Starting phenix.real_space_refine on Sun Aug 9 19:15:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vw8_65391/08_2026/9vw8_65391.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vw8_65391/08_2026/9vw8_65391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vw8_65391/08_2026/9vw8_65391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vw8_65391/08_2026/9vw8_65391.map" model { file = "/net/cci-nas-00/data/ceres_data/9vw8_65391/08_2026/9vw8_65391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vw8_65391/08_2026/9vw8_65391.cif" } resolution = 3.36 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 170 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 146 5.49 5 S 147 5.16 5 C 22406 2.51 5 N 6539 2.21 5 O 7262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36500 Number of models: 1 Model: "" Number of chains: 13 Chain: "1" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1482 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "2" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1524 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10560 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 10362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10362 Classifications: {'peptide': 1333} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1279} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3977 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1074 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "P" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 548 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 65} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 873 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1026 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "L" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 894 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.91, per 1000 atoms: 0.19 Number of scatterers: 36500 At special positions: 0 Unit cell: (214.8, 175.2, 180, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 147 16.00 P 146 15.00 O 7262 8.00 N 6539 7.00 C 22406 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 8406 Ramachandran restraints generated. 4203 Oldfield, 0 Emsley, 4203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7912 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 44 sheets defined 48.2% alpha, 12.6% beta 51 base pairs and 105 stacking pairs defined. Time for finding SS restraints: 3.89 Creating SS restraints... Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.573A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.645A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.928A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.038A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.546A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 233 removed outlier: 5.411A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.768A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.524A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.873A pdb=" N LEU C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.614A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.139A pdb=" N GLU C 382 " --> pdb=" O ARG C 378 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.867A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.736A pdb=" N ILE C 493 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.977A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.766A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.670A pdb=" N GLY C 612 " --> pdb=" O ILE C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.893A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.628A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 907 Processing helix chain 'C' and resid 942 through 976 removed outlier: 3.621A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.844A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 4.233A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1024 removed outlier: 3.621A pdb=" N GLN C1008 " --> pdb=" O ASP C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1100 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 4.253A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1149 Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1177 through 1179 No H-bonds generated for 'chain 'C' and resid 1177 through 1179' Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1261 through 1265 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.889A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.772A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 202 " --> pdb=" O CYS D 198 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.767A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.170A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.542A pdb=" N LEU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.505A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.164A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.858A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.988A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.704A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 1138 through 1147 removed outlier: 4.273A pdb=" N LEU D1144 " --> pdb=" O ARG D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.606A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 4.373A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1291 removed outlier: 4.227A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D1290 " --> pdb=" O LYS D1286 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 removed outlier: 3.609A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.631A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 3.768A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 14 removed outlier: 3.756A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.831A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 4.342A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 66 through 80 removed outlier: 3.653A pdb=" N GLN E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 89 removed outlier: 3.756A pdb=" N LEU F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.824A pdb=" N THR F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 136 Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.939A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 213 through 237 removed outlier: 4.100A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 258 removed outlier: 3.523A pdb=" N GLN F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 291 removed outlier: 3.688A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 4.019A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 Processing helix chain 'F' and resid 324 through 329 removed outlier: 3.854A pdb=" N LYS F 329 " --> pdb=" O PRO F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.970A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA F 340 " --> pdb=" O GLU F 336 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU F 341 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 382 removed outlier: 3.808A pdb=" N ALA F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 392 Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 401 through 419 removed outlier: 4.028A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.590A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.796A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 482 through 488 removed outlier: 4.185A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 500 removed outlier: 3.652A pdb=" N ILE F 500 " --> pdb=" O LYS F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 523 Processing helix chain 'F' and resid 530 through 550 Processing helix chain 'F' and resid 552 through 563 Processing helix chain 'F' and resid 572 through 580 removed outlier: 3.575A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 600 Processing helix chain 'F' and resid 603 through 609 removed outlier: 4.387A pdb=" N LEU F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER F 609 " --> pdb=" O GLU F 605 " (cutoff:3.500A) Processing helix chain 'F' and resid 610 through 613 Processing helix chain 'J' and resid 4 through 9 removed outlier: 4.023A pdb=" N HIS J 8 " --> pdb=" O ASP J 4 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP J 9 " --> pdb=" O LEU J 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 4 through 9' Processing helix chain 'J' and resid 9 through 19 Processing helix chain 'J' and resid 20 through 22 No H-bonds generated for 'chain 'J' and resid 20 through 22' Processing helix chain 'J' and resid 23 through 31 removed outlier: 3.949A pdb=" N LEU J 27 " --> pdb=" O PRO J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 49 removed outlier: 3.537A pdb=" N VAL J 36 " --> pdb=" O PRO J 32 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG J 48 " --> pdb=" O ASN J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 70 Processing helix chain 'J' and resid 79 through 95 removed outlier: 4.053A pdb=" N LEU J 83 " --> pdb=" O GLY J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 108 Processing helix chain 'J' and resid 110 through 125 Processing helix chain 'P' and resid 256 through 260 removed outlier: 3.515A pdb=" N ASP P 259 " --> pdb=" O PRO P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 263 through 272 Processing helix chain 'P' and resid 278 through 284 Processing helix chain 'P' and resid 285 through 290 removed outlier: 3.523A pdb=" N LEU P 289 " --> pdb=" O THR P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 310 Processing helix chain 'I' and resid 27 through 31 Processing helix chain 'I' and resid 33 through 49 removed outlier: 3.627A pdb=" N ILE I 39 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 70 Processing helix chain 'I' and resid 80 through 95 removed outlier: 3.823A pdb=" N ALA I 85 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 108 Processing helix chain 'I' and resid 110 through 130 Processing helix chain 'K' and resid 4 through 8 removed outlier: 3.901A pdb=" N HIS K 8 " --> pdb=" O LEU K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 17 removed outlier: 3.864A pdb=" N ARG K 13 " --> pdb=" O ASP K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 22 Processing helix chain 'K' and resid 23 through 28 removed outlier: 3.971A pdb=" N LEU K 27 " --> pdb=" O PRO K 23 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU K 28 " --> pdb=" O ALA K 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 23 through 28' Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 32 through 49 removed outlier: 3.775A pdb=" N VAL K 36 " --> pdb=" O PRO K 32 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL K 41 " --> pdb=" O ASP K 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN K 49 " --> pdb=" O GLU K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 69 removed outlier: 3.856A pdb=" N ALA K 64 " --> pdb=" O LYS K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 95 removed outlier: 3.952A pdb=" N LEU K 83 " --> pdb=" O GLY K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 108 Processing helix chain 'K' and resid 110 through 127 removed outlier: 3.663A pdb=" N LYS K 123 " --> pdb=" O ALA K 119 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU K 124 " --> pdb=" O ARG K 120 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS K 125 " --> pdb=" O GLN K 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 30 removed outlier: 4.363A pdb=" N ARG L 30 " --> pdb=" O GLU L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 50 removed outlier: 3.914A pdb=" N VAL L 36 " --> pdb=" O PRO L 32 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL L 41 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU L 42 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG L 48 " --> pdb=" O ASN L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 69 Processing helix chain 'L' and resid 80 through 95 removed outlier: 4.197A pdb=" N ALA L 85 " --> pdb=" O THR L 81 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU L 86 " --> pdb=" O ILE L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 107 Processing helix chain 'L' and resid 110 through 130 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 6.598A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.665A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.568A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.944A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 3.805A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 4.133A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.577A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.597A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 284 through 287 removed outlier: 4.271A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.557A pdb=" N TYR C 301 " --> pdb=" O ILE C 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 598 through 606 removed outlier: 4.097A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.463A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.379A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.387A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.384A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.821A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.024A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD3, first strand: chain 'C' and resid 1335 through 1341 removed outlier: 3.598A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.478A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.079A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 949 through 951 removed outlier: 3.900A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 991 through 996 removed outlier: 6.518A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU D1009 " --> pdb=" O ILE D 958 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1024 through 1026 removed outlier: 3.553A pdb=" N ARG D1123 " --> pdb=" O ILE D1106 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D1106 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1077 through 1079 removed outlier: 3.531A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1156 through 1157 removed outlier: 3.533A pdb=" N ALA D1157 " --> pdb=" O ASP D1208 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP D1208 " --> pdb=" O ALA D1157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'D' and resid 1186 through 1190 Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 4.111A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) 1533 hydrogen bonds defined for protein. 4344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 131 hydrogen bonds 262 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 105 stacking parallelities Total time for adding SS restraints: 9.08 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.55: 36822 1.55 - 1.91: 540 1.91 - 2.27: 0 2.27 - 2.63: 0 2.63 - 2.99: 1 Bond restraints: 37363 Sorted by residual: bond pdb=" C SER D1183 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 1.331 2.991 -1.661 1.31e-02 5.83e+03 1.61e+04 bond pdb=" C6 DA 1 31 " pdb=" N1 DA 1 31 " ideal model delta sigma weight residual 1.351 1.318 0.033 7.00e-03 2.04e+04 2.23e+01 bond pdb=" C2 DT 2 43 " pdb=" N3 DT 2 43 " ideal model delta sigma weight residual 1.373 1.341 0.032 8.00e-03 1.56e+04 1.64e+01 bond pdb=" C3' DA 1 58 " pdb=" C2' DA 1 58 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.33e+01 bond pdb=" C3' DA 1 21 " pdb=" O3' DA 1 21 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.31e+01 ... (remaining 37358 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.51: 51069 6.51 - 13.02: 9 13.02 - 19.52: 0 19.52 - 26.03: 2 26.03 - 32.54: 2 Bond angle restraints: 51082 Sorted by residual: angle pdb=" O SER D1183 " pdb=" C SER D1183 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 121.66 89.12 32.54 1.14e+00 7.69e-01 8.15e+02 angle pdb=" C SER D1183 " pdb=" N PRO D1185 " pdb=" CA PRO D1185 " ideal model delta sigma weight residual 119.85 95.03 24.82 1.01e+00 9.80e-01 6.04e+02 angle pdb=" CA SER D1183 " pdb=" C SER D1183 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 117.38 96.47 20.91 1.18e+00 7.18e-01 3.14e+02 angle pdb=" C SER D1183 " pdb=" N PRO D1185 " pdb=" CD PRO D1185 " ideal model delta sigma weight residual 125.00 152.06 -27.06 4.10e+00 5.95e-02 4.36e+01 angle pdb=" O4' DT 2 43 " pdb=" C4' DT 2 43 " pdb=" C3' DT 2 43 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.87e+01 ... (remaining 51077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 21627 35.73 - 71.46: 987 71.46 - 107.19: 24 107.19 - 142.92: 2 142.92 - 178.65: 5 Dihedral angle restraints: 22645 sinusoidal: 10396 harmonic: 12249 Sorted by residual: dihedral pdb=" CA ARG D 123 " pdb=" C ARG D 123 " pdb=" N ILE D 124 " pdb=" CA ILE D 124 " ideal model delta harmonic sigma weight residual 180.00 153.99 26.01 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA PRO D 584 " pdb=" C PRO D 584 " pdb=" N LYS D 585 " pdb=" CA LYS D 585 " ideal model delta harmonic sigma weight residual 180.00 160.19 19.81 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DT 1 9 " pdb=" C3' DT 1 9 " pdb=" O3' DT 1 9 " pdb=" P DA 1 10 " ideal model delta sinusoidal sigma weight residual 220.00 41.35 178.65 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 22642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3845 0.040 - 0.080: 1401 0.080 - 0.120: 447 0.120 - 0.160: 87 0.160 - 0.200: 14 Chirality restraints: 5794 Sorted by residual: chirality pdb=" CA LEU J 83 " pdb=" N LEU J 83 " pdb=" C LEU J 83 " pdb=" CB LEU J 83 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA LEU D 374 " pdb=" N LEU D 374 " pdb=" C LEU D 374 " pdb=" CB LEU D 374 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" P DC 2 44 " pdb=" OP1 DC 2 44 " pdb=" OP2 DC 2 44 " pdb=" O5' DC 2 44 " both_signs ideal model delta sigma weight residual True 2.34 -2.52 -0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 5791 not shown) Planarity restraints: 6171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D1183 " 0.178 2.00e-02 2.50e+03 2.65e-01 7.01e+02 pdb=" C SER D1183 " -0.438 2.00e-02 2.50e+03 pdb=" O SER D1183 " 0.237 2.00e-02 2.50e+03 pdb=" N PRO D1185 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 2 43 " -0.032 2.00e-02 2.50e+03 1.89e-02 8.89e+00 pdb=" N1 DT 2 43 " 0.049 2.00e-02 2.50e+03 pdb=" C2 DT 2 43 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT 2 43 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT 2 43 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DT 2 43 " -0.002 2.00e-02 2.50e+03 pdb=" O4 DT 2 43 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT 2 43 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT 2 43 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT 2 43 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 297 " -0.235 9.50e-02 1.11e+02 1.05e-01 6.82e+00 pdb=" NE ARG D 297 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 297 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 297 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 297 " -0.009 2.00e-02 2.50e+03 ... (remaining 6168 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4193 2.74 - 3.28: 38252 3.28 - 3.82: 62274 3.82 - 4.36: 73870 4.36 - 4.90: 120877 Nonbonded interactions: 299466 Sorted by model distance: nonbonded pdb=" OG SER D1321 " pdb=" OE2 GLU D1349 " model vdw 2.197 3.040 nonbonded pdb=" O ASP D 812 " pdb=" ND1 HIS D 897 " model vdw 2.200 3.120 nonbonded pdb=" O GLY D 358 " pdb=" N TYR D 360 " model vdw 2.203 3.120 nonbonded pdb=" CD1 LEU D 807 " pdb=" OE1 GLN D1259 " model vdw 2.210 3.460 nonbonded pdb=" OE1 GLU D1030 " pdb=" OH TYR D1099 " model vdw 2.214 3.040 ... (remaining 299461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } ncs_group { reference = (chain 'I' and (resid 27 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB )) or resid 73 through 131)) selection = (chain 'L' and (resid 27 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 131)) } ncs_group { reference = (chain 'J' and resid 4 through 127) selection = chain 'K' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.250 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.011 1.661 37363 Z= 0.751 Angle : 0.743 32.539 51082 Z= 0.504 Chirality : 0.046 0.200 5794 Planarity : 0.006 0.265 6171 Dihedral : 17.423 178.650 14733 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.81 % Allowed : 10.85 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: -0.03 (0.13), residues: 4203 helix: 0.69 (0.13), residues: 1763 sheet: 0.26 (0.26), residues: 396 loop : -0.64 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 120 TYR 0.016 0.001 TYR D1365 PHE 0.013 0.002 PHE L 74 TRP 0.011 0.001 TRP D 868 HIS 0.007 0.001 HIS C 447 Details of bonding type rmsd/Z covalent geometry : bond 0.01057 / 0.75 (37363) covalent geometry : angle 0.74291 / 0.50 (51082) hydrogen bonds : bond 0.15699 / 17.30 ( 1664) hydrogen bonds : angle 6.36395 / 8.40 ( 4606) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8406 Ramachandran restraints generated. 4203 Oldfield, 0 Emsley, 4203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8406 Ramachandran restraints generated. 4203 Oldfield, 0 Emsley, 4203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 534 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 25 LYS cc_start: 0.9032 (mttt) cc_final: 0.8651 (mttm) REVERT: B 10 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8604 (mmmm) REVERT: B 205 MET cc_start: 0.8020 (ttm) cc_final: 0.7819 (ttp) REVERT: C 102 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8281 (tt) REVERT: C 160 ASP cc_start: 0.8568 (m-30) cc_final: 0.8244 (p0) REVERT: C 479 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8838 (mp) REVERT: C 681 MET cc_start: 0.9107 (mtp) cc_final: 0.8849 (mtt) REVERT: C 696 ASP cc_start: 0.8168 (t0) cc_final: 0.7934 (t70) REVERT: C 903 ARG cc_start: 0.9014 (mmt-90) cc_final: 0.8034 (mmt90) REVERT: C 1132 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8932 (tt) REVERT: C 1135 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8492 (pm20) REVERT: D 180 MET cc_start: 0.8265 (ttm) cc_final: 0.7859 (ttm) REVERT: D 330 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8372 (ptp) REVERT: D 666 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: D 983 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8045 (mmtm) REVERT: D 999 TYR cc_start: 0.6927 (t80) cc_final: 0.6700 (t80) REVERT: D 1189 MET cc_start: 0.7156 (tpp) cc_final: 0.6916 (tpp) REVERT: D 1290 ARG cc_start: 0.7469 (mmt90) cc_final: 0.7206 (mtp180) REVERT: F 137 TYR cc_start: 0.8196 (t80) cc_final: 0.7925 (t80) REVERT: F 505 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8019 (tt) REVERT: F 611 LEU cc_start: 0.8504 (mt) cc_final: 0.8255 (pp) REVERT: J 42 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8789 (mm) REVERT: J 47 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8710 (mtmm) REVERT: J 60 LYS cc_start: 0.9423 (mttt) cc_final: 0.9212 (mmtp) REVERT: J 76 ILE cc_start: 0.8900 (mm) cc_final: 0.8681 (mm) REVERT: J 88 ASP cc_start: 0.8617 (m-30) cc_final: 0.7834 (t0) REVERT: J 91 LEU cc_start: 0.9488 (tt) cc_final: 0.9058 (tp) REVERT: J 96 ASN cc_start: 0.8343 (p0) cc_final: 0.8077 (p0) REVERT: J 117 ILE cc_start: 0.8063 (mt) cc_final: 0.7790 (mt) REVERT: P 310 ARG cc_start: 0.7978 (ptp90) cc_final: 0.7776 (ptt180) REVERT: K 43 GLU cc_start: 0.8025 (tt0) cc_final: 0.7483 (tm-30) REVERT: K 56 GLU cc_start: 0.8899 (mp0) cc_final: 0.8645 (mp0) REVERT: K 84 THR cc_start: 0.8741 (m) cc_final: 0.8487 (m) REVERT: L 35 VAL cc_start: 0.9146 (t) cc_final: 0.8759 (t) REVERT: L 123 LYS cc_start: 0.8869 (mttt) cc_final: 0.8616 (mtpt) outliers start: 175 outliers final: 77 residues processed: 681 average time/residue: 0.2346 time to fit residues: 252.4233 Evaluate side-chains 375 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 290 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 234 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1135 GLN Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1325 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 495 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 545 HIS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 506 SER Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 98 ARG Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 108 ARG Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN B 84 ASN B 128 HIS ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN C 613 ASN C 677 ASN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 HIS C 932 GLN C1209 GLN C1268 GLN D 206 ASN D 294 ASN D 489 ASN D1195 GLN D1326 GLN F 317 ASN F 346 GLN F 406 GLN F 409 ASN F 579 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 61 GLN J 113 GLN ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 294 ASN I 49 GLN I 73 GLN I 125 HIS ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 ASN ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.100944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070807 restraints weight = 111219.192| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 3.34 r_work: 0.2982 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37363 Z= 0.197 Angle : 0.652 8.368 51082 Z= 0.352 Chirality : 0.045 0.301 5794 Planarity : 0.005 0.100 6171 Dihedral : 18.746 179.388 6434 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.12 % Allowed : 14.73 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % 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: 0.09 (0.13), residues: 4205 helix: 0.82 (0.12), residues: 1805 sheet: 0.33 (0.26), residues: 417 loop : -0.65 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 88 TYR 0.018 0.001 TYR D 631 PHE 0.018 0.002 PHE A 231 TRP 0.022 0.002 TRP L 31 HIS 0.013 0.001 HIS D1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (37363) covalent geometry : angle 0.65201 / 0.35 (51082) hydrogen bonds : bond 0.05030 / 5.62 ( 1664) hydrogen bonds : angle 5.05350 / 6.51 ( 4606) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 330 time to evaluate : 1.213 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 17 GLU cc_start: 0.8594 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 25 LYS cc_start: 0.8987 (mttt) cc_final: 0.8595 (mttm) REVERT: B 10 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8473 (mmmm) REVERT: B 28 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8658 (tp) REVERT: B 41 ASN cc_start: 0.9225 (t0) cc_final: 0.9017 (t0) REVERT: B 95 LYS cc_start: 0.8255 (ptmt) cc_final: 0.8024 (ptmt) REVERT: C 102 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8475 (tt) REVERT: C 160 ASP cc_start: 0.8863 (m-30) cc_final: 0.8210 (p0) REVERT: C 653 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8689 (tpp) REVERT: C 667 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9115 (mt) REVERT: C 778 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: C 903 ARG cc_start: 0.9395 (mmt-90) cc_final: 0.8755 (mmt90) REVERT: C 1021 LEU cc_start: 0.5376 (mt) cc_final: 0.4496 (mt) REVERT: C 1132 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9174 (tt) REVERT: D 129 ASP cc_start: 0.9065 (t0) cc_final: 0.8753 (t0) REVERT: D 180 MET cc_start: 0.8744 (ttm) cc_final: 0.8333 (ttm) REVERT: D 237 MET cc_start: 0.9412 (mtm) cc_final: 0.9186 (mtm) REVERT: D 330 MET cc_start: 0.8967 (ptp) cc_final: 0.8638 (ptp) REVERT: D 429 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9308 (mt) REVERT: D 649 LYS cc_start: 0.9123 (mmtp) cc_final: 0.8607 (mtpp) REVERT: D 666 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8194 (pt0) REVERT: D 747 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7755 (mtm) REVERT: D 822 MET cc_start: 0.8436 (mmm) cc_final: 0.8202 (mmm) REVERT: D 918 ILE cc_start: 0.9155 (pt) cc_final: 0.8920 (mt) REVERT: D 1140 ARG cc_start: 0.6906 (mtp85) cc_final: 0.6452 (tpt170) REVERT: D 1200 GLU cc_start: 0.7408 (tp30) cc_final: 0.7086 (tt0) REVERT: D 1290 ARG cc_start: 0.7669 (mmt90) cc_final: 0.7244 (mtp180) REVERT: D 1291 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6312 (pp20) REVERT: F 148 TYR cc_start: 0.5935 (t80) cc_final: 0.5730 (t80) REVERT: F 487 MET cc_start: 0.9055 (mmm) cc_final: 0.8614 (mmm) REVERT: F 505 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8025 (tt) REVERT: F 561 MET cc_start: 0.8146 (ptp) cc_final: 0.7806 (ttp) REVERT: F 611 LEU cc_start: 0.8444 (mt) cc_final: 0.8231 (pp) REVERT: J 45 GLU cc_start: 0.7872 (pp20) cc_final: 0.6414 (pp20) REVERT: J 47 LYS cc_start: 0.9017 (mtmm) cc_final: 0.8801 (mtmm) REVERT: J 88 ASP cc_start: 0.8797 (m-30) cc_final: 0.8198 (t0) REVERT: J 91 LEU cc_start: 0.9525 (tt) cc_final: 0.9161 (tp) REVERT: J 117 ILE cc_start: 0.8257 (mt) cc_final: 0.7969 (mt) REVERT: I 49 GLN cc_start: 0.6965 (mt0) cc_final: 0.6252 (tm-30) REVERT: I 61 GLN cc_start: 0.7773 (mt0) cc_final: 0.6821 (mm-40) REVERT: K 43 GLU cc_start: 0.8220 (tt0) cc_final: 0.7635 (tm-30) REVERT: K 56 GLU cc_start: 0.8973 (mp0) cc_final: 0.8578 (mp0) REVERT: K 115 TYR cc_start: 0.8451 (t80) cc_final: 0.8242 (m-80) REVERT: L 33 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7791 (ppt170) REVERT: L 61 GLN cc_start: 0.9136 (mt0) cc_final: 0.8728 (tp40) REVERT: L 106 GLN cc_start: 0.8127 (pp30) cc_final: 0.7785 (pp30) REVERT: L 109 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6715 (tp) REVERT: L 123 LYS cc_start: 0.8871 (mttt) cc_final: 0.8573 (mtpt) outliers start: 150 outliers final: 88 residues processed: 458 average time/residue: 0.2017 time to fit residues: 151.3854 Evaluate side-chains 384 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 284 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1132 LEU Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 75 TYR Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 79 optimal weight: 0.1980 chunk 36 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 141 optimal weight: 0.4980 chunk 198 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 329 optimal weight: 2.9990 chunk 223 optimal weight: 0.0670 chunk 354 optimal weight: 8.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 327 GLN C 510 GLN C 519 ASN C 799 ASN D1326 GLN ** F 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 94 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.102343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072152 restraints weight = 111074.906| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.42 r_work: 0.3015 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 37363 Z= 0.133 Angle : 0.582 9.281 51082 Z= 0.316 Chirality : 0.043 0.299 5794 Planarity : 0.004 0.107 6171 Dihedral : 18.548 179.466 6379 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.01 % Allowed : 15.30 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % 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: 0.20 (0.13), residues: 4205 helix: 0.94 (0.12), residues: 1814 sheet: 0.29 (0.26), residues: 414 loop : -0.60 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG J 120 TYR 0.014 0.001 TYR C 5 PHE 0.015 0.001 PHE A 231 TRP 0.017 0.001 TRP L 31 HIS 0.006 0.001 HIS C 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (37363) covalent geometry : angle 0.58158 / 0.32 (51082) hydrogen bonds : bond 0.04269 / 4.75 ( 1664) hydrogen bonds : angle 4.76342 / 6.15 ( 4606) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 329 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 25 LYS cc_start: 0.8961 (mttt) cc_final: 0.8696 (mttm) REVERT: B 28 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8704 (tp) REVERT: C 14 ASP cc_start: 0.8830 (t0) cc_final: 0.8564 (t0) REVERT: C 42 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8630 (p0) REVERT: C 160 ASP cc_start: 0.8848 (m-30) cc_final: 0.8171 (p0) REVERT: C 510 GLN cc_start: 0.8709 (tt0) cc_final: 0.8436 (tm-30) REVERT: C 542 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7656 (ttm110) REVERT: C 653 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8724 (tpp) REVERT: C 778 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8116 (pt0) REVERT: C 951 MET cc_start: 0.9131 (ttm) cc_final: 0.8898 (tpp) REVERT: C 1034 ARG cc_start: 0.8906 (tmm-80) cc_final: 0.8637 (tmm-80) REVERT: C 1106 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.7228 (mpp-170) REVERT: D 180 MET cc_start: 0.8736 (ttm) cc_final: 0.8344 (ttm) REVERT: D 235 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8519 (mm-30) REVERT: D 237 MET cc_start: 0.9282 (mtm) cc_final: 0.9069 (mtm) REVERT: D 330 MET cc_start: 0.8712 (ptp) cc_final: 0.8365 (ptp) REVERT: D 386 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: D 429 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9224 (mt) REVERT: D 649 LYS cc_start: 0.8999 (mmtp) cc_final: 0.8553 (mtpp) REVERT: D 666 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8128 (pt0) REVERT: D 747 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7679 (mtm) REVERT: D 790 THR cc_start: 0.8640 (p) cc_final: 0.8375 (t) REVERT: D 918 ILE cc_start: 0.9158 (pt) cc_final: 0.8892 (mt) REVERT: D 1140 ARG cc_start: 0.6849 (mtp85) cc_final: 0.6460 (tpt170) REVERT: D 1200 GLU cc_start: 0.7308 (tp30) cc_final: 0.6791 (tt0) REVERT: D 1274 PHE cc_start: 0.7377 (t80) cc_final: 0.6896 (p90) REVERT: D 1290 ARG cc_start: 0.7607 (mmt90) cc_final: 0.7209 (mtp180) REVERT: D 1291 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6339 (pp20) REVERT: D 1355 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8079 (mtp85) REVERT: F 143 TYR cc_start: 0.8993 (t80) cc_final: 0.8526 (t80) REVERT: F 148 TYR cc_start: 0.6148 (t80) cc_final: 0.5935 (t80) REVERT: F 470 MET cc_start: 0.8718 (mmm) cc_final: 0.8223 (mmm) REVERT: F 487 MET cc_start: 0.9043 (mmm) cc_final: 0.8630 (mmm) REVERT: F 561 MET cc_start: 0.8021 (ptp) cc_final: 0.7673 (ttp) REVERT: F 578 LYS cc_start: 0.7210 (mmtm) cc_final: 0.6855 (mmmt) REVERT: F 595 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9131 (tt) REVERT: F 611 LEU cc_start: 0.8448 (mt) cc_final: 0.8232 (pp) REVERT: J 88 ASP cc_start: 0.8763 (m-30) cc_final: 0.8198 (t0) REVERT: J 91 LEU cc_start: 0.9462 (tt) cc_final: 0.9217 (tt) REVERT: J 113 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8565 (mp10) REVERT: I 49 GLN cc_start: 0.6861 (mt0) cc_final: 0.6117 (tm-30) REVERT: I 61 GLN cc_start: 0.7732 (mt0) cc_final: 0.6753 (mm-40) REVERT: I 104 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.5584 (ttp80) REVERT: K 43 GLU cc_start: 0.8203 (tt0) cc_final: 0.7613 (tm-30) REVERT: K 56 GLU cc_start: 0.9044 (mp0) cc_final: 0.8757 (mp0) REVERT: K 115 TYR cc_start: 0.8444 (t80) cc_final: 0.8221 (m-80) REVERT: L 61 GLN cc_start: 0.9158 (mt0) cc_final: 0.8539 (mt0) REVERT: L 106 GLN cc_start: 0.7925 (pp30) cc_final: 0.7669 (pp30) outliers start: 146 outliers final: 81 residues processed: 456 average time/residue: 0.2051 time to fit residues: 153.1578 Evaluate side-chains 376 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 280 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1106 ARG Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 457 ILE Chi-restraints excluded: chain F residue 511 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 113 GLN Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 145 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 430 optimal weight: 0.5980 chunk 131 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 369 optimal weight: 0.6980 chunk 190 optimal weight: 8.9990 chunk 370 optimal weight: 8.9990 chunk 316 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 234 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** 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 = 0.3820 r_free = 0.3820 target = 0.102807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072823 restraints weight = 110205.241| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.34 r_work: 0.3030 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 37363 Z= 0.120 Angle : 0.564 9.173 51082 Z= 0.304 Chirality : 0.043 0.297 5794 Planarity : 0.004 0.109 6171 Dihedral : 18.463 178.574 6364 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.76 % Allowed : 16.35 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % 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: 0.26 (0.13), residues: 4205 helix: 0.97 (0.12), residues: 1815 sheet: 0.36 (0.26), residues: 417 loop : -0.57 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1330 TYR 0.018 0.001 TYR F 137 PHE 0.016 0.001 PHE A 231 TRP 0.014 0.001 TRP L 31 HIS 0.007 0.001 HIS C 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (37363) covalent geometry : angle 0.56386 / 0.30 (51082) hydrogen bonds : bond 0.03901 / 4.34 ( 1664) hydrogen bonds : angle 4.58828 / 5.91 ( 4606) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 319 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 28 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8703 (tp) REVERT: C 14 ASP cc_start: 0.8789 (t0) cc_final: 0.8531 (t0) REVERT: C 42 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8622 (p0) REVERT: C 160 ASP cc_start: 0.8832 (m-30) cc_final: 0.8176 (p0) REVERT: C 542 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7714 (ttm110) REVERT: C 653 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.7923 (tpt) REVERT: C 778 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8397 (pt0) REVERT: C 903 ARG cc_start: 0.9004 (mmt90) cc_final: 0.8799 (mmt90) REVERT: D 386 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: D 429 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9206 (mt) REVERT: D 649 LYS cc_start: 0.8973 (mmtp) cc_final: 0.8526 (mtpp) REVERT: D 666 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: D 790 THR cc_start: 0.8669 (p) cc_final: 0.8445 (t) REVERT: D 811 GLU cc_start: 0.8998 (mp0) cc_final: 0.8794 (mt-10) REVERT: D 918 ILE cc_start: 0.9095 (pt) cc_final: 0.8847 (mt) REVERT: D 981 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7110 (mm-30) REVERT: D 1140 ARG cc_start: 0.6813 (mtp85) cc_final: 0.6418 (tpt170) REVERT: D 1200 GLU cc_start: 0.7348 (tp30) cc_final: 0.6838 (tt0) REVERT: D 1274 PHE cc_start: 0.7285 (t80) cc_final: 0.6917 (p90) REVERT: D 1290 ARG cc_start: 0.7550 (mmt90) cc_final: 0.7003 (mtp85) REVERT: D 1291 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6385 (pp20) REVERT: D 1355 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8076 (mtp85) REVERT: F 143 TYR cc_start: 0.9065 (t80) cc_final: 0.8675 (t80) REVERT: F 487 MET cc_start: 0.9061 (mmm) cc_final: 0.8571 (mmm) REVERT: F 561 MET cc_start: 0.7980 (ptp) cc_final: 0.7684 (ttp) REVERT: F 578 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6823 (mmmt) REVERT: F 595 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9125 (tt) REVERT: F 611 LEU cc_start: 0.8447 (mt) cc_final: 0.8233 (pp) REVERT: J 47 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8731 (pttt) REVERT: J 88 ASP cc_start: 0.8805 (m-30) cc_final: 0.8232 (t0) REVERT: J 109 LEU cc_start: 0.7827 (tp) cc_final: 0.7504 (tp) REVERT: I 61 GLN cc_start: 0.7631 (mt0) cc_final: 0.6631 (mm-40) REVERT: K 43 GLU cc_start: 0.8224 (tt0) cc_final: 0.7651 (tm-30) REVERT: K 56 GLU cc_start: 0.9048 (mp0) cc_final: 0.8770 (mp0) REVERT: K 115 TYR cc_start: 0.8443 (t80) cc_final: 0.8226 (m-80) outliers start: 137 outliers final: 89 residues processed: 439 average time/residue: 0.2064 time to fit residues: 148.1478 Evaluate side-chains 376 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 277 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 799 ASN Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 386 GLU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 48 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 361 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 chunk 209 optimal weight: 5.9990 chunk 395 optimal weight: 0.4980 chunk 416 optimal weight: 2.9990 chunk 289 optimal weight: 0.0070 overall best weight: 2.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** 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 = 0.3800 r_free = 0.3800 target = 0.101580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071602 restraints weight = 110584.102| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.30 r_work: 0.3004 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 37363 Z= 0.156 Angle : 0.566 8.212 51082 Z= 0.305 Chirality : 0.043 0.274 5794 Planarity : 0.004 0.104 6171 Dihedral : 18.433 178.697 6347 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.18 % Allowed : 16.29 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % 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: 0.31 (0.13), residues: 4205 helix: 1.00 (0.12), residues: 1821 sheet: 0.29 (0.26), residues: 432 loop : -0.51 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 120 TYR 0.029 0.001 TYR F 137 PHE 0.016 0.001 PHE I 74 TRP 0.015 0.001 TRP L 31 HIS 0.009 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (37363) covalent geometry : angle 0.56634 / 0.31 (51082) hydrogen bonds : bond 0.03899 / 4.32 ( 1664) hydrogen bonds : angle 4.56471 / 5.89 ( 4606) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 294 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 28 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8661 (tp) REVERT: B 142 MET cc_start: 0.8914 (pmm) cc_final: 0.8689 (pmm) REVERT: C 14 ASP cc_start: 0.8829 (t0) cc_final: 0.8566 (t0) REVERT: C 42 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8582 (p0) REVERT: C 59 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7821 (tp) REVERT: C 160 ASP cc_start: 0.8864 (m-30) cc_final: 0.8231 (p0) REVERT: C 189 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8612 (t0) REVERT: C 239 MET cc_start: 0.7023 (tmm) cc_final: 0.6817 (tmm) REVERT: C 542 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7942 (ttm110) REVERT: C 653 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.7928 (tpt) REVERT: C 748 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8447 (mp) REVERT: C 778 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: C 1217 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8556 (p) REVERT: C 1219 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: C 1319 MET cc_start: 0.8754 (tpp) cc_final: 0.8462 (tpp) REVERT: D 94 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8799 (pm20) REVERT: D 429 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9210 (mt) REVERT: D 649 LYS cc_start: 0.9062 (mmtp) cc_final: 0.8556 (mtpp) REVERT: D 666 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: D 811 GLU cc_start: 0.9030 (mp0) cc_final: 0.8826 (mt-10) REVERT: D 918 ILE cc_start: 0.9132 (pt) cc_final: 0.8873 (mt) REVERT: D 981 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7055 (mm-30) REVERT: D 1025 MET cc_start: 0.7799 (mmp) cc_final: 0.7472 (mmp) REVERT: D 1140 ARG cc_start: 0.6977 (mtp85) cc_final: 0.6480 (tpt170) REVERT: D 1189 MET cc_start: 0.7192 (tpt) cc_final: 0.6615 (tpp) REVERT: D 1200 GLU cc_start: 0.7484 (tp30) cc_final: 0.7124 (tt0) REVERT: D 1274 PHE cc_start: 0.7361 (t80) cc_final: 0.7024 (p90) REVERT: D 1290 ARG cc_start: 0.7579 (mmt90) cc_final: 0.7207 (mtp180) REVERT: D 1291 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6555 (pp20) REVERT: D 1355 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8093 (mtp85) REVERT: F 137 TYR cc_start: 0.8201 (t80) cc_final: 0.7944 (t80) REVERT: F 143 TYR cc_start: 0.9043 (t80) cc_final: 0.8729 (t80) REVERT: F 273 MET cc_start: 0.9081 (mmp) cc_final: 0.8843 (mmm) REVERT: F 326 TRP cc_start: 0.3673 (p-90) cc_final: 0.3314 (p90) REVERT: F 470 MET cc_start: 0.8637 (mmm) cc_final: 0.8218 (mmm) REVERT: F 487 MET cc_start: 0.9039 (mmm) cc_final: 0.8501 (mmm) REVERT: F 489 MET cc_start: 0.8898 (mtp) cc_final: 0.8620 (mtp) REVERT: F 561 MET cc_start: 0.8095 (ptp) cc_final: 0.7677 (ttp) REVERT: F 578 LYS cc_start: 0.7308 (mmtm) cc_final: 0.6911 (mmmt) REVERT: F 595 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9135 (tt) REVERT: F 611 LEU cc_start: 0.8476 (mt) cc_final: 0.8228 (pp) REVERT: J 47 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8829 (mtmm) REVERT: J 88 ASP cc_start: 0.8819 (m-30) cc_final: 0.8161 (t0) REVERT: I 61 GLN cc_start: 0.7699 (mt0) cc_final: 0.6686 (mm-40) REVERT: K 43 GLU cc_start: 0.8238 (tt0) cc_final: 0.7662 (tm-30) REVERT: K 56 GLU cc_start: 0.9085 (mp0) cc_final: 0.8788 (mp0) REVERT: K 115 TYR cc_start: 0.8446 (t80) cc_final: 0.8200 (m-80) REVERT: L 61 GLN cc_start: 0.9180 (mm110) cc_final: 0.8949 (mm110) REVERT: L 103 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7140 (pp) REVERT: L 106 GLN cc_start: 0.8031 (pp30) cc_final: 0.7567 (pp30) outliers start: 152 outliers final: 96 residues processed: 425 average time/residue: 0.1938 time to fit residues: 136.8890 Evaluate side-chains 383 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 271 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 880 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 67 CYS Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 268 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 326 optimal weight: 0.0030 chunk 197 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 399 optimal weight: 9.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 327 GLN ** C1023 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS F 227 GLN ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.102991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073229 restraints weight = 110557.794| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 3.31 r_work: 0.3038 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 37363 Z= 0.111 Angle : 0.553 9.301 51082 Z= 0.295 Chirality : 0.042 0.261 5794 Planarity : 0.004 0.104 6171 Dihedral : 18.369 176.704 6344 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.38 % Allowed : 17.03 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % 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: 0.42 (0.13), residues: 4205 helix: 1.13 (0.13), residues: 1805 sheet: 0.41 (0.26), residues: 434 loop : -0.50 (0.14), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 120 TYR 0.023 0.001 TYR F 137 PHE 0.018 0.001 PHE K 6 TRP 0.017 0.001 TRP L 31 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (37363) covalent geometry : angle 0.55284 / 0.30 (51082) hydrogen bonds : bond 0.03563 / 3.94 ( 1664) hydrogen bonds : angle 4.41872 / 5.73 ( 4606) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 310 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7432 (tm-30) REVERT: A 122 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: B 28 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8632 (tp) REVERT: B 142 MET cc_start: 0.8953 (pmm) cc_final: 0.8709 (pmm) REVERT: C 14 ASP cc_start: 0.8809 (t0) cc_final: 0.8556 (t0) REVERT: C 42 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8583 (p0) REVERT: C 160 ASP cc_start: 0.8830 (m-30) cc_final: 0.8220 (p0) REVERT: C 185 ASP cc_start: 0.8827 (m-30) cc_final: 0.8520 (m-30) REVERT: C 189 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8589 (t0) REVERT: C 653 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8684 (tpp) REVERT: C 778 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8483 (pt0) REVERT: C 899 GLU cc_start: 0.9071 (pt0) cc_final: 0.8256 (tm-30) REVERT: C 1025 PHE cc_start: 0.4926 (m-80) cc_final: 0.4522 (m-80) REVERT: C 1319 MET cc_start: 0.8686 (tpp) cc_final: 0.8461 (tpp) REVERT: D 94 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8800 (pm20) REVERT: D 180 MET cc_start: 0.8629 (ttm) cc_final: 0.8114 (ttm) REVERT: D 283 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9193 (mt) REVERT: D 429 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9164 (mt) REVERT: D 649 LYS cc_start: 0.9012 (mmtp) cc_final: 0.8528 (mtpp) REVERT: D 811 GLU cc_start: 0.9040 (mp0) cc_final: 0.8836 (mt-10) REVERT: D 918 ILE cc_start: 0.9117 (pt) cc_final: 0.8841 (mt) REVERT: D 981 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7210 (mm-30) REVERT: D 1140 ARG cc_start: 0.6919 (mtp85) cc_final: 0.6460 (tpt170) REVERT: D 1189 MET cc_start: 0.7239 (tpt) cc_final: 0.6713 (tpt) REVERT: D 1193 TRP cc_start: 0.6743 (m-90) cc_final: 0.5964 (m-90) REVERT: D 1200 GLU cc_start: 0.7234 (tp30) cc_final: 0.6753 (tt0) REVERT: D 1274 PHE cc_start: 0.7262 (t80) cc_final: 0.6884 (p90) REVERT: D 1290 ARG cc_start: 0.7481 (mmt90) cc_final: 0.6902 (mtp85) REVERT: D 1291 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6426 (pp20) REVERT: D 1355 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8028 (mtp85) REVERT: E 29 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: F 137 TYR cc_start: 0.8143 (t80) cc_final: 0.7919 (t80) REVERT: F 143 TYR cc_start: 0.8972 (t80) cc_final: 0.8716 (t80) REVERT: F 273 MET cc_start: 0.9031 (mmp) cc_final: 0.8795 (mmm) REVERT: F 288 MET cc_start: 0.6132 (mmp) cc_final: 0.5868 (mmp) REVERT: F 326 TRP cc_start: 0.3603 (p-90) cc_final: 0.3203 (p90) REVERT: F 470 MET cc_start: 0.8669 (mmm) cc_final: 0.8226 (mmm) REVERT: F 487 MET cc_start: 0.9034 (mmm) cc_final: 0.8477 (mmm) REVERT: F 489 MET cc_start: 0.8897 (mtp) cc_final: 0.8547 (mtp) REVERT: F 561 MET cc_start: 0.8019 (ptp) cc_final: 0.7631 (ttp) REVERT: F 578 LYS cc_start: 0.7234 (mmtm) cc_final: 0.6826 (mmmt) REVERT: F 595 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9132 (tt) REVERT: F 611 LEU cc_start: 0.8482 (mt) cc_final: 0.8247 (pp) REVERT: J 88 ASP cc_start: 0.8786 (m-30) cc_final: 0.8226 (t0) REVERT: I 61 GLN cc_start: 0.7704 (mt0) cc_final: 0.6693 (mm-40) REVERT: K 26 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8075 (pm20) REVERT: K 43 GLU cc_start: 0.8232 (tt0) cc_final: 0.7650 (tm-30) REVERT: K 56 GLU cc_start: 0.9081 (mp0) cc_final: 0.8700 (tm-30) REVERT: K 115 TYR cc_start: 0.8451 (t80) cc_final: 0.8226 (m-80) REVERT: L 106 GLN cc_start: 0.8040 (pp30) cc_final: 0.7716 (pp30) outliers start: 123 outliers final: 74 residues processed: 413 average time/residue: 0.1961 time to fit residues: 134.6127 Evaluate side-chains 374 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 287 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 165 optimal weight: 0.2980 chunk 151 optimal weight: 9.9990 chunk 424 optimal weight: 0.9990 chunk 363 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 237 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 86 GLN C 327 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS F 346 GLN J 73 GLN ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.102117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072327 restraints weight = 110188.074| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.28 r_work: 0.3019 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 37363 Z= 0.132 Angle : 0.559 8.621 51082 Z= 0.298 Chirality : 0.042 0.251 5794 Planarity : 0.004 0.104 6171 Dihedral : 18.329 177.292 6328 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.65 % Allowed : 16.92 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % 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: 0.43 (0.13), residues: 4205 helix: 1.15 (0.13), residues: 1818 sheet: 0.21 (0.25), residues: 442 loop : -0.46 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 200 TYR 0.017 0.001 TYR F 137 PHE 0.017 0.001 PHE C 545 TRP 0.017 0.001 TRP L 31 HIS 0.008 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (37363) covalent geometry : angle 0.55884 / 0.30 (51082) hydrogen bonds : bond 0.03565 / 3.94 ( 1664) hydrogen bonds : angle 4.41591 / 5.72 ( 4606) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 307 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 122 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: B 15 ASP cc_start: 0.7844 (p0) cc_final: 0.7609 (p0) REVERT: B 28 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8492 (tp) REVERT: B 142 MET cc_start: 0.8938 (pmm) cc_final: 0.8701 (pmm) REVERT: B 181 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8318 (mt-10) REVERT: B 200 LYS cc_start: 0.8771 (ptmm) cc_final: 0.8368 (ptmm) REVERT: C 14 ASP cc_start: 0.8764 (t0) cc_final: 0.8527 (t0) REVERT: C 42 ASP cc_start: 0.8806 (OUTLIER) cc_final: 0.8600 (p0) REVERT: C 160 ASP cc_start: 0.8845 (m-30) cc_final: 0.8234 (p0) REVERT: C 653 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.7912 (tpt) REVERT: C 748 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8456 (mp) REVERT: C 876 GLU cc_start: 0.8493 (pm20) cc_final: 0.8155 (pm20) REVERT: C 1319 MET cc_start: 0.8732 (tpp) cc_final: 0.8511 (tpp) REVERT: D 94 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8801 (pm20) REVERT: D 429 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9195 (mm) REVERT: D 649 LYS cc_start: 0.9033 (mmtp) cc_final: 0.8545 (mtpp) REVERT: D 811 GLU cc_start: 0.9065 (mp0) cc_final: 0.8864 (mt-10) REVERT: D 918 ILE cc_start: 0.9157 (pt) cc_final: 0.8848 (mt) REVERT: D 981 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7186 (mm-30) REVERT: D 1025 MET cc_start: 0.7954 (mmp) cc_final: 0.7497 (mmt) REVERT: D 1140 ARG cc_start: 0.6971 (mtp85) cc_final: 0.6489 (tpt170) REVERT: D 1188 GLU cc_start: 0.8110 (pt0) cc_final: 0.7807 (pt0) REVERT: D 1189 MET cc_start: 0.7408 (tpt) cc_final: 0.7202 (tpt) REVERT: D 1193 TRP cc_start: 0.6896 (m-90) cc_final: 0.6210 (m-90) REVERT: D 1200 GLU cc_start: 0.7327 (tp30) cc_final: 0.6780 (tt0) REVERT: D 1258 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8757 (tmt-80) REVERT: D 1274 PHE cc_start: 0.7271 (t80) cc_final: 0.6925 (p90) REVERT: D 1290 ARG cc_start: 0.7523 (mmt90) cc_final: 0.6915 (mtp85) REVERT: D 1291 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6570 (pp20) REVERT: D 1355 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8103 (mtp85) REVERT: E 29 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: F 137 TYR cc_start: 0.8231 (t80) cc_final: 0.8021 (t80) REVERT: F 143 TYR cc_start: 0.8965 (t80) cc_final: 0.8749 (t80) REVERT: F 273 MET cc_start: 0.9049 (mmp) cc_final: 0.8798 (mmm) REVERT: F 288 MET cc_start: 0.6204 (mmp) cc_final: 0.5925 (mmp) REVERT: F 487 MET cc_start: 0.9038 (mmm) cc_final: 0.8487 (mmm) REVERT: F 489 MET cc_start: 0.8877 (mtp) cc_final: 0.8514 (mtp) REVERT: F 561 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7656 (ttp) REVERT: F 578 LYS cc_start: 0.7261 (mmtm) cc_final: 0.6864 (mmmt) REVERT: F 595 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9149 (tt) REVERT: F 611 LEU cc_start: 0.8508 (mt) cc_final: 0.8260 (pp) REVERT: J 47 LYS cc_start: 0.9079 (mtmm) cc_final: 0.8837 (mtmm) REVERT: J 88 ASP cc_start: 0.8793 (m-30) cc_final: 0.8252 (t0) REVERT: I 61 GLN cc_start: 0.7719 (mt0) cc_final: 0.6697 (mm-40) REVERT: K 26 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: K 43 GLU cc_start: 0.8332 (tt0) cc_final: 0.7669 (tm-30) REVERT: K 56 GLU cc_start: 0.9096 (mp0) cc_final: 0.8785 (mp0) REVERT: K 115 TYR cc_start: 0.8440 (t80) cc_final: 0.8203 (m-80) REVERT: L 103 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.6918 (pp) REVERT: L 106 GLN cc_start: 0.7981 (pp30) cc_final: 0.7679 (pp30) outliers start: 133 outliers final: 93 residues processed: 415 average time/residue: 0.2013 time to fit residues: 137.7491 Evaluate side-chains 388 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 281 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1258 ARG Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 278 ILE Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 389 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 309 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 295 optimal weight: 30.0000 chunk 92 optimal weight: 0.1980 chunk 264 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 149 optimal weight: 0.0050 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 327 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** 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 = 0.3804 r_free = 0.3804 target = 0.102928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.074262 restraints weight = 112268.746| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 3.24 r_work: 0.3019 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 37363 Z= 0.137 Angle : 0.567 10.838 51082 Z= 0.300 Chirality : 0.043 0.254 5794 Planarity : 0.004 0.104 6171 Dihedral : 18.317 176.892 6324 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.52 % Allowed : 17.55 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % 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: 0.44 (0.13), residues: 4205 helix: 1.15 (0.13), residues: 1812 sheet: 0.23 (0.25), residues: 441 loop : -0.45 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1034 TYR 0.016 0.001 TYR F 137 PHE 0.021 0.001 PHE K 6 TRP 0.059 0.002 TRP F 326 HIS 0.007 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (37363) covalent geometry : angle 0.56656 / 0.30 (51082) hydrogen bonds : bond 0.03560 / 3.94 ( 1664) hydrogen bonds : angle 4.41771 / 5.71 ( 4606) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 288 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8538 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 122 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8601 (tt0) REVERT: B 15 ASP cc_start: 0.7850 (p0) cc_final: 0.7615 (p0) REVERT: B 142 MET cc_start: 0.8936 (pmm) cc_final: 0.8692 (pmm) REVERT: B 181 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8320 (mt-10) REVERT: C 14 ASP cc_start: 0.8758 (t0) cc_final: 0.8526 (t0) REVERT: C 42 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8623 (p0) REVERT: C 160 ASP cc_start: 0.8852 (m-30) cc_final: 0.8244 (p0) REVERT: C 653 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.7910 (tpt) REVERT: C 748 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8452 (mp) REVERT: C 876 GLU cc_start: 0.8513 (pm20) cc_final: 0.8217 (pm20) REVERT: C 1319 MET cc_start: 0.8711 (tpp) cc_final: 0.8494 (tpp) REVERT: D 94 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8812 (pm20) REVERT: D 649 LYS cc_start: 0.9027 (mmtp) cc_final: 0.8540 (mtpp) REVERT: D 666 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: D 918 ILE cc_start: 0.9160 (pt) cc_final: 0.8857 (mt) REVERT: D 981 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7243 (mm-30) REVERT: D 1025 MET cc_start: 0.8047 (mmp) cc_final: 0.7615 (mmt) REVERT: D 1140 ARG cc_start: 0.6892 (mtp85) cc_final: 0.6383 (tpt170) REVERT: D 1188 GLU cc_start: 0.8137 (pt0) cc_final: 0.7839 (pt0) REVERT: D 1193 TRP cc_start: 0.6820 (m-90) cc_final: 0.6168 (m-90) REVERT: D 1200 GLU cc_start: 0.7319 (tp30) cc_final: 0.6900 (tt0) REVERT: D 1258 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8756 (tmt-80) REVERT: D 1274 PHE cc_start: 0.7279 (t80) cc_final: 0.6946 (p90) REVERT: D 1290 ARG cc_start: 0.7511 (mmt90) cc_final: 0.7006 (mtp180) REVERT: D 1291 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6440 (pp20) REVERT: D 1355 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8110 (mtp85) REVERT: E 29 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7321 (pm20) REVERT: F 143 TYR cc_start: 0.8942 (t80) cc_final: 0.8741 (t80) REVERT: F 288 MET cc_start: 0.6443 (mmp) cc_final: 0.6117 (mmp) REVERT: F 458 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8639 (mp0) REVERT: F 470 MET cc_start: 0.8578 (mmm) cc_final: 0.8248 (mmm) REVERT: F 487 MET cc_start: 0.9040 (mmm) cc_final: 0.8488 (mmm) REVERT: F 489 MET cc_start: 0.8820 (mtp) cc_final: 0.8429 (mtp) REVERT: F 561 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7675 (ttp) REVERT: F 578 LYS cc_start: 0.7289 (mmtm) cc_final: 0.6887 (mmmt) REVERT: F 595 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9143 (tt) REVERT: F 611 LEU cc_start: 0.8526 (mt) cc_final: 0.8250 (pp) REVERT: J 47 LYS cc_start: 0.9071 (mtmm) cc_final: 0.8813 (mtmm) REVERT: J 88 ASP cc_start: 0.8857 (m-30) cc_final: 0.8315 (t0) REVERT: I 61 GLN cc_start: 0.7650 (mt0) cc_final: 0.6595 (mm-40) REVERT: K 26 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8139 (pm20) REVERT: K 43 GLU cc_start: 0.8330 (tt0) cc_final: 0.7666 (tm-30) REVERT: K 56 GLU cc_start: 0.9114 (mp0) cc_final: 0.8815 (mp0) REVERT: K 115 TYR cc_start: 0.8402 (t80) cc_final: 0.8163 (m-80) REVERT: L 106 GLN cc_start: 0.7977 (pp30) cc_final: 0.7663 (pp30) outliers start: 128 outliers final: 98 residues processed: 396 average time/residue: 0.2003 time to fit residues: 131.3087 Evaluate side-chains 393 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 283 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1258 ARG Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 532 LEU Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 278 ILE Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 257 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 214 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 GLN C 327 GLN C1157 GLN D 157 GLN D 777 HIS ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.100047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.070244 restraints weight = 111335.886| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.27 r_work: 0.2975 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 37363 Z= 0.202 Angle : 0.606 10.007 51082 Z= 0.320 Chirality : 0.044 0.267 5794 Planarity : 0.004 0.103 6171 Dihedral : 18.367 177.737 6324 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.68 % Allowed : 17.64 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % 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: 0.38 (0.13), residues: 4205 helix: 1.12 (0.13), residues: 1816 sheet: 0.14 (0.25), residues: 444 loop : -0.49 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 120 TYR 0.017 0.001 TYR F 137 PHE 0.015 0.001 PHE C 545 TRP 0.050 0.002 TRP F 326 HIS 0.008 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (37363) covalent geometry : angle 0.60608 / 0.32 (51082) hydrogen bonds : bond 0.03868 / 4.28 ( 1664) hydrogen bonds : angle 4.50676 / 5.84 ( 4606) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 281 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 122 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: B 142 MET cc_start: 0.8917 (pmm) cc_final: 0.8673 (pmm) REVERT: B 181 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8581 (mm-30) REVERT: C 14 ASP cc_start: 0.8837 (t0) cc_final: 0.8611 (t0) REVERT: C 42 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8663 (p0) REVERT: C 160 ASP cc_start: 0.8897 (m-30) cc_final: 0.8272 (p0) REVERT: C 538 LEU cc_start: 0.9302 (mp) cc_final: 0.9027 (mt) REVERT: C 653 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.7881 (tpt) REVERT: C 892 GLU cc_start: 0.7759 (tp30) cc_final: 0.7445 (tp30) REVERT: D 94 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8805 (pm20) REVERT: D 649 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8533 (mtpp) REVERT: D 666 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: D 918 ILE cc_start: 0.9184 (pt) cc_final: 0.8870 (mt) REVERT: D 981 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6487 (pm20) REVERT: D 1025 MET cc_start: 0.8090 (mmp) cc_final: 0.7702 (mmt) REVERT: D 1140 ARG cc_start: 0.6926 (mtp85) cc_final: 0.6410 (tpt170) REVERT: D 1188 GLU cc_start: 0.8265 (pt0) cc_final: 0.8058 (pt0) REVERT: D 1193 TRP cc_start: 0.6919 (m-90) cc_final: 0.6316 (m-90) REVERT: D 1200 GLU cc_start: 0.7382 (tp30) cc_final: 0.6977 (tt0) REVERT: D 1274 PHE cc_start: 0.7477 (t80) cc_final: 0.7090 (p90) REVERT: D 1290 ARG cc_start: 0.7617 (mmt90) cc_final: 0.6885 (mtp85) REVERT: D 1291 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6541 (pp20) REVERT: D 1355 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8094 (mtp85) REVERT: E 29 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: E 41 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7156 (tm-30) REVERT: F 273 MET cc_start: 0.8971 (mmm) cc_final: 0.8666 (mmm) REVERT: F 288 MET cc_start: 0.6521 (mmp) cc_final: 0.6191 (mmp) REVERT: F 458 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8652 (mp0) REVERT: F 470 MET cc_start: 0.8607 (mmm) cc_final: 0.8265 (mmm) REVERT: F 487 MET cc_start: 0.9011 (mmm) cc_final: 0.8534 (mmm) REVERT: F 489 MET cc_start: 0.8713 (mtp) cc_final: 0.8265 (mtp) REVERT: F 561 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7788 (ttp) REVERT: F 578 LYS cc_start: 0.7447 (mmtm) cc_final: 0.7060 (mmmt) REVERT: F 581 ASP cc_start: 0.4350 (OUTLIER) cc_final: 0.3911 (m-30) REVERT: F 595 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9130 (tt) REVERT: F 611 LEU cc_start: 0.8537 (mt) cc_final: 0.8231 (pp) REVERT: J 47 LYS cc_start: 0.9093 (mtmm) cc_final: 0.8850 (mtmm) REVERT: J 88 ASP cc_start: 0.8906 (m-30) cc_final: 0.8339 (t0) REVERT: P 319 GLU cc_start: 0.8483 (tp30) cc_final: 0.8252 (tp30) REVERT: I 61 GLN cc_start: 0.7746 (mt0) cc_final: 0.6721 (mm-40) REVERT: K 26 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: K 43 GLU cc_start: 0.8402 (tt0) cc_final: 0.7678 (tm-30) REVERT: K 56 GLU cc_start: 0.9118 (mp0) cc_final: 0.8838 (mp0) REVERT: K 115 TYR cc_start: 0.8451 (t80) cc_final: 0.8167 (m-80) REVERT: L 33 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.6441 (ppt170) REVERT: L 61 GLN cc_start: 0.9288 (mm110) cc_final: 0.9079 (mm110) outliers start: 134 outliers final: 94 residues processed: 394 average time/residue: 0.2023 time to fit residues: 131.9605 Evaluate side-chains 379 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 273 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 581 ASP Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 278 ILE Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 162 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 368 optimal weight: 0.9980 chunk 405 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 327 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN D 157 GLN D 777 HIS ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.100362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070449 restraints weight = 110975.083| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.32 r_work: 0.2981 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 37363 Z= 0.182 Angle : 0.703 59.199 51082 Z= 0.386 Chirality : 0.044 0.631 5794 Planarity : 0.004 0.103 6171 Dihedral : 18.363 177.581 6321 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.02 % Allowed : 18.41 % Favored : 78.57 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.87 % 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: 0.40 (0.13), residues: 4205 helix: 1.15 (0.13), residues: 1815 sheet: 0.12 (0.25), residues: 444 loop : -0.49 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG L 127 TYR 0.023 0.001 TYR L 107 PHE 0.018 0.001 PHE F 221 TRP 0.047 0.002 TRP F 326 HIS 0.008 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (37363) covalent geometry : angle 0.70284 / 0.39 (51082) hydrogen bonds : bond 0.03832 / 4.25 ( 1664) hydrogen bonds : angle 4.50341 / 5.84 ( 4606) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8410 Ramachandran restraints generated. 4205 Oldfield, 0 Emsley, 4205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 274 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 122 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: B 142 MET cc_start: 0.8916 (pmm) cc_final: 0.8673 (pmm) REVERT: B 181 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8584 (mm-30) REVERT: C 14 ASP cc_start: 0.8776 (t0) cc_final: 0.8564 (t0) REVERT: C 42 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8657 (p0) REVERT: C 160 ASP cc_start: 0.8896 (m-30) cc_final: 0.8272 (p0) REVERT: C 538 LEU cc_start: 0.9293 (mp) cc_final: 0.9016 (mt) REVERT: C 653 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.7894 (tpt) REVERT: C 892 GLU cc_start: 0.7736 (tp30) cc_final: 0.7425 (tp30) REVERT: D 94 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8790 (pm20) REVERT: D 649 LYS cc_start: 0.9025 (mmtp) cc_final: 0.8532 (mtpp) REVERT: D 666 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: D 918 ILE cc_start: 0.9171 (pt) cc_final: 0.8860 (mt) REVERT: D 981 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6493 (pm20) REVERT: D 1025 MET cc_start: 0.8056 (mmp) cc_final: 0.7763 (mmp) REVERT: D 1140 ARG cc_start: 0.6906 (mtp85) cc_final: 0.6393 (tpt170) REVERT: D 1188 GLU cc_start: 0.8259 (pt0) cc_final: 0.8044 (pt0) REVERT: D 1193 TRP cc_start: 0.6911 (m-90) cc_final: 0.6304 (m-90) REVERT: D 1200 GLU cc_start: 0.7372 (tp30) cc_final: 0.6962 (tt0) REVERT: D 1274 PHE cc_start: 0.7470 (t80) cc_final: 0.7088 (p90) REVERT: D 1290 ARG cc_start: 0.7622 (mmt90) cc_final: 0.6888 (mtp85) REVERT: D 1291 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6534 (pp20) REVERT: D 1355 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8058 (mtp85) REVERT: E 29 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: F 273 MET cc_start: 0.8951 (mmm) cc_final: 0.8634 (mmm) REVERT: F 288 MET cc_start: 0.6545 (mmp) cc_final: 0.6223 (mmp) REVERT: F 458 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8640 (mp0) REVERT: F 470 MET cc_start: 0.8633 (mmm) cc_final: 0.8296 (mmm) REVERT: F 487 MET cc_start: 0.9016 (mmm) cc_final: 0.8599 (mmm) REVERT: F 489 MET cc_start: 0.8721 (mtp) cc_final: 0.8368 (mtp) REVERT: F 561 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7779 (ttp) REVERT: F 578 LYS cc_start: 0.7444 (mmtm) cc_final: 0.7054 (mmmt) REVERT: F 581 ASP cc_start: 0.4363 (OUTLIER) cc_final: 0.3916 (m-30) REVERT: F 595 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9126 (tt) REVERT: F 611 LEU cc_start: 0.8531 (mt) cc_final: 0.8228 (pp) REVERT: J 47 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8828 (mtmm) REVERT: J 88 ASP cc_start: 0.8903 (m-30) cc_final: 0.8335 (t0) REVERT: P 319 GLU cc_start: 0.8481 (tp30) cc_final: 0.8246 (tp30) REVERT: I 61 GLN cc_start: 0.7734 (mt0) cc_final: 0.6709 (mm-40) REVERT: K 26 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: K 43 GLU cc_start: 0.8399 (tt0) cc_final: 0.7675 (tm-30) REVERT: K 56 GLU cc_start: 0.9119 (mp0) cc_final: 0.8841 (mp0) REVERT: K 65 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8784 (pp) REVERT: K 115 TYR cc_start: 0.8457 (t80) cc_final: 0.8174 (m-80) REVERT: L 33 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.6347 (ppt170) REVERT: L 61 GLN cc_start: 0.9289 (mm110) cc_final: 0.9069 (mm110) outliers start: 110 outliers final: 95 residues processed: 367 average time/residue: 0.2015 time to fit residues: 122.7626 Evaluate side-chains 381 residues out of total 3656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 273 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 653 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 876 GLU Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1264 GLN Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 739 GLN Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 931 THR Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1355 ARG Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 63 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 567 MET Chi-restraints excluded: chain F residue 581 ASP Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 67 CYS Chi-restraints excluded: chain J residue 91 LEU Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 278 ILE Chi-restraints excluded: chain P residue 285 THR Chi-restraints excluded: chain P residue 290 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 113 GLN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 44 ASN Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 123 LYS Chi-restraints excluded: chain L residue 33 ARG Chi-restraints excluded: chain L residue 44 ASN Chi-restraints excluded: chain L residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 385 optimal weight: 0.2980 chunk 199 optimal weight: 7.9990 chunk 332 optimal weight: 0.0570 chunk 189 optimal weight: 3.9990 chunk 417 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 60 optimal weight: 0.0470 chunk 124 optimal weight: 0.8980 chunk 353 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 327 GLN ** C 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 777 HIS ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.100322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.070549 restraints weight = 110219.931| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.26 r_work: 0.2983 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 37363 Z= 0.182 Angle : 0.703 59.199 51082 Z= 0.386 Chirality : 0.044 0.631 5794 Planarity : 0.004 0.103 6171 Dihedral : 18.363 177.581 6321 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.99 % Allowed : 18.38 % Favored : 78.63 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.87 % 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: 0.40 (0.13), residues: 4205 helix: 1.15 (0.13), residues: 1815 sheet: 0.12 (0.25), residues: 444 loop : -0.49 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG L 127 TYR 0.023 0.001 TYR L 107 PHE 0.018 0.001 PHE F 221 TRP 0.047 0.002 TRP F 326 HIS 0.008 0.001 HIS C1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (37363) covalent geometry : angle 0.70284 / 0.39 (51082) hydrogen bonds : bond 0.03832 / 4.25 ( 1664) hydrogen bonds : angle 4.50341 / 5.84 ( 4606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9138.40 seconds wall clock time: 156 minutes 57.86 seconds (9417.86 seconds total)