) REVERT: D 1070 MET cc_start: 0.5375 (ppp) cc_final: 0.5004 (ppp) REVERT: D 1184 PHE cc_start: 0.7738 (m-10) cc_final: 0.7363 (m-10) REVERT: D 1247 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8132 (ttpt) REVERT: D 1341 GLU cc_start: 0.7529 (mp0) cc_final: 0.7204 (mp0) REVERT: E 11 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7918 (tm-30) REVERT: E 12 LYS cc_start: 0.8140 (tppp) cc_final: 0.7374 (tptm) REVERT: F 121 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7888 (ttp-170) REVERT: F 148 MET cc_start: 0.6934 (mmm) cc_final: 0.6601 (mmm) REVERT: F 248 MET cc_start: 0.7924 (mtm) cc_final: 0.7625 (mtm) REVERT: F 452 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8156 (mm) REVERT: F 474 TRP cc_start: 0.6965 (OUTLIER) cc_final: 0.5483 (m-90) REVERT: F 535 ARG cc_start: 0.8376 (mtp180) cc_final: 0.8034 (mtp180) REVERT: F 543 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6682 (tm-30) REVERT: F 579 ASN cc_start: 0.8833 (t0) cc_final: 0.8621 (t0) REVERT: F 637 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7569 (tttm) REVERT: Q 100 ARG cc_start: 0.7099 (ttp-110) cc_final: 0.6327 (mmp80) REVERT: Q 211 MET cc_start: 0.0811 (mtm) cc_final: -0.0718 (mmm) REVERT: R 36 ARG cc_start: 0.5410 (tpt90) cc_final: 0.5202 (tpp80) REVERT: R 86 ARG cc_start: 0.8202 (tmm160) cc_final: 0.7775 (tmm160) outliers start: 106 outliers final: 86 residues processed: 840 average time/residue: 0.2155 time to fit residues: 291.9820 Evaluate side-chains 872 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 780 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 88 ILE Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 177 SER 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 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 204 ILE Chi-restraints excluded: chain C residue 210 LEU 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 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 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 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 1307 VAL 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 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 431 LEU 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 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 828 LEU 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 1195 HIS 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 1337 THR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 453 MET Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 536 LYS Chi-restraints excluded: chain F residue 592 THR 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 280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 226 optimal weight: 0.7980 chunk 231 optimal weight: 0.6980 chunk 378 optimal weight: 3.9990 chunk 391 optimal weight: 10.0000 chunk 355 optimal weight: 1.9990 chunk 427 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 370 optimal weight: 0.0020 chunk 151 optimal weight: 2.9990 chunk 404 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.212893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.145231 restraints weight = 46610.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.145361 restraints weight = 24575.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.145318 restraints weight = 17538.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.145780 restraints weight = 16543.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.146174 restraints weight = 13905.590| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1820 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= 0.130 Angle : 0.609 16.541 50848 Z= 0.309 Chirality : 0.042 0.279 5847 Planarity : 0.004 0.059 6237 Dihedral : 16.014 172.707 6164 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.28 % Allowed : 22.16 % Favored : 74.56 % 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: 0.78 (0.13), residues: 1705 sheet: -1.02 (0.25), residues: 462 loop : -1.82 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 288 TYR 0.021 0.001 TYR C 403 PHE 0.020 0.001 PHE D 18 TRP 0.030 0.001 TRP D 34 HIS 0.007 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (37164) covalent geometry : angle 0.60618 / 0.31 (50842) hydrogen bonds : bond 0.03382 / 2.21 ( 1434) hydrogen bonds : angle 4.36102 / 3.10 ( 3947) metal coordination : bond 0.00886 / 0.53 ( 6) metal coordination : angle 5.25126 / 2.70 ( 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 902 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 789 time to evaluate : 1.260 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: 0.8327 (tmmt) cc_final: 0.8001 (ttpp) REVERT: A 28 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7653 (ttm-80) REVERT: A 119 GLU cc_start: 0.8307 (tp30) cc_final: 0.8087 (tp30) REVERT: B 16 GLN cc_start: 0.8184 (pp30) cc_final: 0.7881 (pp30) REVERT: B 70 GLU cc_start: 0.8021 (pp20) cc_final: 0.7653 (pp20) REVERT: B 87 ASN cc_start: 0.8868 (m110) cc_final: 0.8516 (m110) REVERT: B 103 MET cc_start: 0.8256 (ttt) cc_final: 0.8029 (ttm) REVERT: B 226 GLN cc_start: 0.8946 (tp40) cc_final: 0.8497 (tp-100) REVERT: C 205 ASP cc_start: 0.8698 (t0) cc_final: 0.8314 (t0) REVERT: C 404 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.7532 (t0) REVERT: C 429 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.7298 (mtm110) REVERT: C 487 MET cc_start: 0.7538 (tmm) cc_final: 0.7321 (tmm) REVERT: C 613 TYR cc_start: 0.8629 (m-80) cc_final: 0.8314 (m-80) REVERT: C 701 GLN cc_start: 0.8568 (tt0) cc_final: 0.8290 (tt0) REVERT: C 807 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8477 (tt) REVERT: C 843 GLU cc_start: 0.7609 (tt0) cc_final: 0.7156 (tt0) REVERT: C 1067 MET cc_start: 0.8429 (ptt) cc_final: 0.8052 (ptp) REVERT: C 1097 ILE cc_start: 0.8980 (mm) cc_final: 0.8580 (mt) REVERT: C 1189 ASN cc_start: 0.8909 (m-40) cc_final: 0.8575 (m-40) REVERT: C 1206 MET cc_start: 0.7630 (mmm) cc_final: 0.7333 (mmp) REVERT: C 1278 GLN cc_start: 0.8991 (pm20) cc_final: 0.8557 (pm20) REVERT: C 1299 TYR cc_start: 0.8824 (m-80) cc_final: 0.8366 (m-80) REVERT: D 216 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8317 (tm-30) REVERT: D 398 GLN cc_start: 0.8655 (tp40) cc_final: 0.8283 (tp40) REVERT: D 406 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7221 (tm-30) REVERT: D 431 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8325 (mm) REVERT: D 703 MET cc_start: 0.7848 (ppp) cc_final: 0.7297 (ppp) REVERT: D 734 LYS cc_start: 0.8908 (tttm) cc_final: 0.8687 (tttp) REVERT: D 796 LEU cc_start: 0.9543 (mm) cc_final: 0.9215 (mm) REVERT: D 807 GLU cc_start: 0.7652 (tt0) cc_final: 0.7356 (tt0) REVERT: D 1070 MET cc_start: 0.5401 (ppp) cc_final: 0.5099 (tmm) REVERT: D 1184 PHE cc_start: 0.7779 (m-10) cc_final: 0.7437 (m-10) REVERT: D 1247 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8154 (ttpt) REVERT: D 1341 GLU cc_start: 0.7508 (mp0) cc_final: 0.7131 (mp0) REVERT: E 11 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 12 LYS cc_start: 0.8177 (tppp) cc_final: 0.7410 (tptm) REVERT: F 121 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7907 (ttp-170) REVERT: F 148 MET cc_start: 0.6920 (mmm) cc_final: 0.6574 (mmm) REVERT: F 248 MET cc_start: 0.7880 (mtm) cc_final: 0.7593 (mtm) REVERT: F 452 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8222 (mm) REVERT: F 474 TRP cc_start: 0.7011 (OUTLIER) cc_final: 0.5522 (m-90) REVERT: F 535 ARG cc_start: 0.8370 (mtp180) cc_final: 0.8063 (mtp180) REVERT: F 543 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6746 (tm-30) REVERT: F 579 ASN cc_start: 0.8834 (t0) cc_final: 0.8621 (t0) REVERT: F 601 MET cc_start: 0.7928 (ttp) cc_final: 0.7672 (ttp) REVERT: F 637 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7574 (tttm) REVERT: Q 42 MET cc_start: 0.7432 (tpp) cc_final: 0.7199 (tpp) REVERT: Q 100 ARG cc_start: 0.7085 (ttp-110) cc_final: 0.6321 (mmp80) REVERT: Q 211 MET cc_start: 0.0517 (mtm) cc_final: -0.0912 (mmm) REVERT: R 86 ARG cc_start: 0.8221 (tmm160) cc_final: 0.7780 (tmm160) outliers start: 113 outliers final: 97 residues processed: 843 average time/residue: 0.2209 time to fit residues: 299.1737 Evaluate side-chains 880 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 777 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 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 204 ILE Chi-restraints excluded: chain C residue 210 LEU 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 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 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 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 431 LEU 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 828 LEU 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 1144 CYS Chi-restraints excluded: chain D residue 1195 HIS 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 1337 THR 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 453 MET Chi-restraints excluded: chain F residue 474 TRP Chi-restraints excluded: chain F residue 495 HIS Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 536 LYS Chi-restraints excluded: chain F residue 592 THR 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 90 ASP Chi-restraints excluded: chain R residue 280 VAL 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: 0.4980 chunk 437 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 375 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 416 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN B 224 GLN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.213304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.147853 restraints weight = 46950.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.145561 restraints weight = 26792.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.145555 restraints weight = 20176.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.146263 restraints weight = 16929.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.146398 restraints weight = 13411.750| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1856 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= 0.127 Angle : 0.623 16.588 50848 Z= 0.314 Chirality : 0.042 0.279 5847 Planarity : 0.004 0.060 6237 Dihedral : 16.015 172.797 6164 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.99 % Allowed : 22.60 % Favored : 74.41 % 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: -1.02 (0.13), residues: 4437 helix: 0.78 (0.13), residues: 1706 sheet: -0.95 (0.25), residues: 448 loop : -1.82 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 956 TYR 0.015 0.001 TYR C 403 PHE 0.020 0.001 PHE C 178 TRP 0.024 0.001 TRP D 34 HIS 0.007 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (37164) covalent geometry : angle 0.62041 / 0.31 (50842) hydrogen bonds : bond 0.03355 / 2.19 ( 1434) hydrogen bonds : angle 4.34684 / 3.09 ( 3947) metal coordination : bond 0.00868 / 0.52 ( 6) metal coordination : angle 5.35725 / 2.71 ( 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 894 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 791 time to evaluate : 1.260 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: 0.8322 (tmmt) cc_final: 0.7989 (ttpp) REVERT: A 28 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7701 (ttm-80) REVERT: A 119 GLU cc_start: 0.8348 (tp30) cc_final: 0.8101 (tp30) REVERT: B 16 GLN cc_start: 0.8183 (pp30) cc_final: 0.7897 (pp30) REVERT: B 70 GLU cc_start: 0.8010 (pp20) cc_final: 0.7617 (pp20) REVERT: B 87 ASN cc_start: 0.8844 (m110) cc_final: 0.8487 (m110) REVERT: B 103 MET cc_start: 0.8216 (ttt) cc_final: 0.7991 (ttm) REVERT: B 226 GLN cc_start: 0.8935 (tp40) cc_final: 0.8483 (tp-100) REVERT: C 198 ASP cc_start: 0.7954 (m-30) cc_final: 0.6978 (t70) REVERT: C 205 ASP cc_start: 0.8680 (t0) cc_final: 0.8300 (t0) REVERT: C 392 MET cc_start: 0.8743 (tmm) cc_final: 0.8458 (tmm) REVERT: C 404 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7540 (t0) REVERT: C 429 ARG cc_start: 0.7528 (mtm-85) cc_final: 0.7284 (mtm110) REVERT: C 460 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8084 (ttt-90) REVERT: C 487 MET cc_start: 0.7539 (tmm) cc_final: 0.7298 (tmm) REVERT: C 613 TYR cc_start: 0.8615 (m-80) cc_final: 0.8256 (m-80) REVERT: C 701 GLN cc_start: 0.8568 (tt0) cc_final: 0.8296 (tt0) REVERT: C 732 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7626 (mm-30) REVERT: C 776 LEU cc_start: 0.9207 (tp) cc_final: 0.8994 (tp) REVERT: C 807 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8459 (tt) REVERT: C 843 GLU cc_start: 0.7595 (tt0) cc_final: 0.7091 (tt0) REVERT: C 1069 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8561 (mtpp) REVERT: C 1097 ILE cc_start: 0.8965 (mm) cc_final: 0.8603 (mt) REVERT: C 1189 ASN cc_start: 0.8898 (m-40) cc_final: 0.8568 (m-40) REVERT: C 1206 MET cc_start: 0.7605 (mmm) cc_final: 0.7318 (mmp) REVERT: C 1278 GLN cc_start: 0.9013 (pm20) cc_final: 0.8584 (pm20) REVERT: C 1299 TYR cc_start: 0.8809 (m-80) cc_final: 0.8369 (m-80) REVERT: D 216 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 276 ASN cc_start: 0.8390 (t0) cc_final: 0.7886 (m-40) REVERT: D 398 GLN cc_start: 0.8628 (tp40) cc_final: 0.8277 (tp40) REVERT: D 406 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7243 (tm-30) REVERT: D 431 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8314 (mm) REVERT: D 703 MET cc_start: 0.7861 (ppp) cc_final: 0.7303 (ppp) REVERT: D 734 LYS cc_start: 0.8896 (tttm) cc_final: 0.8680 (tttp) REVERT: D 796 LEU cc_start: 0.9529 (mm) cc_final: 0.9189 (mm) REVERT: D 807 GLU cc_start: 0.7667 (tt0) cc_final: 0.7363 (tt0) REVERT: D 1070 MET cc_start: 0.5162 (ppp) cc_final: 0.4873 (tmm) REVERT: D 1184 PHE cc_start: 0.7815 (m-10) cc_final: 0.7430 (m-10) REVERT: D 1247 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8154 (ttpt) REVERT: D 1341 GLU cc_start: 0.7188 (mp0) cc_final: 0.6820 (mp0) REVERT: E 11 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7922 (tm-30) REVERT: E 12 LYS cc_start: 0.8170 (tppp) cc_final: 0.7399 (tptm) REVERT: F 121 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7912 (ttp-170) REVERT: F 131 ARG cc_start: 0.8415 (tpt90) cc_final: 0.7910 (tpt90) REVERT: F 148 MET cc_start: 0.6927 (mmm) cc_final: 0.6566 (mmm) REVERT: F 248 MET cc_start: 0.7756 (mtm) cc_final: 0.7537 (mtm) REVERT: F 452 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8233 (mm) REVERT: F 474 TRP cc_start: 0.7000 (OUTLIER) cc_final: 0.5578 (m-90) REVERT: F 535 ARG cc_start: 0.8345 (mtp180) cc_final: 0.8043 (mtp180) REVERT: F 543 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6765 (tm-30) REVERT: F 619 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8179 (tm-30) REVERT: F 637 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7520 (tttm) REVERT: Q 42 MET cc_start: 0.7519 (tpp) cc_final: 0.7265 (tpp) REVERT: Q 100 ARG cc_start: 0.7188 (ttp-110) cc_final: 0.6733 (tpp-160) REVERT: Q 211 MET cc_start: 0.0337 (mtm) cc_final: -0.1038 (mmm) REVERT: R 86 ARG cc_start: 0.8276 (tmm160) cc_final: 0.7809 (tmm160) outliers start: 103 outliers final: 94 residues processed: 840 average time/residue: 0.2140 time to fit residues: 290.0863 Evaluate side-chains 882 residues out of total 3692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 782 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 A residue 177 SER 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 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 204 ILE Chi-restraints excluded: chain C residue 210 LEU 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 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 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 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 431 LEU 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 828 LEU 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 1144 CYS Chi-restraints excluded: chain D residue 1195 HIS 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 1337 THR 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 498 GLU Chi-restraints excluded: chain F residue 536 LYS 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 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 90 ASP Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 173 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 chunk 200 optimal weight: 0.0070 chunk 292 optimal weight: 0.0570 chunk 58 optimal weight: 0.2980 chunk 294 optimal weight: 0.9980 chunk 395 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 278 optimal weight: 0.0570 chunk 72 optimal weight: 5.9990 chunk 442 optimal weight: 9.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 GLN C 26 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1365 GLN R 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.209907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.145093 restraints weight = 46912.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.142524 restraints weight = 28947.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.143049 restraints weight = 20520.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.143135 restraints weight = 20753.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.143677 restraints weight = 15956.562| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 37170 Z= 0.113 Angle : 0.611 16.730 50848 Z= 0.308 Chirality : 0.041 0.279 5847 Planarity : 0.004 0.056 6237 Dihedral : 15.988 172.825 6164 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.96 % Allowed : 22.57 % Favored : 74.47 % 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: -0.97 (0.13), residues: 4437 helix: 0.82 (0.13), residues: 1709 sheet: -0.92 (0.25), residues: 453 loop : -1.80 (0.13), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 120 TYR 0.019 0.001 TYR D 271 PHE 0.019 0.001 PHE D 18 TRP 0.032 0.001 TRP D 34 HIS 0.008 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (37164) covalent geometry : angle 0.60910 / 0.31 (50842) hydrogen bonds : bond 0.03152 / 2.05 ( 1434) hydrogen bonds : angle 4.27607 / 3.04 ( 3947) metal coordination : bond 0.00848 / 0.48 ( 6) metal coordination : angle 4.28263 / 2.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7279.13 seconds wall clock time: 125 minutes 31.75 seconds (7531.75 seconds total)