Starting phenix.real_space_refine on Wed Aug 27 00:59:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lxo_63483/08_2025/9lxo_63483.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lxo_63483/08_2025/9lxo_63483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lxo_63483/08_2025/9lxo_63483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lxo_63483/08_2025/9lxo_63483.map" model { file = "/net/cci-nas-00/data/ceres_data/9lxo_63483/08_2025/9lxo_63483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lxo_63483/08_2025/9lxo_63483.cif" } resolution = 3.6 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= 0.004 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 110 5.49 5 Mg 1 5.21 5 S 285 5.16 5 C 27789 2.51 5 N 7738 2.21 5 O 8563 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44496 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 10814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10814 Classifications: {'peptide': 1378} Link IDs: {'PTRANS': 64, 'TRANS': 1313} Chain: "B" Number of atoms: 8736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8736 Classifications: {'peptide': 1105} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1053} Chain breaks: 1 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: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3382 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 754 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 12, 'TRANS': 74} Chain: "V" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 246 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "X" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1048 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Y" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1043 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Z" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 57.602 113.916 84.607 1.00103.58 S ATOM 565 SG CYS A 72 58.242 117.414 86.013 1.00106.71 S ATOM 613 SG CYS A 79 61.509 115.287 84.707 1.00104.11 S ATOM 854 SG CYS A 109 67.803 86.995 123.209 1.00114.77 S ATOM 876 SG CYS A 112 65.753 89.286 125.305 1.00118.64 S ATOM 1245 SG CYS A 156 68.428 88.114 127.489 1.00130.18 S ATOM 1271 SG CYS A 159 65.710 86.098 126.708 1.00130.36 S ATOM 19137 SG CYS B1080 59.836 119.906 102.603 1.00102.14 S ATOM 19156 SG CYS B1083 61.064 116.165 102.800 1.00101.99 S ATOM 19222 SG CYS B1092 58.687 117.343 100.294 1.00 97.16 S ATOM 19250 SG CYS B1095 57.401 116.509 104.390 1.00100.21 S ATOM 28160 SG CYS I 5 116.397 46.403 105.515 1.00130.73 S ATOM 28177 SG CYS I 8 112.834 47.622 103.993 1.00130.05 S ATOM 28307 SG CYS I 25 112.603 49.165 107.118 1.00130.27 S ATOM 28328 SG CYS I 28 112.966 45.698 107.037 1.00128.16 S ATOM 28600 SG CYS J 7 115.793 124.851 44.422 1.00 75.41 S ATOM 28624 SG CYS J 10 117.287 128.127 43.237 1.00 75.83 S ATOM 28888 SG CYS J 44 119.570 125.824 44.598 1.00 81.33 S ATOM 28894 SG CYS J 45 118.777 125.234 41.040 1.00 82.39 S ATOM 29937 SG CYS L 19 82.646 99.645 34.471 1.00103.46 S ATOM 29956 SG CYS L 22 83.631 97.768 30.511 1.00109.30 S ATOM 30073 SG CYS L 36 79.595 99.654 32.135 1.00117.09 S ATOM 30099 SG CYS L 39 81.303 96.342 32.683 1.00117.30 S ATOM 41169 SG CYS P 307 41.361 99.473 107.397 1.00108.29 S Time building chain proxies: 8.18, per 1000 atoms: 0.18 Number of scatterers: 44496 At special positions: 0 Unit cell: (173.23, 181.225, 173.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 285 16.00 P 110 15.00 Mg 1 11.99 O 8563 8.00 N 7738 7.00 C 27789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.4 microseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " Number of angles added : 9 Zn2+ tetrahedral coordination pdb=" ZN A1401 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1401 " - pdb=" NE2 HIS A 82 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1080 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1083 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 33 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10004 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 57 sheets defined 42.5% alpha, 17.0% beta 34 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 135 through 153 removed outlier: 3.729A pdb=" N LYS A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 212 Proline residue: A 209 - end of helix removed outlier: 4.465A pdb=" N GLY A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.597A pdb=" N ARG A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 5.923A pdb=" N GLU A 233 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 277 through 300 removed outlier: 3.788A pdb=" N MET A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.787A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 572 No H-bonds generated for 'chain 'A' and resid 571 through 572' Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.647A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.768A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 656 Processing helix chain 'A' and resid 662 through 672 Processing helix chain 'A' and resid 672 through 695 removed outlier: 3.919A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 733 Processing helix chain 'A' and resid 743 through 771 Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 843 through 880 removed outlier: 3.708A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.518A pdb=" N ASP A 905 " --> pdb=" O TYR A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 941 through 954 removed outlier: 3.541A pdb=" N LYS A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 987 Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1007 through 1025 Processing helix chain 'A' and resid 1032 through 1048 Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1094 through 1106 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1133 through 1141 Processing helix chain 'A' and resid 1145 through 1153 Processing helix chain 'A' and resid 1161 through 1163 No H-bonds generated for 'chain 'A' and resid 1161 through 1163' Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1188 through 1196 removed outlier: 3.949A pdb=" N GLU A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1238 removed outlier: 3.571A pdb=" N VAL A1235 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1278 removed outlier: 7.738A pdb=" N ILE A1260 " --> pdb=" O LYS A1256 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N GLU A1261 " --> pdb=" O THR A1257 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.957A pdb=" N VAL A1287 " --> pdb=" O ASP A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1312 Processing helix chain 'A' and resid 1314 through 1322 Processing helix chain 'A' and resid 1323 through 1335 Processing helix chain 'A' and resid 1342 through 1350 removed outlier: 3.553A pdb=" N CYS A1346 " --> pdb=" O GLY A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1360 removed outlier: 3.670A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A1359 " --> pdb=" O GLY A1356 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N PHE A1360 " --> pdb=" O THR A1357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1355 through 1360' Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.260A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.834A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.583A pdb=" N ILE B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 258 through 275 Proline residue: B 267 - end of helix removed outlier: 3.674A pdb=" N ALA B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'B' and resid 304 through 315 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.641A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 422 removed outlier: 4.186A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 452 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 518 Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.599A pdb=" N LEU B 526 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.592A pdb=" N GLU B 530 " --> pdb=" O CYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 566 removed outlier: 3.734A pdb=" N LEU B 555 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 617 Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 635 through 639 Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.589A pdb=" N THR B 663 " --> pdb=" O GLU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 691 Processing helix chain 'B' and resid 722 through 729 Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.411A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.764A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 removed outlier: 3.589A pdb=" N VAL B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1048 through 1059 Processing helix chain 'B' and resid 1060 through 1069 Processing helix chain 'B' and resid 1108 through 1120 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.538A pdb=" N ILE C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.519A pdb=" N LEU C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 162' Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 247 through 257 removed outlier: 3.739A pdb=" N GLU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 317 through 344 Processing helix chain 'D' and resid 12 through 30 removed outlier: 3.830A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.583A pdb=" N GLN D 39 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.140A pdb=" N ALA D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.850A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.541A pdb=" N GLY K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 126 Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 140 through 159 Processing helix chain 'M' and resid 182 through 191 Processing helix chain 'M' and resid 192 through 203 removed outlier: 3.982A pdb=" N GLU M 203 " --> pdb=" O LYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 222 removed outlier: 3.905A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 226 Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'M' and resid 269 through 275 Processing helix chain 'M' and resid 277 through 289 Processing helix chain 'M' and resid 293 through 302 Processing helix chain 'M' and resid 306 through 315 Processing helix chain 'M' and resid 328 through 333 removed outlier: 3.809A pdb=" N LEU M 332 " --> pdb=" O LYS M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 363 removed outlier: 3.560A pdb=" N LEU M 349 " --> pdb=" O PRO M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 376 Processing helix chain 'M' and resid 378 through 388 Processing helix chain 'M' and resid 405 through 412 removed outlier: 4.010A pdb=" N ILE M 409 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 435 Processing helix chain 'N' and resid 147 through 151 removed outlier: 4.095A pdb=" N THR N 151 " --> pdb=" O ASP N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 259 Processing helix chain 'N' and resid 333 through 335 No H-bonds generated for 'chain 'N' and resid 333 through 335' Processing helix chain 'N' and resid 388 through 396 removed outlier: 3.944A pdb=" N LYS N 396 " --> pdb=" O LEU N 392 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 21 through 32 Processing helix chain 'O' and resid 35 through 44 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.786A pdb=" N HIS O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 78 through 85 Processing helix chain 'O' and resid 87 through 99 Processing helix chain 'O' and resid 100 through 114 Processing helix chain 'O' and resid 117 through 133 removed outlier: 4.017A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 154 removed outlier: 4.063A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 Processing helix chain 'O' and resid 260 through 278 removed outlier: 4.516A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR O 277 " --> pdb=" O MET O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 297 Processing helix chain 'O' and resid 304 through 317 Processing helix chain 'O' and resid 337 through 359 Processing helix chain 'O' and resid 359 through 372 Processing helix chain 'O' and resid 376 through 385 Processing helix chain 'O' and resid 390 through 401 Processing helix chain 'O' and resid 416 through 418 No H-bonds generated for 'chain 'O' and resid 416 through 418' Processing helix chain 'O' and resid 427 through 457 Processing helix chain 'O' and resid 457 through 473 removed outlier: 4.188A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 3.570A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 491 through 530 removed outlier: 4.040A pdb=" N GLU O 495 " --> pdb=" O ILE O 491 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 29 Processing helix chain 'P' and resid 34 through 42 Processing helix chain 'P' and resid 46 through 60 Processing helix chain 'P' and resid 88 through 103 removed outlier: 3.670A pdb=" N GLU P 92 " --> pdb=" O SER P 88 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'P' and resid 108 through 117 Processing helix chain 'P' and resid 119 through 133 removed outlier: 3.539A pdb=" N LYS P 133 " --> pdb=" O ASN P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 199 removed outlier: 3.575A pdb=" N LYS P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 210 Processing helix chain 'P' and resid 213 through 224 Processing helix chain 'P' and resid 231 through 245 Processing helix chain 'P' and resid 281 through 285 Processing helix chain 'P' and resid 292 through 296 Processing helix chain 'P' and resid 307 through 316 Processing helix chain 'Q' and resid 51 through 69 removed outlier: 3.877A pdb=" N LYS Q 69 " --> pdb=" O ARG Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 93 Processing helix chain 'Q' and resid 107 through 111 removed outlier: 3.799A pdb=" N MET Q 110 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1337 through 1339 removed outlier: 7.350A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B1123 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 93 removed outlier: 6.850A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.521A pdb=" N ILE A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 266 through 268 removed outlier: 3.703A pdb=" N SER A 268 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.795A pdb=" N LYS A 359 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 3.548A pdb=" N ARG A 487 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N PHE A 486 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 368 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N PHE A 488 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER A 370 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 395 removed outlier: 4.258A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA9, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.658A pdb=" N GLN A 641 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 883 through 884 removed outlier: 6.915A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1210 through 1215 removed outlier: 7.185A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N THR A1086 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR A1244 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN A1088 " --> pdb=" O LYS A1242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 6.948A pdb=" N THR A1108 " --> pdb=" O VAL A1201 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1114 through 1121 removed outlier: 7.246A pdb=" N LYS A1131 " --> pdb=" O GLU A1115 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE A1117 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A1129 " --> pdb=" O ILE A1117 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU A1119 " --> pdb=" O PHE A1127 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE A1127 " --> pdb=" O GLU A1119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1361 through 1364 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 65 removed outlier: 7.285A pdb=" N LEU B 75 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 79 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 111 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG B 135 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 113 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 131 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE B 117 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN B 129 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR B 119 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE B 127 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'B' and resid 360 through 363 removed outlier: 6.692A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 189 through 193 Processing sheet with id=AC1, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AC2, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC3, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC4, first strand: chain 'B' and resid 544 through 550 removed outlier: 5.379A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N VAL B 583 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.573A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.573A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 986 through 987 removed outlier: 7.343A pdb=" N LEU B 755 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 910 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU B 757 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 927 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 929 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AC9, first strand: chain 'B' and resid 795 through 796 removed outlier: 3.520A pdb=" N LYS B 801 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 918 through 919 Processing sheet with id=AD2, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.270A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 21 through 22 removed outlier: 7.114A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.752A pdb=" N HIS C 305 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.318A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 88 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.779A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.715A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 240 through 241 removed outlier: 3.720A pdb=" N THR C 240 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE1, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.767A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA D 6 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU G 4 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N HIS G 67 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA G 57 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LYS G 69 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU G 55 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL G 75 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE G 49 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N PHE G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N CYS G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 72 through 75 Processing sheet with id=AE3, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.759A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.600A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 105 through 108 removed outlier: 3.951A pdb=" N ASP G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 101 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ILE G 107 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL G 99 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER G 189 " --> pdb=" O ARG G 151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.925A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 12 through 16 Processing sheet with id=AE8, first strand: chain 'K' and resid 26 through 30 Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 17 removed outlier: 3.545A pdb=" N ALA M 115 " --> pdb=" O LEU N 269 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY N 327 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 25 through 34 removed outlier: 6.963A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG M 33 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 11.698A pdb=" N GLU N 359 " --> pdb=" O PRO M 31 " (cutoff:3.500A) removed outlier: 10.894A pdb=" N VAL N 361 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N GLN M 29 " --> pdb=" O VAL N 361 " (cutoff:3.500A) removed outlier: 9.847A pdb=" N VAL N 363 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LEU M 27 " --> pdb=" O VAL N 363 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 291 through 292 removed outlier: 3.544A pdb=" N TRP M 325 " --> pdb=" O MET M 292 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AF4, first strand: chain 'O' and resid 63 through 67 Processing sheet with id=AF5, first strand: chain 'O' and resid 157 through 159 Processing sheet with id=AF6, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AF7, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AF8, first strand: chain 'O' and resid 409 through 410 Processing sheet with id=AF9, first strand: chain 'P' and resid 63 through 68 Processing sheet with id=AG1, first strand: chain 'P' and resid 136 through 140 Processing sheet with id=AG2, first strand: chain 'P' and resid 211 through 212 Processing sheet with id=AG3, first strand: chain 'V' and resid 15 through 17 removed outlier: 6.461A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1904 hydrogen bonds defined for protein. 5382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 12.89 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.38: 15133 1.38 - 1.60: 29835 1.60 - 1.83: 559 1.83 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 45539 Sorted by residual: bond pdb=" O3' C Z 4 " pdb=" P U Z 5 " ideal model delta sigma weight residual 1.607 1.464 0.143 1.50e-02 4.44e+03 9.07e+01 bond pdb=" C LEU I 46 " pdb=" O LEU I 46 " ideal model delta sigma weight residual 1.234 1.149 0.085 1.07e-02 8.73e+03 6.32e+01 bond pdb=" O3' U Z 2 " pdb=" P G Z 3 " ideal model delta sigma weight residual 1.607 1.507 0.100 1.50e-02 4.44e+03 4.43e+01 bond pdb=" O3' U Z 5 " pdb=" P C Z 6 " ideal model delta sigma weight residual 1.607 1.518 0.089 1.50e-02 4.44e+03 3.49e+01 bond pdb=" CA LYS I 47 " pdb=" C LYS I 47 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.33e-02 5.65e+03 2.77e+01 ... (remaining 45534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 61893 4.38 - 8.76: 50 8.76 - 13.13: 9 13.13 - 17.51: 2 17.51 - 21.89: 3 Bond angle restraints: 61957 Sorted by residual: angle pdb=" C3' U Z 2 " pdb=" O3' U Z 2 " pdb=" P G Z 3 " ideal model delta sigma weight residual 120.20 98.31 21.89 1.50e+00 4.44e-01 2.13e+02 angle pdb=" O3' U Z 2 " pdb=" P G Z 3 " pdb=" O5' G Z 3 " ideal model delta sigma weight residual 104.00 125.70 -21.70 1.50e+00 4.44e-01 2.09e+02 angle pdb=" C3' U Z 5 " pdb=" C2' U Z 5 " pdb=" O2' U Z 5 " ideal model delta sigma weight residual 110.70 130.53 -19.83 1.50e+00 4.44e-01 1.75e+02 angle pdb=" N ASP I 51 " pdb=" CA ASP I 51 " pdb=" C ASP I 51 " ideal model delta sigma weight residual 110.17 121.95 -11.78 1.51e+00 4.39e-01 6.09e+01 angle pdb=" O4' C Z 6 " pdb=" C4' C Z 6 " pdb=" C3' C Z 6 " ideal model delta sigma weight residual 104.00 96.93 7.07 1.00e+00 1.00e+00 5.00e+01 ... (remaining 61952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 27186 35.75 - 71.51: 515 71.51 - 107.26: 18 107.26 - 143.01: 2 143.01 - 178.77: 7 Dihedral angle restraints: 27728 sinusoidal: 12249 harmonic: 15479 Sorted by residual: dihedral pdb=" O3A GTP Z 101 " pdb=" O3B GTP Z 101 " pdb=" PB GTP Z 101 " pdb=" PG GTP Z 101 " ideal model delta sinusoidal sigma weight residual 303.79 154.94 148.85 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C8 GTP Z 101 " pdb=" C1' GTP Z 101 " pdb=" N9 GTP Z 101 " pdb=" O4' GTP Z 101 " ideal model delta sinusoidal sigma weight residual 104.59 -32.99 137.58 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' GTP Z 101 " pdb=" O5' GTP Z 101 " pdb=" PA GTP Z 101 " pdb=" O3A GTP Z 101 " ideal model delta sinusoidal sigma weight residual 69.27 168.70 -99.43 1 2.00e+01 2.50e-03 2.79e+01 ... (remaining 27725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 6868 0.119 - 0.239: 98 0.239 - 0.358: 5 0.358 - 0.478: 2 0.478 - 0.597: 1 Chirality restraints: 6974 Sorted by residual: chirality pdb=" C2' U Z 5 " pdb=" C3' U Z 5 " pdb=" O2' U Z 5 " pdb=" C1' U Z 5 " both_signs ideal model delta sigma weight residual False -2.75 -2.16 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" CA ASP I 51 " pdb=" N ASP I 51 " pdb=" C ASP I 51 " pdb=" CB ASP I 51 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C3' U Z 5 " pdb=" C4' U Z 5 " pdb=" O3' U Z 5 " pdb=" C2' U Z 5 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.40 2.00e-01 2.50e+01 4.03e+00 ... (remaining 6971 not shown) Planarity restraints: 7602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 46 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C LEU I 46 " -0.063 2.00e-02 2.50e+03 pdb=" O LEU I 46 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS I 47 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C Z 6 " 0.030 2.00e-02 2.50e+03 2.03e-02 9.26e+00 pdb=" N1 C Z 6 " -0.023 2.00e-02 2.50e+03 pdb=" C2 C Z 6 " -0.030 2.00e-02 2.50e+03 pdb=" O2 C Z 6 " 0.010 2.00e-02 2.50e+03 pdb=" N3 C Z 6 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C Z 6 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C Z 6 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C Z 6 " 0.021 2.00e-02 2.50e+03 pdb=" C6 C Z 6 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G Z 3 " -0.021 2.00e-02 2.50e+03 1.71e-02 8.72e+00 pdb=" N9 G Z 3 " 0.023 2.00e-02 2.50e+03 pdb=" C8 G Z 3 " 0.018 2.00e-02 2.50e+03 pdb=" N7 G Z 3 " 0.012 2.00e-02 2.50e+03 pdb=" C5 G Z 3 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G Z 3 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G Z 3 " 0.003 2.00e-02 2.50e+03 pdb=" N1 G Z 3 " -0.015 2.00e-02 2.50e+03 pdb=" C2 G Z 3 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G Z 3 " 0.028 2.00e-02 2.50e+03 pdb=" N3 G Z 3 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G Z 3 " -0.028 2.00e-02 2.50e+03 ... (remaining 7599 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 78 2.32 - 2.97: 21214 2.97 - 3.61: 65832 3.61 - 4.26: 103416 4.26 - 4.90: 170742 Nonbonded interactions: 361282 Sorted by model distance: nonbonded pdb=" OG1 THR A 303 " pdb=" NE2 GLN O 377 " model vdw 1.679 3.120 nonbonded pdb=" O6 DG X 11 " pdb=" N4 DC Y -11 " model vdw 1.827 3.120 nonbonded pdb=" OG1 THR A 303 " pdb=" OH TYR O 424 " model vdw 1.834 3.040 nonbonded pdb=" O ILE A 230 " pdb=" N THR O 2 " model vdw 1.878 3.120 nonbonded pdb=" OE1 GLN E 95 " pdb=" OH TYR E 125 " model vdw 2.009 3.040 ... (remaining 361277 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 51.680 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 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 : 0.009 1.021 45566 Z= 0.333 Angle : 0.791 59.506 61999 Z= 0.318 Chirality : 0.042 0.597 6974 Planarity : 0.003 0.046 7602 Dihedral : 12.061 178.766 17724 Min Nonbonded Distance : 1.679 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.53 % Allowed : 2.45 % Favored : 97.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.25 (0.11), residues: 5269 helix: 0.38 (0.11), residues: 2026 sheet: -1.35 (0.17), residues: 707 loop : -1.68 (0.11), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 452 TYR 0.008 0.001 TYR L 41 PHE 0.006 0.001 PHE B1004 TRP 0.005 0.001 TRP P 313 HIS 0.003 0.001 HIS B 676 Details of bonding type rmsd covalent geometry : bond 0.00363 (45539) covalent geometry : angle 0.52307 (61957) hydrogen bonds : bond 0.14437 ( 1957) hydrogen bonds : angle 5.45234 ( 5538) metal coordination : bond 0.35605 ( 27) metal coordination : angle 22.80729 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 1501 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7975 (t80) cc_final: 0.7554 (t80) REVERT: A 75 ASN cc_start: 0.7348 (m-40) cc_final: 0.6567 (p0) REVERT: A 115 ILE cc_start: 0.8403 (tt) cc_final: 0.8090 (tp) REVERT: A 175 ILE cc_start: 0.7111 (tt) cc_final: 0.6498 (mt) REVERT: A 176 HIS cc_start: 0.8082 (t-170) cc_final: 0.7459 (t-90) REVERT: A 445 LYS cc_start: 0.7810 (mmpt) cc_final: 0.7521 (mmtt) REVERT: A 465 GLN cc_start: 0.7595 (tp40) cc_final: 0.7187 (tp40) REVERT: A 490 GLU cc_start: 0.7707 (mp0) cc_final: 0.7017 (mp0) REVERT: A 497 ASN cc_start: 0.9190 (t0) cc_final: 0.8940 (t0) REVERT: A 560 ASP cc_start: 0.7101 (p0) cc_final: 0.6878 (p0) REVERT: A 634 ASN cc_start: 0.8803 (m-40) cc_final: 0.8157 (t0) REVERT: A 650 MET cc_start: 0.8388 (mmm) cc_final: 0.8154 (mmt) REVERT: A 727 TYR cc_start: 0.5799 (m-10) cc_final: 0.5541 (m-10) REVERT: A 743 THR cc_start: 0.7605 (t) cc_final: 0.5866 (m) REVERT: A 758 VAL cc_start: 0.7009 (t) cc_final: 0.6740 (p) REVERT: A 946 ILE cc_start: 0.8242 (mm) cc_final: 0.7907 (mt) REVERT: A 962 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7434 (mt0) REVERT: A 1078 LYS cc_start: 0.8631 (mttp) cc_final: 0.7978 (mmtt) REVERT: A 1100 LEU cc_start: 0.9138 (tp) cc_final: 0.8898 (tp) REVERT: A 1175 VAL cc_start: 0.9048 (t) cc_final: 0.8748 (m) REVERT: A 1273 TYR cc_start: 0.8078 (t80) cc_final: 0.7496 (t80) REVERT: A 1337 LYS cc_start: 0.7978 (ptpt) cc_final: 0.7480 (mttt) REVERT: B 64 LYS cc_start: 0.6039 (ttmt) cc_final: 0.5209 (tttp) REVERT: B 150 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7719 (mmtm) REVERT: B 154 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7758 (mt-10) REVERT: B 249 GLN cc_start: 0.6597 (tt0) cc_final: 0.5758 (tp40) REVERT: B 254 MET cc_start: 0.7121 (mtp) cc_final: 0.6302 (mtp) REVERT: B 260 HIS cc_start: 0.8573 (p-80) cc_final: 0.8157 (p-80) REVERT: B 338 MET cc_start: 0.7903 (ttp) cc_final: 0.7676 (ttm) REVERT: B 412 THR cc_start: 0.8035 (m) cc_final: 0.7762 (p) REVERT: B 471 LEU cc_start: 0.8262 (tp) cc_final: 0.8009 (tp) REVERT: B 508 ASP cc_start: 0.5869 (t0) cc_final: 0.5400 (t0) REVERT: B 545 ILE cc_start: 0.8057 (mt) cc_final: 0.7589 (mt) REVERT: B 561 LEU cc_start: 0.8643 (tp) cc_final: 0.8141 (mt) REVERT: B 628 SER cc_start: 0.8870 (m) cc_final: 0.8549 (p) REVERT: B 721 LYS cc_start: 0.8449 (pttt) cc_final: 0.8121 (pttm) REVERT: B 869 VAL cc_start: 0.9254 (t) cc_final: 0.8951 (m) REVERT: B 916 MET cc_start: 0.9319 (mmt) cc_final: 0.8854 (mmt) REVERT: B 923 ILE cc_start: 0.8984 (mt) cc_final: 0.8779 (pt) REVERT: B 996 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7557 (mp0) REVERT: B 1002 ILE cc_start: 0.8856 (mm) cc_final: 0.8392 (mm) REVERT: B 1037 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7660 (mt-10) REVERT: B 1076 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7894 (mp0) REVERT: B 1105 ARG cc_start: 0.8276 (mmm160) cc_final: 0.7895 (ttt90) REVERT: C 19 PHE cc_start: 0.9027 (m-80) cc_final: 0.8581 (m-80) REVERT: C 55 HIS cc_start: 0.7140 (t70) cc_final: 0.6834 (t-170) REVERT: C 65 MET cc_start: 0.8355 (mtp) cc_final: 0.8110 (mtm) REVERT: C 83 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8004 (mm-30) REVERT: C 87 MET cc_start: 0.8423 (mmm) cc_final: 0.7680 (mmm) REVERT: C 190 ILE cc_start: 0.9210 (mm) cc_final: 0.8964 (mm) REVERT: C 246 GLU cc_start: 0.7792 (pm20) cc_final: 0.7570 (pm20) REVERT: D 3 VAL cc_start: 0.8679 (m) cc_final: 0.7718 (m) REVERT: D 14 TYR cc_start: 0.7422 (t80) cc_final: 0.6668 (t80) REVERT: D 45 ILE cc_start: 0.6468 (tp) cc_final: 0.6024 (tt) REVERT: D 58 CYS cc_start: 0.8034 (t) cc_final: 0.7426 (p) REVERT: E 70 ASP cc_start: 0.5699 (t0) cc_final: 0.4807 (p0) REVERT: E 108 GLN cc_start: 0.8276 (mm110) cc_final: 0.7800 (tm-30) REVERT: E 154 GLU cc_start: 0.8092 (mp0) cc_final: 0.7747 (tp30) REVERT: F 84 GLU cc_start: 0.7251 (mp0) cc_final: 0.6766 (mp0) REVERT: F 87 THR cc_start: 0.8443 (p) cc_final: 0.8160 (t) REVERT: G 41 ASN cc_start: 0.8605 (m-40) cc_final: 0.8393 (m110) REVERT: G 104 PHE cc_start: 0.6798 (t80) cc_final: 0.5667 (t80) REVERT: H 13 LYS cc_start: 0.8739 (mmtp) cc_final: 0.8473 (mmtp) REVERT: H 14 ASP cc_start: 0.7906 (t0) cc_final: 0.7545 (t0) REVERT: H 42 ASP cc_start: 0.8342 (m-30) cc_final: 0.7542 (m-30) REVERT: H 64 LEU cc_start: 0.8485 (tp) cc_final: 0.8229 (tt) REVERT: I 26 ASN cc_start: 0.8911 (m-40) cc_final: 0.8400 (m-40) REVERT: I 40 ASN cc_start: 0.7772 (t0) cc_final: 0.6068 (t0) REVERT: J 64 PRO cc_start: 0.8343 (Cg_exo) cc_final: 0.8135 (Cg_endo) REVERT: K 24 LYS cc_start: 0.7678 (ptpp) cc_final: 0.7443 (ptmm) REVERT: K 39 CYS cc_start: 0.8382 (t) cc_final: 0.7884 (p) REVERT: K 66 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7323 (mm-30) REVERT: K 77 GLU cc_start: 0.7169 (pt0) cc_final: 0.6752 (pt0) REVERT: K 78 SER cc_start: 0.8291 (m) cc_final: 0.7621 (p) REVERT: L 24 THR cc_start: 0.9034 (p) cc_final: 0.8833 (p) REVERT: M 44 HIS cc_start: 0.7127 (m90) cc_final: 0.6461 (m170) REVERT: M 49 ILE cc_start: 0.7565 (tt) cc_final: 0.7192 (mp) REVERT: M 54 GLN cc_start: 0.6508 (pt0) cc_final: 0.4740 (tt0) REVERT: M 80 ASN cc_start: 0.9364 (m-40) cc_final: 0.8902 (m110) REVERT: M 91 THR cc_start: 0.8117 (p) cc_final: 0.7877 (p) REVERT: M 129 LEU cc_start: 0.7130 (mp) cc_final: 0.6894 (mp) REVERT: M 298 MET cc_start: 0.7045 (mmm) cc_final: 0.6567 (mmm) REVERT: M 389 MET cc_start: 0.3447 (ptp) cc_final: 0.2894 (ptp) REVERT: N 150 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7112 (tp30) REVERT: N 380 LYS cc_start: 0.8175 (tppp) cc_final: 0.7684 (mttp) REVERT: O 31 THR cc_start: 0.7825 (p) cc_final: 0.7226 (p) REVERT: O 133 MET cc_start: 0.3556 (ptt) cc_final: 0.3043 (ptt) REVERT: O 235 TRP cc_start: 0.9062 (m100) cc_final: 0.8531 (m100) REVERT: O 321 GLU cc_start: 0.7745 (mp0) cc_final: 0.7437 (mp0) REVERT: O 333 MET cc_start: 0.8514 (tpt) cc_final: 0.8068 (tpp) REVERT: O 382 ASP cc_start: 0.8313 (m-30) cc_final: 0.8014 (m-30) REVERT: O 435 LEU cc_start: 0.8638 (tp) cc_final: 0.8128 (tp) REVERT: O 530 THR cc_start: 0.8680 (t) cc_final: 0.8237 (p) REVERT: P 267 MET cc_start: 0.7384 (mmt) cc_final: 0.7064 (mmt) REVERT: P 303 SER cc_start: 0.8104 (t) cc_final: 0.7851 (m) REVERT: Q 43 TYR cc_start: 0.7345 (m-80) cc_final: 0.7004 (m-10) REVERT: Q 58 LEU cc_start: 0.9427 (tp) cc_final: 0.9204 (tp) REVERT: Q 67 THR cc_start: 0.8548 (t) cc_final: 0.8342 (t) REVERT: Q 71 MET cc_start: 0.8808 (tpt) cc_final: 0.8270 (tpp) outliers start: 25 outliers final: 5 residues processed: 1517 average time/residue: 0.2781 time to fit residues: 670.9436 Evaluate side-chains 896 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 891 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain O residue 55 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 80.0000 chunk 497 optimal weight: 0.0770 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 0.9980 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.5980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 290 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN A 599 GLN A 739 GLN A 836 ASN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 HIS A1336 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS B 273 GLN B 423 ASN B 616 GLN B 692 GLN C 160 ASN C 268 GLN C 290 ASN D 18 GLN D 35 HIS D 43 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 GLN E 108 GLN E 168 ASN G 115 GLN H 29 HIS H 126 GLN ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN N 381 HIS ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 457 ASN P 182 GLN P 214 HIS P 297 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.211359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155212 restraints weight = 63482.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149426 restraints weight = 40129.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151037 restraints weight = 46610.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151828 restraints weight = 30519.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.156239 restraints weight = 26322.231| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 45566 Z= 0.153 Angle : 0.654 22.882 61999 Z= 0.316 Chirality : 0.044 0.207 6974 Planarity : 0.004 0.042 7602 Dihedral : 15.493 179.926 7014 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.47 % Allowed : 11.22 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.40 (0.11), residues: 5269 helix: 1.04 (0.11), residues: 2061 sheet: -0.82 (0.18), residues: 694 loop : -1.20 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 33 TYR 0.022 0.001 TYR A 53 PHE 0.040 0.002 PHE D 69 TRP 0.008 0.001 TRP B 476 HIS 0.018 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00356 (45539) covalent geometry : angle 0.62296 (61957) hydrogen bonds : bond 0.03832 ( 1957) hydrogen bonds : angle 4.32623 ( 5538) metal coordination : bond 0.00955 ( 27) metal coordination : angle 7.73655 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 930 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 75 ASN cc_start: 0.7490 (m-40) cc_final: 0.7061 (p0) REVERT: A 146 ILE cc_start: 0.8679 (mt) cc_final: 0.8241 (mt) REVERT: A 150 CYS cc_start: 0.7958 (m) cc_final: 0.7662 (m) REVERT: A 167 LYS cc_start: 0.7213 (tttt) cc_final: 0.6813 (ttpp) REVERT: A 176 HIS cc_start: 0.7599 (t-170) cc_final: 0.7352 (t-90) REVERT: A 203 HIS cc_start: 0.8490 (t-90) cc_final: 0.8146 (t-170) REVERT: A 243 GLU cc_start: 0.8108 (mp0) cc_final: 0.7884 (mp0) REVERT: A 465 GLN cc_start: 0.7640 (tp40) cc_final: 0.7299 (tp40) REVERT: A 589 LEU cc_start: 0.8215 (pp) cc_final: 0.7960 (pp) REVERT: A 650 MET cc_start: 0.8593 (mmm) cc_final: 0.8363 (mmt) REVERT: A 680 MET cc_start: 0.7725 (mtp) cc_final: 0.7347 (mtp) REVERT: A 747 THR cc_start: 0.8357 (m) cc_final: 0.8076 (m) REVERT: A 946 ILE cc_start: 0.8557 (mm) cc_final: 0.8101 (mt) REVERT: A 947 LEU cc_start: 0.9073 (tt) cc_final: 0.8831 (mm) REVERT: A 1105 ILE cc_start: 0.8427 (pt) cc_final: 0.8140 (pt) REVERT: A 1138 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7794 (mtm110) REVERT: A 1194 GLU cc_start: 0.8616 (tp30) cc_final: 0.8395 (pp20) REVERT: A 1198 LYS cc_start: 0.8466 (mtmm) cc_final: 0.8178 (mtmm) REVERT: A 1273 TYR cc_start: 0.8328 (t80) cc_final: 0.7607 (t80) REVERT: A 1337 LYS cc_start: 0.8396 (ptpt) cc_final: 0.8047 (mttt) REVERT: B 59 MET cc_start: 0.7228 (tmm) cc_final: 0.6601 (ttp) REVERT: B 64 LYS cc_start: 0.6110 (ttmt) cc_final: 0.5081 (tttp) REVERT: B 190 ILE cc_start: 0.8820 (mt) cc_final: 0.8493 (tt) REVERT: B 260 HIS cc_start: 0.8182 (p90) cc_final: 0.7835 (p-80) REVERT: B 389 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: B 409 ASP cc_start: 0.7760 (p0) cc_final: 0.7513 (p0) REVERT: B 412 THR cc_start: 0.8077 (m) cc_final: 0.7724 (p) REVERT: B 530 GLU cc_start: 0.7373 (mp0) cc_final: 0.7145 (mm-30) REVERT: B 549 ILE cc_start: 0.8297 (tp) cc_final: 0.7959 (tp) REVERT: B 561 LEU cc_start: 0.8588 (tp) cc_final: 0.8275 (mt) REVERT: B 628 SER cc_start: 0.9045 (m) cc_final: 0.8580 (p) REVERT: B 899 SER cc_start: 0.8711 (p) cc_final: 0.8430 (p) REVERT: B 916 MET cc_start: 0.9372 (mmt) cc_final: 0.9133 (mmt) REVERT: B 996 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7551 (mp0) REVERT: C 19 PHE cc_start: 0.8856 (m-80) cc_final: 0.8471 (m-80) REVERT: C 65 MET cc_start: 0.8545 (mtp) cc_final: 0.8100 (mtp) REVERT: C 83 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7897 (mm-30) REVERT: C 87 MET cc_start: 0.8535 (mmm) cc_final: 0.8138 (mmm) REVERT: C 189 THR cc_start: 0.8588 (m) cc_final: 0.8383 (m) REVERT: C 190 ILE cc_start: 0.9067 (mm) cc_final: 0.8769 (mm) REVERT: D 14 TYR cc_start: 0.7388 (t80) cc_final: 0.6901 (t80) REVERT: E 18 MET cc_start: 0.8623 (mmm) cc_final: 0.8376 (mmm) REVERT: E 19 GLN cc_start: 0.8404 (mm-40) cc_final: 0.7877 (tp40) REVERT: E 73 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6924 (m-80) REVERT: E 99 ILE cc_start: 0.7743 (mt) cc_final: 0.7088 (mt) REVERT: G 24 ASP cc_start: 0.8454 (m-30) cc_final: 0.8167 (t0) REVERT: G 104 PHE cc_start: 0.6646 (t80) cc_final: 0.5910 (t80) REVERT: G 121 ASP cc_start: 0.5598 (m-30) cc_final: 0.4971 (m-30) REVERT: G 148 ILE cc_start: 0.8887 (mt) cc_final: 0.8473 (mp) REVERT: G 149 ARG cc_start: 0.7999 (tpt-90) cc_final: 0.7683 (tpt-90) REVERT: H 42 ASP cc_start: 0.8207 (m-30) cc_final: 0.7901 (m-30) REVERT: H 123 MET cc_start: 0.7894 (ttt) cc_final: 0.7566 (ttt) REVERT: I 40 ASN cc_start: 0.7421 (t0) cc_final: 0.7057 (t0) REVERT: I 42 LYS cc_start: 0.8191 (mmtt) cc_final: 0.7788 (mmtt) REVERT: J 58 LYS cc_start: 0.7719 (mmtp) cc_final: 0.7485 (mptt) REVERT: K 78 SER cc_start: 0.8200 (m) cc_final: 0.7749 (p) REVERT: L 44 MET cc_start: 0.8630 (mmm) cc_final: 0.8050 (mmm) REVERT: M 129 LEU cc_start: 0.7389 (mp) cc_final: 0.7167 (mp) REVERT: M 250 MET cc_start: 0.8472 (mmm) cc_final: 0.8258 (tpt) REVERT: M 270 MET cc_start: 0.3568 (tpp) cc_final: 0.3365 (ptt) REVERT: M 298 MET cc_start: 0.7582 (mmm) cc_final: 0.6923 (mmm) REVERT: N 274 THR cc_start: 0.7097 (p) cc_final: 0.6872 (p) REVERT: N 325 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7278 (tp40) REVERT: N 359 GLU cc_start: 0.7106 (pt0) cc_final: 0.6723 (pt0) REVERT: O 5 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7186 (mt-10) REVERT: O 31 THR cc_start: 0.8045 (p) cc_final: 0.7772 (p) REVERT: O 268 ARG cc_start: 0.8837 (ttm110) cc_final: 0.8442 (ptm160) REVERT: O 528 GLU cc_start: 0.8158 (tp30) cc_final: 0.7951 (tp30) REVERT: P 104 ASN cc_start: 0.8469 (t0) cc_final: 0.8248 (t0) REVERT: P 207 ASN cc_start: 0.9295 (m110) cc_final: 0.8902 (p0) REVERT: P 219 TYR cc_start: 0.8602 (t80) cc_final: 0.8317 (t80) REVERT: P 271 ARG cc_start: 0.6365 (ptm-80) cc_final: 0.6152 (ptm160) REVERT: P 311 THR cc_start: 0.9159 (m) cc_final: 0.8946 (p) REVERT: P 315 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7287 (tm-30) REVERT: Q 33 LYS cc_start: 0.8302 (tttp) cc_final: 0.7906 (tmtt) REVERT: Q 43 TYR cc_start: 0.7555 (m-80) cc_final: 0.7166 (m-10) REVERT: Q 86 ARG cc_start: 0.8395 (ptt-90) cc_final: 0.8104 (ttp-170) outliers start: 116 outliers final: 70 residues processed: 1001 average time/residue: 0.2733 time to fit residues: 448.5823 Evaluate side-chains 827 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 755 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 820 LYS Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 29 HIS Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain V residue 29 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 415 optimal weight: 50.0000 chunk 462 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 182 optimal weight: 0.4980 chunk 360 optimal weight: 0.7980 chunk 1 optimal weight: 0.0060 chunk 491 optimal weight: 40.0000 chunk 123 optimal weight: 0.5980 chunk 265 optimal weight: 0.0970 chunk 185 optimal weight: 0.9980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 641 GLN A 791 ASN A 836 ASN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 282 GLN ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN D 18 GLN D 88 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 HIS K 81 ASN ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN M 235 ASN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 381 HIS ** O 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 168 ASN ** O 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 407 GLN P 189 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.210470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154447 restraints weight = 63156.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.148148 restraints weight = 40094.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.150098 restraints weight = 45318.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.150443 restraints weight = 29431.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.152225 restraints weight = 25375.481| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 45566 Z= 0.124 Angle : 0.609 16.838 61999 Z= 0.299 Chirality : 0.042 0.277 6974 Planarity : 0.004 0.047 7602 Dihedral : 15.441 178.875 7008 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.87 % Allowed : 13.54 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.13 (0.11), residues: 5269 helix: 1.27 (0.11), residues: 2064 sheet: -0.59 (0.19), residues: 677 loop : -1.09 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 70 TYR 0.029 0.001 TYR E 90 PHE 0.033 0.001 PHE P 210 TRP 0.026 0.001 TRP Q 103 HIS 0.021 0.001 HIS H 29 Details of bonding type rmsd covalent geometry : bond 0.00285 (45539) covalent geometry : angle 0.59006 (61957) hydrogen bonds : bond 0.03396 ( 1957) hydrogen bonds : angle 4.21946 ( 5538) metal coordination : bond 0.00695 ( 27) metal coordination : angle 5.74922 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 841 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.7533 (m-40) cc_final: 0.7086 (p0) REVERT: A 146 ILE cc_start: 0.8817 (mt) cc_final: 0.8469 (mt) REVERT: A 150 CYS cc_start: 0.7882 (m) cc_final: 0.7556 (m) REVERT: A 167 LYS cc_start: 0.7344 (tttt) cc_final: 0.6922 (ttpp) REVERT: A 176 HIS cc_start: 0.7426 (t-170) cc_final: 0.7176 (t-90) REVERT: A 428 MET cc_start: 0.8515 (ppp) cc_final: 0.7510 (ppp) REVERT: A 465 GLN cc_start: 0.7673 (tp40) cc_final: 0.7241 (tp40) REVERT: A 650 MET cc_start: 0.8644 (mmm) cc_final: 0.8427 (mmt) REVERT: A 680 MET cc_start: 0.7661 (mtp) cc_final: 0.7309 (mtp) REVERT: A 946 ILE cc_start: 0.8529 (mm) cc_final: 0.8033 (mt) REVERT: A 947 LEU cc_start: 0.9095 (tt) cc_final: 0.8834 (mm) REVERT: A 1105 ILE cc_start: 0.8414 (pt) cc_final: 0.8152 (pt) REVERT: A 1138 ARG cc_start: 0.8164 (mtm110) cc_final: 0.7860 (mtm110) REVERT: A 1273 TYR cc_start: 0.8328 (t80) cc_final: 0.7683 (t80) REVERT: A 1275 MET cc_start: 0.9058 (tpp) cc_final: 0.8674 (mmt) REVERT: A 1337 LYS cc_start: 0.8413 (ptpt) cc_final: 0.8095 (mttt) REVERT: B 59 MET cc_start: 0.7111 (tmm) cc_final: 0.6622 (ttp) REVERT: B 64 LYS cc_start: 0.5899 (ttmt) cc_final: 0.4990 (tttp) REVERT: B 222 ARG cc_start: 0.6878 (ptp-170) cc_final: 0.6595 (ptp-110) REVERT: B 260 HIS cc_start: 0.8247 (p90) cc_final: 0.8046 (p-80) REVERT: B 281 MET cc_start: 0.8869 (tpp) cc_final: 0.8244 (tpt) REVERT: B 389 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: B 409 ASP cc_start: 0.7861 (p0) cc_final: 0.7587 (p0) REVERT: B 412 THR cc_start: 0.8081 (m) cc_final: 0.7695 (p) REVERT: B 529 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6594 (tm-30) REVERT: B 533 TYR cc_start: 0.8647 (m-10) cc_final: 0.7802 (m-80) REVERT: B 561 LEU cc_start: 0.8549 (tp) cc_final: 0.8228 (mt) REVERT: B 628 SER cc_start: 0.9089 (m) cc_final: 0.8573 (p) REVERT: B 709 MET cc_start: 0.9229 (ttp) cc_final: 0.8973 (ttp) REVERT: B 719 MET cc_start: 0.6761 (mmm) cc_final: 0.6426 (mmm) REVERT: B 899 SER cc_start: 0.8694 (p) cc_final: 0.8368 (p) REVERT: B 996 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7577 (mp0) REVERT: B 1042 ASP cc_start: 0.5915 (t0) cc_final: 0.5237 (t0) REVERT: C 19 PHE cc_start: 0.8985 (m-80) cc_final: 0.8400 (m-10) REVERT: C 65 MET cc_start: 0.8598 (mtp) cc_final: 0.8185 (mtp) REVERT: C 83 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7757 (mm-30) REVERT: C 87 MET cc_start: 0.8548 (mmm) cc_final: 0.8329 (mmm) REVERT: C 190 ILE cc_start: 0.9113 (mm) cc_final: 0.8850 (mm) REVERT: D 14 TYR cc_start: 0.7410 (t80) cc_final: 0.7097 (t80) REVERT: D 43 ASN cc_start: 0.8302 (m-40) cc_final: 0.7999 (m-40) REVERT: D 45 ILE cc_start: 0.6432 (tp) cc_final: 0.6169 (tt) REVERT: D 69 PHE cc_start: 0.9272 (t80) cc_final: 0.9006 (t80) REVERT: D 88 ASN cc_start: 0.7668 (m-40) cc_final: 0.6893 (m-40) REVERT: E 19 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7890 (tp40) REVERT: E 73 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.7000 (m-80) REVERT: E 99 ILE cc_start: 0.7443 (mt) cc_final: 0.6821 (mt) REVERT: E 105 VAL cc_start: 0.8647 (t) cc_final: 0.8281 (p) REVERT: F 115 TYR cc_start: 0.8285 (p90) cc_final: 0.7760 (p90) REVERT: G 2 PHE cc_start: 0.7414 (m-80) cc_final: 0.7073 (m-10) REVERT: G 7 MET cc_start: 0.8558 (mmm) cc_final: 0.8345 (mmm) REVERT: G 19 GLU cc_start: 0.7297 (pp20) cc_final: 0.6789 (pp20) REVERT: G 104 PHE cc_start: 0.6691 (t80) cc_final: 0.6055 (t80) REVERT: G 121 ASP cc_start: 0.6024 (m-30) cc_final: 0.5230 (m-30) REVERT: G 149 ARG cc_start: 0.8230 (tpt-90) cc_final: 0.7956 (tpt-90) REVERT: H 33 GLU cc_start: 0.6184 (mp0) cc_final: 0.5593 (mm-30) REVERT: H 37 MET cc_start: 0.7612 (mmt) cc_final: 0.7356 (mmp) REVERT: H 42 ASP cc_start: 0.8372 (m-30) cc_final: 0.8006 (m-30) REVERT: H 123 MET cc_start: 0.8067 (ttt) cc_final: 0.7696 (ttt) REVERT: I 40 ASN cc_start: 0.7400 (t0) cc_final: 0.6933 (t0) REVERT: I 42 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7970 (mmtt) REVERT: J 58 LYS cc_start: 0.7834 (mmtp) cc_final: 0.7495 (mptt) REVERT: K 77 GLU cc_start: 0.7512 (pt0) cc_final: 0.7302 (pt0) REVERT: K 78 SER cc_start: 0.8276 (m) cc_final: 0.7793 (p) REVERT: L 44 MET cc_start: 0.8663 (mmm) cc_final: 0.7926 (mmm) REVERT: M 37 MET cc_start: 0.7755 (ptp) cc_final: 0.7550 (pmm) REVERT: M 44 HIS cc_start: 0.7707 (m90) cc_final: 0.7397 (m-70) REVERT: M 80 ASN cc_start: 0.8880 (m110) cc_final: 0.8560 (m110) REVERT: M 97 MET cc_start: 0.5083 (mmp) cc_final: 0.4533 (mmm) REVERT: M 286 MET cc_start: 0.6663 (mmm) cc_final: 0.6094 (mmm) REVERT: M 298 MET cc_start: 0.7633 (mmm) cc_final: 0.6982 (mmm) REVERT: M 389 MET cc_start: 0.6265 (ptp) cc_final: 0.6051 (ptp) REVERT: N 325 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7453 (tp40) REVERT: N 328 LYS cc_start: 0.7612 (mtpp) cc_final: 0.7183 (mtpp) REVERT: N 350 MET cc_start: 0.8503 (ttm) cc_final: 0.7967 (mtm) REVERT: N 380 LYS cc_start: 0.8389 (tppp) cc_final: 0.7819 (mttp) REVERT: O 5 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7294 (mt-10) REVERT: O 139 MET cc_start: 0.7756 (mmm) cc_final: 0.7533 (mmm) REVERT: O 321 GLU cc_start: 0.7649 (mp0) cc_final: 0.7378 (mp0) REVERT: O 385 MET cc_start: 0.8021 (ppp) cc_final: 0.7738 (ppp) REVERT: O 528 GLU cc_start: 0.8262 (tp30) cc_final: 0.7710 (tp30) REVERT: P 311 THR cc_start: 0.9207 (m) cc_final: 0.8987 (p) REVERT: P 315 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7618 (tm-30) REVERT: Q 33 LYS cc_start: 0.8165 (tttp) cc_final: 0.7962 (ttmt) REVERT: Q 43 TYR cc_start: 0.7645 (m-80) cc_final: 0.7308 (m-10) REVERT: Q 92 MET cc_start: 0.3763 (ppp) cc_final: 0.3445 (ppp) REVERT: Q 102 ASP cc_start: 0.7913 (t0) cc_final: 0.7630 (t0) REVERT: Q 105 ARG cc_start: 0.8445 (ptp-110) cc_final: 0.8221 (ptp90) outliers start: 135 outliers final: 80 residues processed: 927 average time/residue: 0.2167 time to fit residues: 331.8527 Evaluate side-chains 828 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 745 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 820 LYS Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 325 GLN Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 381 HIS Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 285 THR Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 510 ASP Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 270 TYR Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 138 optimal weight: 0.7980 chunk 269 optimal weight: 1.9990 chunk 370 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 492 optimal weight: 0.0770 chunk 491 optimal weight: 40.0000 chunk 283 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 458 optimal weight: 5.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN B 253 GLN B 282 GLN B 501 HIS D 98 GLN E 107 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 HIS N 381 HIS ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 ASN ** V 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.194507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119447 restraints weight = 62567.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.123074 restraints weight = 34993.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123033 restraints weight = 21891.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123585 restraints weight = 24429.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123574 restraints weight = 21413.954| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 45566 Z= 0.250 Angle : 0.699 15.007 61999 Z= 0.349 Chirality : 0.046 0.262 6974 Planarity : 0.004 0.049 7602 Dihedral : 15.490 177.741 7008 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.66 % Allowed : 13.65 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.09 (0.11), residues: 5269 helix: 1.27 (0.12), residues: 2054 sheet: -0.60 (0.19), residues: 685 loop : -1.02 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 67 TYR 0.036 0.002 TYR B1058 PHE 0.034 0.002 PHE E 75 TRP 0.022 0.002 TRP P 217 HIS 0.021 0.002 HIS N 381 Details of bonding type rmsd covalent geometry : bond 0.00596 (45539) covalent geometry : angle 0.68252 (61957) hydrogen bonds : bond 0.03906 ( 1957) hydrogen bonds : angle 4.44431 ( 5538) metal coordination : bond 0.01210 ( 27) metal coordination : angle 5.89844 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 804 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7298 (p-80) REVERT: A 67 ARG cc_start: 0.8645 (ttp-110) cc_final: 0.8394 (ttp-110) REVERT: A 107 MET cc_start: 0.8020 (mmp) cc_final: 0.7760 (mmt) REVERT: A 146 ILE cc_start: 0.8840 (mt) cc_final: 0.8519 (mp) REVERT: A 150 CYS cc_start: 0.8237 (m) cc_final: 0.7967 (m) REVERT: A 176 HIS cc_start: 0.8032 (t-170) cc_final: 0.7731 (t70) REVERT: A 428 MET cc_start: 0.8714 (ppp) cc_final: 0.7643 (ppp) REVERT: A 440 MET cc_start: 0.8818 (mtt) cc_final: 0.8568 (mtp) REVERT: A 589 LEU cc_start: 0.8872 (pp) cc_final: 0.8546 (pp) REVERT: A 657 SER cc_start: 0.9079 (p) cc_final: 0.8842 (p) REVERT: A 831 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8150 (tptm) REVERT: A 915 LYS cc_start: 0.8158 (ptpt) cc_final: 0.7895 (ptpt) REVERT: A 947 LEU cc_start: 0.9219 (tt) cc_final: 0.8904 (mm) REVERT: A 1105 ILE cc_start: 0.8530 (pt) cc_final: 0.8200 (pt) REVERT: A 1138 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7913 (mtm110) REVERT: A 1198 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8291 (mtmm) REVERT: A 1215 ASP cc_start: 0.7784 (t0) cc_final: 0.7552 (t0) REVERT: A 1273 TYR cc_start: 0.8406 (t80) cc_final: 0.7370 (t80) REVERT: A 1288 MET cc_start: 0.7919 (mtm) cc_final: 0.7641 (mtm) REVERT: A 1308 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8836 (tt) REVERT: A 1333 TYR cc_start: 0.9073 (t80) cc_final: 0.8740 (t80) REVERT: B 59 MET cc_start: 0.7232 (tmm) cc_final: 0.6965 (ttp) REVERT: B 64 LYS cc_start: 0.5904 (ttmt) cc_final: 0.4910 (tttp) REVERT: B 190 ILE cc_start: 0.8883 (mt) cc_final: 0.8369 (tt) REVERT: B 281 MET cc_start: 0.9080 (tpp) cc_final: 0.8838 (tpp) REVERT: B 290 LYS cc_start: 0.8129 (mmtm) cc_final: 0.7598 (mmtm) REVERT: B 332 CYS cc_start: 0.8356 (m) cc_final: 0.7993 (m) REVERT: B 378 LYS cc_start: 0.7035 (mttm) cc_final: 0.6801 (mtpt) REVERT: B 409 ASP cc_start: 0.7917 (p0) cc_final: 0.7698 (p0) REVERT: B 412 THR cc_start: 0.8197 (m) cc_final: 0.7880 (p) REVERT: B 526 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7363 (pp) REVERT: B 529 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6666 (tm-30) REVERT: B 533 TYR cc_start: 0.8597 (m-10) cc_final: 0.7682 (m-10) REVERT: B 537 PHE cc_start: 0.7843 (m-80) cc_final: 0.7357 (m-80) REVERT: B 561 LEU cc_start: 0.8861 (tp) cc_final: 0.8315 (mt) REVERT: B 719 MET cc_start: 0.8125 (mmm) cc_final: 0.7849 (mmm) REVERT: B 781 ARG cc_start: 0.8635 (ptp-110) cc_final: 0.8363 (ptp-110) REVERT: B 899 SER cc_start: 0.8947 (p) cc_final: 0.8657 (p) REVERT: C 83 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7907 (mm-30) REVERT: C 324 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7359 (tp30) REVERT: D 69 PHE cc_start: 0.9433 (t80) cc_final: 0.9019 (t80) REVERT: E 19 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7952 (tp40) REVERT: E 33 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7309 (mp) REVERT: E 73 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: E 105 VAL cc_start: 0.8705 (t) cc_final: 0.8415 (p) REVERT: E 209 VAL cc_start: 0.9303 (t) cc_final: 0.9085 (m) REVERT: F 115 TYR cc_start: 0.8546 (p90) cc_final: 0.8138 (p90) REVERT: G 19 GLU cc_start: 0.7513 (pp20) cc_final: 0.7010 (pp20) REVERT: G 89 ILE cc_start: 0.7735 (mm) cc_final: 0.7526 (pt) REVERT: G 121 ASP cc_start: 0.5704 (m-30) cc_final: 0.4955 (m-30) REVERT: H 42 ASP cc_start: 0.8374 (m-30) cc_final: 0.7931 (m-30) REVERT: H 122 LEU cc_start: 0.8337 (mt) cc_final: 0.8097 (mm) REVERT: H 123 MET cc_start: 0.8385 (ttt) cc_final: 0.8123 (ttt) REVERT: I 4 PHE cc_start: 0.7310 (m-80) cc_final: 0.7026 (m-80) REVERT: I 40 ASN cc_start: 0.7548 (t0) cc_final: 0.6914 (t0) REVERT: I 42 LYS cc_start: 0.8430 (mmtt) cc_final: 0.7962 (mmtt) REVERT: J 26 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8111 (tp40) REVERT: J 54 ASP cc_start: 0.8105 (t0) cc_final: 0.7662 (t0) REVERT: K 39 CYS cc_start: 0.7703 (t) cc_final: 0.7494 (p) REVERT: K 77 GLU cc_start: 0.7844 (pt0) cc_final: 0.7626 (pt0) REVERT: K 78 SER cc_start: 0.8472 (m) cc_final: 0.8088 (p) REVERT: L 18 ILE cc_start: 0.9150 (mt) cc_final: 0.8721 (mm) REVERT: L 44 MET cc_start: 0.8798 (mmm) cc_final: 0.7992 (mmm) REVERT: M 11 GLN cc_start: 0.7665 (tp40) cc_final: 0.6716 (mp10) REVERT: M 37 MET cc_start: 0.7918 (ptp) cc_final: 0.7389 (pmm) REVERT: M 44 HIS cc_start: 0.7560 (m90) cc_final: 0.7046 (m-70) REVERT: M 214 ARG cc_start: 0.8501 (pmt-80) cc_final: 0.7577 (mtt180) REVERT: M 286 MET cc_start: 0.6742 (mmm) cc_final: 0.6127 (mmm) REVERT: M 298 MET cc_start: 0.7609 (mmm) cc_final: 0.7001 (mmm) REVERT: N 350 MET cc_start: 0.8503 (ttm) cc_final: 0.8150 (mtm) REVERT: O 139 MET cc_start: 0.7968 (mmm) cc_final: 0.7714 (mmm) REVERT: O 275 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7275 (tp30) REVERT: O 321 GLU cc_start: 0.7920 (mp0) cc_final: 0.7656 (mp0) REVERT: O 351 GLU cc_start: 0.8465 (pt0) cc_final: 0.8183 (mt-10) REVERT: O 385 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7683 (ppp) REVERT: O 407 GLN cc_start: 0.8007 (tp40) cc_final: 0.7593 (tp40) REVERT: O 528 GLU cc_start: 0.8448 (tp30) cc_final: 0.8057 (tp30) REVERT: O 531 MET cc_start: 0.8010 (mtt) cc_final: 0.7618 (mtt) REVERT: P 217 TRP cc_start: 0.8921 (t60) cc_final: 0.8542 (t60) REVERT: P 311 THR cc_start: 0.9189 (m) cc_final: 0.8980 (p) REVERT: P 315 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7562 (tm-30) REVERT: Q 37 LEU cc_start: 0.8939 (tp) cc_final: 0.8728 (tp) REVERT: Q 43 TYR cc_start: 0.7569 (m-80) cc_final: 0.7336 (m-10) REVERT: Q 57 MET cc_start: 0.7842 (mmt) cc_final: 0.7619 (mmt) REVERT: Q 71 MET cc_start: 0.8960 (tpp) cc_final: 0.8365 (tpp) REVERT: Q 102 ASP cc_start: 0.8031 (t0) cc_final: 0.7731 (t0) outliers start: 172 outliers final: 114 residues processed: 920 average time/residue: 0.2212 time to fit residues: 336.3235 Evaluate side-chains 829 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 707 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 820 LYS Chi-restraints excluded: chain B residue 870 MET Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 285 THR Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 385 MET Chi-restraints excluded: chain O residue 399 LEU Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain V residue 16 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 111 optimal weight: 5.9990 chunk 505 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 427 optimal weight: 7.9990 chunk 398 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 521 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 412 optimal weight: 50.0000 chunk 70 optimal weight: 0.5980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 423 GLN A 508 HIS ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN B 273 GLN B 806 HIS C 139 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 381 HIS O 402 ASN O 407 GLN P 189 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.195411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121650 restraints weight = 62498.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124741 restraints weight = 36744.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124656 restraints weight = 23536.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125068 restraints weight = 24660.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125134 restraints weight = 23422.223| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 45566 Z= 0.248 Angle : 0.693 15.898 61999 Z= 0.346 Chirality : 0.046 0.243 6974 Planarity : 0.004 0.046 7602 Dihedral : 15.515 177.727 7008 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.87 % Allowed : 15.24 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.15 (0.11), residues: 5269 helix: 1.19 (0.12), residues: 2057 sheet: -0.75 (0.19), residues: 691 loop : -0.98 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG Q 70 TYR 0.031 0.002 TYR B1058 PHE 0.042 0.002 PHE E 75 TRP 0.041 0.002 TRP Q 103 HIS 0.010 0.002 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00594 (45539) covalent geometry : angle 0.67505 (61957) hydrogen bonds : bond 0.03851 ( 1957) hydrogen bonds : angle 4.50510 ( 5538) metal coordination : bond 0.01262 ( 27) metal coordination : angle 6.06691 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 769 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7554 (p-80) REVERT: A 107 MET cc_start: 0.8396 (mmp) cc_final: 0.8112 (mmt) REVERT: A 158 HIS cc_start: 0.7124 (t-170) cc_final: 0.6583 (t-170) REVERT: A 428 MET cc_start: 0.8854 (ppp) cc_final: 0.7953 (ppp) REVERT: A 511 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8299 (mm-40) REVERT: A 831 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8121 (tptm) REVERT: A 915 LYS cc_start: 0.8235 (ptpt) cc_final: 0.7998 (ptpt) REVERT: A 916 ASP cc_start: 0.6754 (m-30) cc_final: 0.6503 (m-30) REVERT: A 947 LEU cc_start: 0.9243 (tt) cc_final: 0.8930 (mm) REVERT: A 1061 MET cc_start: 0.6964 (tpp) cc_final: 0.6699 (tpp) REVERT: A 1091 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8585 (mmmm) REVERT: A 1105 ILE cc_start: 0.8702 (pt) cc_final: 0.8416 (pt) REVERT: A 1138 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7942 (mtm110) REVERT: A 1215 ASP cc_start: 0.7846 (t0) cc_final: 0.7476 (t0) REVERT: A 1273 TYR cc_start: 0.8446 (t80) cc_final: 0.7245 (t80) REVERT: A 1288 MET cc_start: 0.8063 (mtm) cc_final: 0.7860 (mtm) REVERT: A 1333 TYR cc_start: 0.9102 (t80) cc_final: 0.8638 (t80) REVERT: B 59 MET cc_start: 0.7639 (tmm) cc_final: 0.7135 (ttp) REVERT: B 64 LYS cc_start: 0.5944 (ttmt) cc_final: 0.4980 (tttp) REVERT: B 154 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7530 (mt-10) REVERT: B 190 ILE cc_start: 0.8917 (mt) cc_final: 0.8303 (tt) REVERT: B 281 MET cc_start: 0.9065 (tpp) cc_final: 0.8781 (tpp) REVERT: B 290 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7757 (mmtm) REVERT: B 332 CYS cc_start: 0.8107 (m) cc_final: 0.7903 (m) REVERT: B 378 LYS cc_start: 0.7047 (mttm) cc_final: 0.6808 (mtpt) REVERT: B 412 THR cc_start: 0.8193 (m) cc_final: 0.7901 (p) REVERT: B 488 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7478 (tp30) REVERT: B 526 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7322 (pp) REVERT: B 529 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7319 (tm-30) REVERT: B 537 PHE cc_start: 0.8224 (m-80) cc_final: 0.7745 (m-80) REVERT: B 550 ARG cc_start: 0.7323 (tpp80) cc_final: 0.6999 (tpp80) REVERT: B 719 MET cc_start: 0.8007 (mmm) cc_final: 0.7492 (mmm) REVERT: B 781 ARG cc_start: 0.8727 (ptp-110) cc_final: 0.8475 (ptp-110) REVERT: B 899 SER cc_start: 0.8988 (p) cc_final: 0.8654 (p) REVERT: B 999 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: D 5 ASP cc_start: 0.6341 (t0) cc_final: 0.6008 (t0) REVERT: D 14 TYR cc_start: 0.7504 (t80) cc_final: 0.7247 (t80) REVERT: D 69 PHE cc_start: 0.9429 (t80) cc_final: 0.9173 (t80) REVERT: D 88 ASN cc_start: 0.8004 (m-40) cc_final: 0.7534 (m-40) REVERT: E 19 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8022 (tp40) REVERT: E 73 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: E 90 TYR cc_start: 0.7977 (m-80) cc_final: 0.7732 (m-80) REVERT: E 105 VAL cc_start: 0.8910 (t) cc_final: 0.8631 (p) REVERT: E 124 LYS cc_start: 0.8749 (ptpp) cc_final: 0.8525 (pttm) REVERT: E 141 GLU cc_start: 0.8252 (tt0) cc_final: 0.7905 (tp30) REVERT: F 115 TYR cc_start: 0.8637 (p90) cc_final: 0.8269 (p90) REVERT: G 88 LYS cc_start: 0.7748 (tptt) cc_final: 0.7165 (mmtm) REVERT: G 121 ASP cc_start: 0.5699 (m-30) cc_final: 0.4925 (m-30) REVERT: H 42 ASP cc_start: 0.8384 (m-30) cc_final: 0.8050 (m-30) REVERT: I 4 PHE cc_start: 0.7601 (m-80) cc_final: 0.7164 (m-80) REVERT: I 36 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7624 (mtm-85) REVERT: I 40 ASN cc_start: 0.7616 (t0) cc_final: 0.7275 (t0) REVERT: K 60 MET cc_start: 0.8775 (tpp) cc_final: 0.8252 (mmt) REVERT: K 66 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7850 (tt0) REVERT: K 77 GLU cc_start: 0.7745 (pt0) cc_final: 0.7514 (pt0) REVERT: K 78 SER cc_start: 0.8571 (m) cc_final: 0.8236 (p) REVERT: L 18 ILE cc_start: 0.9158 (mt) cc_final: 0.8760 (mm) REVERT: L 44 MET cc_start: 0.8939 (mmm) cc_final: 0.8162 (mmm) REVERT: M 37 MET cc_start: 0.7945 (ptp) cc_final: 0.7575 (pmm) REVERT: M 44 HIS cc_start: 0.7896 (m90) cc_final: 0.7502 (m170) REVERT: M 49 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7349 (mp) REVERT: M 66 ASN cc_start: 0.8055 (p0) cc_final: 0.7840 (t0) REVERT: M 214 ARG cc_start: 0.8556 (pmt-80) cc_final: 0.7740 (mtt180) REVERT: M 245 TYR cc_start: 0.7875 (t80) cc_final: 0.7475 (t80) REVERT: M 286 MET cc_start: 0.6751 (mmm) cc_final: 0.6129 (mmm) REVERT: M 298 MET cc_start: 0.7639 (mmm) cc_final: 0.7268 (mmm) REVERT: N 350 MET cc_start: 0.8750 (ttm) cc_final: 0.8483 (mtm) REVERT: O 5 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7654 (pt0) REVERT: O 38 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.9013 (p) REVERT: O 270 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9193 (ttt) REVERT: O 275 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: O 321 GLU cc_start: 0.8037 (mp0) cc_final: 0.7786 (mp0) REVERT: O 351 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8235 (mt-10) REVERT: O 385 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7843 (ppp) REVERT: O 490 MET cc_start: 0.5980 (mpp) cc_final: 0.4747 (ptm) REVERT: O 528 GLU cc_start: 0.8429 (tp30) cc_final: 0.8044 (tp30) REVERT: O 531 MET cc_start: 0.7986 (mtt) cc_final: 0.7416 (mtt) REVERT: P 207 ASN cc_start: 0.9536 (m110) cc_final: 0.9192 (p0) REVERT: P 217 TRP cc_start: 0.8932 (t60) cc_final: 0.8495 (t60) REVERT: P 311 THR cc_start: 0.9160 (m) cc_final: 0.8947 (p) REVERT: Q 33 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8349 (ttmm) outliers start: 182 outliers final: 125 residues processed: 887 average time/residue: 0.2333 time to fit residues: 343.9761 Evaluate side-chains 836 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 700 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 820 LYS Chi-restraints excluded: chain B residue 870 MET Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 98 LYS Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain K residue 29 MET Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 144 LYS Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 337 VAL Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 396 LYS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 270 MET Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 285 THR Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 351 GLU Chi-restraints excluded: chain O residue 385 MET Chi-restraints excluded: chain O residue 402 ASN Chi-restraints excluded: chain O residue 404 MET Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 417 optimal weight: 8.9990 chunk 532 optimal weight: 50.0000 chunk 372 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 324 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 401 optimal weight: 50.0000 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 ASN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS C 172 HIS ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN E 168 ASN G 71 HIS ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 325 GLN N 381 HIS O 407 GLN ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.189966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114846 restraints weight = 61887.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117193 restraints weight = 36951.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117278 restraints weight = 24644.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117626 restraints weight = 24435.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117739 restraints weight = 24388.319| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 45566 Z= 0.272 Angle : 0.717 21.263 61999 Z= 0.357 Chirality : 0.046 0.257 6974 Planarity : 0.005 0.071 7602 Dihedral : 15.536 178.265 7008 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.39 % Allowed : 15.56 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.22 (0.11), residues: 5269 helix: 1.17 (0.12), residues: 2054 sheet: -0.75 (0.19), residues: 686 loop : -1.06 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 140 TYR 0.033 0.002 TYR E 90 PHE 0.039 0.002 PHE E 75 TRP 0.037 0.001 TRP Q 103 HIS 0.010 0.002 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00651 (45539) covalent geometry : angle 0.69638 (61957) hydrogen bonds : bond 0.03979 ( 1957) hydrogen bonds : angle 4.60287 ( 5538) metal coordination : bond 0.01397 ( 27) metal coordination : angle 6.67232 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 747 time to evaluate : 1.755 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: A 17 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7637 (p-80) REVERT: A 143 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5765 (tmtt) REVERT: A 332 MET cc_start: 0.7751 (mmm) cc_final: 0.7469 (tpt) REVERT: A 428 MET cc_start: 0.8929 (ppp) cc_final: 0.8074 (ppp) REVERT: A 511 GLN cc_start: 0.8577 (mm-40) cc_final: 0.7980 (mm110) REVERT: A 726 GLU cc_start: 0.8371 (tt0) cc_final: 0.8034 (tm-30) REVERT: A 831 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8152 (tptm) REVERT: A 915 LYS cc_start: 0.8303 (ptpt) cc_final: 0.8076 (ptpt) REVERT: A 916 ASP cc_start: 0.7195 (m-30) cc_final: 0.6958 (m-30) REVERT: A 947 LEU cc_start: 0.9217 (tt) cc_final: 0.8914 (mm) REVERT: A 1061 MET cc_start: 0.6949 (tpp) cc_final: 0.6715 (tpp) REVERT: A 1091 LYS cc_start: 0.8881 (mmmm) cc_final: 0.8569 (mmmm) REVERT: A 1105 ILE cc_start: 0.8698 (pt) cc_final: 0.8385 (pt) REVERT: A 1138 ARG cc_start: 0.8437 (mtm110) cc_final: 0.7969 (mtm110) REVERT: A 1215 ASP cc_start: 0.8008 (t0) cc_final: 0.7580 (t0) REVERT: A 1273 TYR cc_start: 0.8498 (t80) cc_final: 0.7313 (t80) REVERT: A 1333 TYR cc_start: 0.9126 (t80) cc_final: 0.8575 (t80) REVERT: B 59 MET cc_start: 0.7756 (tmm) cc_final: 0.7166 (ttp) REVERT: B 64 LYS cc_start: 0.5954 (ttmt) cc_final: 0.5033 (tttp) REVERT: B 154 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 262 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8611 (mpp) REVERT: B 281 MET cc_start: 0.9047 (tpp) cc_final: 0.8749 (tpp) REVERT: B 290 LYS cc_start: 0.8408 (mmtm) cc_final: 0.7861 (mmtm) REVERT: B 409 ASP cc_start: 0.7796 (p0) cc_final: 0.7493 (p0) REVERT: B 412 THR cc_start: 0.8093 (m) cc_final: 0.7787 (p) REVERT: B 488 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7546 (tp30) REVERT: B 526 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7407 (pp) REVERT: B 529 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 550 ARG cc_start: 0.7133 (tpp80) cc_final: 0.6930 (tpp80) REVERT: B 719 MET cc_start: 0.8089 (mmm) cc_final: 0.7868 (mmp) REVERT: B 789 LYS cc_start: 0.7562 (ptmt) cc_final: 0.7292 (ptmt) REVERT: B 801 LYS cc_start: 0.8351 (tppt) cc_final: 0.7870 (mmmm) REVERT: B 899 SER cc_start: 0.8987 (p) cc_final: 0.8669 (p) REVERT: B 999 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7290 (mm-30) REVERT: D 5 ASP cc_start: 0.6276 (t0) cc_final: 0.5943 (t0) REVERT: D 69 PHE cc_start: 0.9460 (t80) cc_final: 0.9203 (t80) REVERT: D 85 GLN cc_start: 0.9190 (mt0) cc_final: 0.8919 (mm-40) REVERT: D 88 ASN cc_start: 0.8286 (m-40) cc_final: 0.7628 (m-40) REVERT: E 19 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8198 (tp40) REVERT: E 38 GLU cc_start: 0.8875 (mp0) cc_final: 0.8591 (pm20) REVERT: E 73 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: E 75 PHE cc_start: 0.7564 (m-10) cc_final: 0.7312 (m-10) REVERT: E 105 VAL cc_start: 0.8990 (t) cc_final: 0.8682 (p) REVERT: E 110 MET cc_start: 0.7584 (mmm) cc_final: 0.7318 (mmm) REVERT: E 124 LYS cc_start: 0.8823 (ptpp) cc_final: 0.8605 (pttm) REVERT: E 141 GLU cc_start: 0.8316 (tt0) cc_final: 0.8005 (tp30) REVERT: G 88 LYS cc_start: 0.7821 (tptt) cc_final: 0.7252 (mmtm) REVERT: G 121 ASP cc_start: 0.5503 (m-30) cc_final: 0.4763 (m-30) REVERT: H 42 ASP cc_start: 0.8413 (m-30) cc_final: 0.7977 (m-30) REVERT: I 4 PHE cc_start: 0.7581 (m-80) cc_final: 0.7165 (m-80) REVERT: K 66 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7916 (tt0) REVERT: K 77 GLU cc_start: 0.7610 (pt0) cc_final: 0.7314 (pt0) REVERT: K 78 SER cc_start: 0.8617 (m) cc_final: 0.8291 (p) REVERT: L 18 ILE cc_start: 0.9148 (mt) cc_final: 0.8724 (mm) REVERT: L 35 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7679 (ttm-80) REVERT: L 44 MET cc_start: 0.8903 (mmm) cc_final: 0.8146 (mmm) REVERT: M 37 MET cc_start: 0.8323 (ptp) cc_final: 0.7856 (pmm) REVERT: M 44 HIS cc_start: 0.7644 (m90) cc_final: 0.7406 (m170) REVERT: M 286 MET cc_start: 0.6897 (mmm) cc_final: 0.6349 (mmm) REVERT: M 298 MET cc_start: 0.7686 (mmm) cc_final: 0.7311 (mmm) REVERT: N 147 THR cc_start: 0.3438 (m) cc_final: 0.3103 (p) REVERT: N 350 MET cc_start: 0.8901 (ttm) cc_final: 0.8690 (mtm) REVERT: O 5 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7486 (pt0) REVERT: O 248 ASP cc_start: 0.8428 (m-30) cc_final: 0.8135 (m-30) REVERT: O 270 MET cc_start: 0.9452 (OUTLIER) cc_final: 0.9211 (ttt) REVERT: O 275 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: O 321 GLU cc_start: 0.8134 (mp0) cc_final: 0.7870 (mp0) REVERT: O 351 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: O 385 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7657 (ppp) REVERT: O 528 GLU cc_start: 0.8437 (tp30) cc_final: 0.8020 (tp30) REVERT: P 151 MET cc_start: 0.7657 (mmp) cc_final: 0.7432 (mtt) REVERT: P 210 PHE cc_start: 0.8163 (m-80) cc_final: 0.7851 (t80) REVERT: P 214 HIS cc_start: 0.9183 (t-90) cc_final: 0.8895 (t70) REVERT: P 217 TRP cc_start: 0.8922 (t60) cc_final: 0.8404 (t60) REVERT: P 311 THR cc_start: 0.9204 (m) cc_final: 0.8985 (p) REVERT: Q 33 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8159 (tmtt) REVERT: Q 43 TYR cc_start: 0.7627 (m-10) cc_final: 0.7397 (m-10) REVERT: Q 71 MET cc_start: 0.8670 (tpp) cc_final: 0.8069 (tpp) REVERT: Q 73 TYR cc_start: 0.8229 (m-80) cc_final: 0.7844 (m-80) REVERT: Q 102 ASP cc_start: 0.7965 (t0) cc_final: 0.7686 (t0) outliers start: 206 outliers final: 149 residues processed: 884 average time/residue: 0.2483 time to fit residues: 364.5592 Evaluate side-chains 856 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 696 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 901 ILE Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 820 LYS Chi-restraints excluded: chain B residue 870 MET Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 98 HIS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 25 CYS Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 144 LYS Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 368 SER Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 381 HIS Chi-restraints excluded: chain N residue 396 LYS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 28 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 270 MET Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 285 THR Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 351 GLU Chi-restraints excluded: chain O residue 369 VAL Chi-restraints excluded: chain O residue 385 MET Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 91 optimal weight: 0.6980 chunk 434 optimal weight: 1.9990 chunk 178 optimal weight: 0.0370 chunk 204 optimal weight: 0.9990 chunk 472 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 359 optimal weight: 0.6980 chunk 362 optimal weight: 1.9990 chunk 393 optimal weight: 20.0000 chunk 145 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN M 235 ASN N 381 HIS O 379 GLN ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.196360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137865 restraints weight = 61483.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132096 restraints weight = 41051.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.132992 restraints weight = 51284.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133239 restraints weight = 32502.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133498 restraints weight = 26030.838| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45566 Z= 0.135 Angle : 0.648 22.964 61999 Z= 0.320 Chirality : 0.043 0.292 6974 Planarity : 0.004 0.077 7602 Dihedral : 15.461 178.784 7008 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.21 % Allowed : 17.65 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.05 (0.11), residues: 5269 helix: 1.29 (0.12), residues: 2061 sheet: -0.62 (0.19), residues: 684 loop : -0.96 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 70 TYR 0.025 0.001 TYR E 90 PHE 0.030 0.001 PHE A1379 TRP 0.019 0.001 TRP Q 103 HIS 0.028 0.001 HIS N 381 Details of bonding type rmsd covalent geometry : bond 0.00312 (45539) covalent geometry : angle 0.63024 (61957) hydrogen bonds : bond 0.03419 ( 1957) hydrogen bonds : angle 4.36951 ( 5538) metal coordination : bond 0.00790 ( 27) metal coordination : angle 5.85034 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 782 time to evaluate : 1.651 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 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7411 (p-80) REVERT: A 332 MET cc_start: 0.7595 (mmm) cc_final: 0.7306 (tpt) REVERT: A 428 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8243 (ppp) REVERT: A 511 GLN cc_start: 0.8419 (mm-40) cc_final: 0.7930 (mm110) REVERT: A 915 LYS cc_start: 0.8200 (ptpt) cc_final: 0.7972 (ptpt) REVERT: A 947 LEU cc_start: 0.9203 (tt) cc_final: 0.8938 (mm) REVERT: A 1091 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8513 (mmmm) REVERT: A 1105 ILE cc_start: 0.8622 (pt) cc_final: 0.8392 (pt) REVERT: A 1106 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7307 (tm-30) REVERT: A 1112 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7726 (mp0) REVERT: A 1138 ARG cc_start: 0.8450 (mtm110) cc_final: 0.7998 (mtm110) REVERT: A 1198 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8027 (pttp) REVERT: A 1215 ASP cc_start: 0.7965 (t0) cc_final: 0.7561 (t0) REVERT: A 1273 TYR cc_start: 0.8362 (t80) cc_final: 0.7226 (t80) REVERT: A 1337 LYS cc_start: 0.8583 (ptpt) cc_final: 0.8170 (mttt) REVERT: B 59 MET cc_start: 0.7687 (tmm) cc_final: 0.7321 (tmm) REVERT: B 64 LYS cc_start: 0.5949 (ttmt) cc_final: 0.5240 (tttp) REVERT: B 262 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8604 (mpp) REVERT: B 281 MET cc_start: 0.8852 (tpp) cc_final: 0.8613 (tpp) REVERT: B 290 LYS cc_start: 0.8357 (mmtm) cc_final: 0.7919 (mmtm) REVERT: B 409 ASP cc_start: 0.7717 (p0) cc_final: 0.7456 (p0) REVERT: B 412 THR cc_start: 0.8066 (m) cc_final: 0.7769 (p) REVERT: B 488 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7539 (tp30) REVERT: B 526 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7432 (pp) REVERT: B 529 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 660 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7742 (mm-30) REVERT: B 719 MET cc_start: 0.7916 (mmm) cc_final: 0.7542 (mmm) REVERT: B 789 LYS cc_start: 0.7746 (ptmt) cc_final: 0.7433 (ptmt) REVERT: B 801 LYS cc_start: 0.8393 (tppt) cc_final: 0.7907 (mmmm) REVERT: B 899 SER cc_start: 0.9000 (p) cc_final: 0.8795 (p) REVERT: B 999 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: D 69 PHE cc_start: 0.9401 (t80) cc_final: 0.9127 (t80) REVERT: D 88 ASN cc_start: 0.8214 (m-40) cc_final: 0.7545 (m-40) REVERT: E 19 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8128 (tp40) REVERT: E 53 PRO cc_start: 0.8403 (Cg_endo) cc_final: 0.7898 (Cg_exo) REVERT: E 73 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: E 105 VAL cc_start: 0.9056 (t) cc_final: 0.8759 (p) REVERT: E 110 MET cc_start: 0.7650 (mmm) cc_final: 0.7363 (mmm) REVERT: F 84 GLU cc_start: 0.7834 (mp0) cc_final: 0.7514 (mp0) REVERT: G 121 ASP cc_start: 0.5371 (m-30) cc_final: 0.4628 (m-30) REVERT: G 148 ILE cc_start: 0.9128 (mt) cc_final: 0.8794 (mm) REVERT: H 42 ASP cc_start: 0.8373 (m-30) cc_final: 0.7814 (m-30) REVERT: J 13 ILE cc_start: 0.9120 (mm) cc_final: 0.8919 (mm) REVERT: K 77 GLU cc_start: 0.7592 (pt0) cc_final: 0.7320 (pt0) REVERT: K 78 SER cc_start: 0.8637 (m) cc_final: 0.8318 (p) REVERT: L 18 ILE cc_start: 0.9162 (mt) cc_final: 0.8820 (mm) REVERT: L 44 MET cc_start: 0.8829 (mmm) cc_final: 0.8146 (mmm) REVERT: M 11 GLN cc_start: 0.7509 (tp40) cc_final: 0.7271 (tp40) REVERT: M 37 MET cc_start: 0.8040 (ptp) cc_final: 0.7746 (pmm) REVERT: M 44 HIS cc_start: 0.7679 (m90) cc_final: 0.7430 (m170) REVERT: M 121 GLN cc_start: 0.8557 (pm20) cc_final: 0.7643 (mm110) REVERT: M 214 ARG cc_start: 0.8503 (pmt-80) cc_final: 0.7578 (mtt180) REVERT: M 286 MET cc_start: 0.6697 (mmm) cc_final: 0.6170 (mmm) REVERT: M 298 MET cc_start: 0.7683 (mmm) cc_final: 0.7238 (mmm) REVERT: N 325 GLN cc_start: 0.7752 (tp-100) cc_final: 0.6025 (tp40) REVERT: N 344 VAL cc_start: 0.7645 (p) cc_final: 0.7395 (m) REVERT: N 350 MET cc_start: 0.8802 (ttm) cc_final: 0.8548 (mtm) REVERT: O 5 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7364 (pt0) REVERT: O 321 GLU cc_start: 0.8070 (mp0) cc_final: 0.7791 (mp0) REVERT: O 351 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: O 385 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7578 (ppp) REVERT: P 214 HIS cc_start: 0.9161 (t-90) cc_final: 0.8859 (t70) REVERT: P 217 TRP cc_start: 0.8883 (t60) cc_final: 0.8420 (t60) REVERT: P 311 THR cc_start: 0.9117 (m) cc_final: 0.8911 (p) REVERT: Q 33 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8119 (tptp) REVERT: Q 43 TYR cc_start: 0.7589 (m-10) cc_final: 0.7374 (m-10) REVERT: Q 65 ARG cc_start: 0.7582 (tpp80) cc_final: 0.6999 (ttm170) REVERT: Q 70 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7366 (mtm110) REVERT: Q 105 ARG cc_start: 0.8129 (ptp90) cc_final: 0.7485 (ptp90) outliers start: 151 outliers final: 113 residues processed: 876 average time/residue: 0.2614 time to fit residues: 380.6977 Evaluate side-chains 833 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 712 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1315 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 820 LYS Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 76 HIS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 98 HIS Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 285 THR Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 351 GLU Chi-restraints excluded: chain O residue 385 MET Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 250 MET Chi-restraints excluded: chain P residue 283 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 140 optimal weight: 2.9990 chunk 504 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 526 optimal weight: 8.9990 chunk 276 optimal weight: 1.9990 chunk 405 optimal weight: 30.0000 chunk 223 optimal weight: 1.9990 chunk 427 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 473 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 235 ASN N 381 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 465 GLN P 182 GLN ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.189322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132283 restraints weight = 61741.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125554 restraints weight = 41848.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127475 restraints weight = 46840.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127419 restraints weight = 33239.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129494 restraints weight = 27293.956| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 45566 Z= 0.220 Angle : 0.704 23.103 61999 Z= 0.349 Chirality : 0.045 0.325 6974 Planarity : 0.005 0.063 7602 Dihedral : 15.479 179.902 7008 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.60 % Allowed : 18.10 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.09 (0.11), residues: 5269 helix: 1.25 (0.12), residues: 2058 sheet: -0.67 (0.19), residues: 679 loop : -0.97 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 70 TYR 0.045 0.002 TYR B1058 PHE 0.050 0.002 PHE E 75 TRP 0.022 0.001 TRP Q 103 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00529 (45539) covalent geometry : angle 0.68440 (61957) hydrogen bonds : bond 0.03795 ( 1957) hydrogen bonds : angle 4.52239 ( 5538) metal coordination : bond 0.01158 ( 27) metal coordination : angle 6.38796 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 722 time to evaluate : 1.725 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: A 17 HIS cc_start: 0.7992 (OUTLIER) cc_final: 0.7483 (p-80) REVERT: A 131 ARG cc_start: 0.8008 (ptp90) cc_final: 0.7316 (ptp90) REVERT: A 243 GLU cc_start: 0.8161 (mp0) cc_final: 0.7645 (pm20) REVERT: A 332 MET cc_start: 0.7680 (mmm) cc_final: 0.7402 (tpt) REVERT: A 428 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8074 (ppp) REVERT: A 511 GLN cc_start: 0.8550 (mm-40) cc_final: 0.7893 (mm110) REVERT: A 589 LEU cc_start: 0.8730 (pp) cc_final: 0.8480 (pp) REVERT: A 647 SER cc_start: 0.8637 (t) cc_final: 0.8424 (t) REVERT: A 831 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8145 (tptm) REVERT: A 915 LYS cc_start: 0.8264 (ptpt) cc_final: 0.8045 (ptpt) REVERT: A 947 LEU cc_start: 0.9200 (tt) cc_final: 0.8960 (mm) REVERT: A 1061 MET cc_start: 0.7706 (tpp) cc_final: 0.6721 (tpt) REVERT: A 1091 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8561 (mmmm) REVERT: A 1105 ILE cc_start: 0.8718 (pt) cc_final: 0.8497 (pt) REVERT: A 1112 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7751 (mp0) REVERT: A 1122 LEU cc_start: 0.7574 (mm) cc_final: 0.7346 (mt) REVERT: A 1138 ARG cc_start: 0.8420 (mtm110) cc_final: 0.7978 (mtm110) REVERT: A 1215 ASP cc_start: 0.8004 (t0) cc_final: 0.7566 (t0) REVERT: A 1273 TYR cc_start: 0.8422 (t80) cc_final: 0.7132 (t80) REVERT: A 1337 LYS cc_start: 0.8512 (ptpt) cc_final: 0.7982 (mttm) REVERT: B 59 MET cc_start: 0.7777 (tmm) cc_final: 0.7324 (tmm) REVERT: B 64 LYS cc_start: 0.5985 (ttmt) cc_final: 0.5174 (tttp) REVERT: B 262 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8642 (mpp) REVERT: B 281 MET cc_start: 0.8918 (tpp) cc_final: 0.8651 (tpp) REVERT: B 409 ASP cc_start: 0.7746 (p0) cc_final: 0.7530 (p0) REVERT: B 412 THR cc_start: 0.8268 (m) cc_final: 0.7935 (p) REVERT: B 488 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7770 (tp30) REVERT: B 525 LEU cc_start: 0.8527 (tp) cc_final: 0.8263 (tt) REVERT: B 526 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7592 (pp) REVERT: B 529 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7491 (tm-30) REVERT: B 562 MET cc_start: 0.9016 (mmm) cc_final: 0.8627 (tpt) REVERT: B 664 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8733 (tp) REVERT: B 719 MET cc_start: 0.8101 (mmm) cc_final: 0.7633 (mmm) REVERT: B 763 ASP cc_start: 0.8245 (m-30) cc_final: 0.7682 (t0) REVERT: B 789 LYS cc_start: 0.7760 (ptmt) cc_final: 0.7417 (ptmt) REVERT: B 801 LYS cc_start: 0.8387 (tppt) cc_final: 0.7905 (mmmm) REVERT: B 899 SER cc_start: 0.9029 (p) cc_final: 0.8826 (p) REVERT: B 999 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7286 (mm-30) REVERT: D 69 PHE cc_start: 0.9312 (t80) cc_final: 0.9062 (t80) REVERT: E 18 MET cc_start: 0.8857 (mmt) cc_final: 0.8638 (mmp) REVERT: E 19 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8278 (tp40) REVERT: E 105 VAL cc_start: 0.9086 (t) cc_final: 0.8801 (p) REVERT: G 121 ASP cc_start: 0.5350 (m-30) cc_final: 0.4641 (m-30) REVERT: G 148 ILE cc_start: 0.9035 (mt) cc_final: 0.8786 (mm) REVERT: H 42 ASP cc_start: 0.8435 (m-30) cc_final: 0.7920 (m-30) REVERT: K 77 GLU cc_start: 0.7490 (pt0) cc_final: 0.7159 (pt0) REVERT: K 78 SER cc_start: 0.8666 (m) cc_final: 0.8332 (p) REVERT: L 18 ILE cc_start: 0.9153 (mt) cc_final: 0.8825 (mm) REVERT: L 29 LYS cc_start: 0.8232 (pttt) cc_final: 0.7945 (mmtt) REVERT: L 35 ARG cc_start: 0.7835 (ttm-80) cc_final: 0.7612 (ttm-80) REVERT: L 44 MET cc_start: 0.8845 (mmm) cc_final: 0.8188 (mmm) REVERT: M 37 MET cc_start: 0.8493 (ptp) cc_final: 0.8041 (pmm) REVERT: M 38 THR cc_start: 0.7724 (m) cc_final: 0.7363 (p) REVERT: M 41 ASP cc_start: 0.8768 (p0) cc_final: 0.8463 (p0) REVERT: M 44 HIS cc_start: 0.7764 (m90) cc_final: 0.7401 (m170) REVERT: M 121 GLN cc_start: 0.8560 (pm20) cc_final: 0.7651 (mm110) REVERT: M 130 HIS cc_start: 0.6691 (t-170) cc_final: 0.6431 (t-170) REVERT: M 188 ARG cc_start: 0.9350 (ptt-90) cc_final: 0.9124 (ptt-90) REVERT: M 205 TRP cc_start: 0.7148 (m-90) cc_final: 0.6670 (m-90) REVERT: M 214 ARG cc_start: 0.8442 (pmt-80) cc_final: 0.7553 (mtt180) REVERT: M 286 MET cc_start: 0.6815 (mmm) cc_final: 0.6264 (mmm) REVERT: M 298 MET cc_start: 0.7664 (mmm) cc_final: 0.7278 (mmm) REVERT: N 344 VAL cc_start: 0.7661 (p) cc_final: 0.7391 (m) REVERT: N 350 MET cc_start: 0.8899 (ttm) cc_final: 0.8629 (mtm) REVERT: O 321 GLU cc_start: 0.8055 (mp0) cc_final: 0.7778 (mp0) REVERT: P 151 MET cc_start: 0.7767 (mtt) cc_final: 0.7099 (mmp) REVERT: P 214 HIS cc_start: 0.9188 (t-90) cc_final: 0.8887 (t70) REVERT: P 217 TRP cc_start: 0.8988 (t60) cc_final: 0.8515 (t60) REVERT: P 311 THR cc_start: 0.9141 (m) cc_final: 0.8938 (p) REVERT: Q 33 LYS cc_start: 0.8597 (ttmt) cc_final: 0.8169 (tmtt) REVERT: Q 65 ARG cc_start: 0.7601 (tpp80) cc_final: 0.7077 (ttm170) REVERT: Q 70 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7483 (mtm110) REVERT: Q 71 MET cc_start: 0.8540 (tpp) cc_final: 0.8266 (tpp) REVERT: Q 73 TYR cc_start: 0.8212 (m-80) cc_final: 0.7784 (m-80) REVERT: Q 105 ARG cc_start: 0.7956 (ptp90) cc_final: 0.7088 (ptp90) outliers start: 169 outliers final: 129 residues processed: 830 average time/residue: 0.2662 time to fit residues: 367.3146 Evaluate side-chains 833 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 697 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 336 LYS Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 702 ASP Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1187 TYR Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 820 LYS Chi-restraints excluded: chain B residue 870 MET Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 98 HIS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 144 LYS Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 381 HIS Chi-restraints excluded: chain N residue 396 LYS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 385 MET Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 250 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 153 optimal weight: 0.8980 chunk 207 optimal weight: 0.3980 chunk 122 optimal weight: 5.9990 chunk 330 optimal weight: 1.9990 chunk 266 optimal weight: 0.1980 chunk 142 optimal weight: 0.5980 chunk 460 optimal weight: 6.9990 chunk 501 optimal weight: 5.9990 chunk 400 optimal weight: 30.0000 chunk 499 optimal weight: 0.3980 chunk 410 optimal weight: 7.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 381 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 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 = 0.4282 r_free = 0.4282 target = 0.192700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135602 restraints weight = 61321.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.129213 restraints weight = 43081.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130836 restraints weight = 50548.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131404 restraints weight = 30439.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134515 restraints weight = 25526.165| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 45566 Z= 0.134 Angle : 0.673 23.146 61999 Z= 0.332 Chirality : 0.044 0.324 6974 Planarity : 0.004 0.061 7602 Dihedral : 15.428 179.255 7008 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.68 % Allowed : 19.14 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.00 (0.12), residues: 5269 helix: 1.32 (0.12), residues: 2056 sheet: -0.54 (0.19), residues: 676 loop : -0.94 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG P 196 TYR 0.032 0.001 TYR B1058 PHE 0.035 0.001 PHE E 75 TRP 0.019 0.001 TRP Q 103 HIS 0.007 0.001 HIS A1054 Details of bonding type rmsd covalent geometry : bond 0.00315 (45539) covalent geometry : angle 0.65596 (61957) hydrogen bonds : bond 0.03421 ( 1957) hydrogen bonds : angle 4.40505 ( 5538) metal coordination : bond 0.00708 ( 27) metal coordination : angle 5.83619 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 733 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7378 (p-80) REVERT: A 34 ILE cc_start: 0.8987 (pp) cc_final: 0.8611 (pt) REVERT: A 194 LEU cc_start: 0.9267 (mt) cc_final: 0.8950 (mt) REVERT: A 226 LEU cc_start: 0.8321 (mp) cc_final: 0.7740 (tp) REVERT: A 243 GLU cc_start: 0.8177 (mp0) cc_final: 0.7681 (pm20) REVERT: A 332 MET cc_start: 0.7540 (mmm) cc_final: 0.7253 (tpt) REVERT: A 428 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.7494 (ppp) REVERT: A 831 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8086 (tptm) REVERT: A 915 LYS cc_start: 0.8132 (ptpt) cc_final: 0.7907 (ptpt) REVERT: A 947 LEU cc_start: 0.9204 (tt) cc_final: 0.8959 (mm) REVERT: A 1091 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8526 (mmmm) REVERT: A 1105 ILE cc_start: 0.8672 (pt) cc_final: 0.8467 (pt) REVERT: A 1106 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7309 (tm-30) REVERT: A 1138 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7961 (mtm110) REVERT: A 1215 ASP cc_start: 0.7824 (t0) cc_final: 0.7435 (t0) REVERT: A 1273 TYR cc_start: 0.8388 (t80) cc_final: 0.7082 (t80) REVERT: A 1337 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8186 (mttt) REVERT: B 59 MET cc_start: 0.7672 (tmm) cc_final: 0.7265 (tmm) REVERT: B 64 LYS cc_start: 0.6089 (ttmt) cc_final: 0.5416 (tttp) REVERT: B 86 ASP cc_start: 0.7801 (m-30) cc_final: 0.7573 (m-30) REVERT: B 262 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8621 (mpp) REVERT: B 281 MET cc_start: 0.8798 (tpp) cc_final: 0.8541 (tpp) REVERT: B 488 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7583 (tp30) REVERT: B 526 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7470 (pp) REVERT: B 529 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7460 (tm-30) REVERT: B 562 MET cc_start: 0.8965 (mmm) cc_final: 0.8567 (tpt) REVERT: B 719 MET cc_start: 0.7905 (mmm) cc_final: 0.7458 (mmm) REVERT: B 789 LYS cc_start: 0.7714 (ptmt) cc_final: 0.7439 (ptmt) REVERT: B 801 LYS cc_start: 0.8366 (tppt) cc_final: 0.7885 (mmmm) REVERT: B 999 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7357 (mm-30) REVERT: B 1025 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7623 (mtm-85) REVERT: D 69 PHE cc_start: 0.9236 (t80) cc_final: 0.8972 (t80) REVERT: E 18 MET cc_start: 0.8833 (mmt) cc_final: 0.8591 (mmp) REVERT: E 19 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8217 (tp40) REVERT: E 53 PRO cc_start: 0.8330 (Cg_endo) cc_final: 0.7832 (Cg_exo) REVERT: E 94 MET cc_start: 0.8106 (mmt) cc_final: 0.7388 (mmt) REVERT: E 105 VAL cc_start: 0.9084 (t) cc_final: 0.8852 (p) REVERT: E 108 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7644 (tt0) REVERT: G 121 ASP cc_start: 0.5166 (m-30) cc_final: 0.4481 (m-30) REVERT: H 42 ASP cc_start: 0.8481 (m-30) cc_final: 0.7926 (m-30) REVERT: J 60 LEU cc_start: 0.8797 (mt) cc_final: 0.8562 (mm) REVERT: K 77 GLU cc_start: 0.7543 (pt0) cc_final: 0.7254 (pt0) REVERT: K 78 SER cc_start: 0.8595 (m) cc_final: 0.8258 (p) REVERT: K 108 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7586 (tt0) REVERT: L 18 ILE cc_start: 0.9065 (mt) cc_final: 0.8757 (mm) REVERT: L 44 MET cc_start: 0.8849 (mmm) cc_final: 0.8131 (mmm) REVERT: M 11 GLN cc_start: 0.7557 (tp40) cc_final: 0.6966 (tp40) REVERT: M 38 THR cc_start: 0.7645 (m) cc_final: 0.7292 (p) REVERT: M 44 HIS cc_start: 0.7604 (m90) cc_final: 0.7365 (m170) REVERT: M 171 LYS cc_start: 0.1334 (OUTLIER) cc_final: 0.1012 (mtmm) REVERT: M 286 MET cc_start: 0.6537 (mmm) cc_final: 0.6048 (mmm) REVERT: M 298 MET cc_start: 0.7551 (mmm) cc_final: 0.6941 (mmm) REVERT: O 321 GLU cc_start: 0.7912 (mp0) cc_final: 0.7638 (mp0) REVERT: P 151 MET cc_start: 0.7295 (mtt) cc_final: 0.6879 (mmp) REVERT: P 188 LEU cc_start: 0.7808 (mt) cc_final: 0.7382 (mt) REVERT: P 214 HIS cc_start: 0.8976 (t-90) cc_final: 0.8683 (t70) REVERT: P 217 TRP cc_start: 0.8884 (t60) cc_final: 0.8424 (t60) REVERT: Q 33 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8219 (tptp) REVERT: Q 65 ARG cc_start: 0.7459 (tpp80) cc_final: 0.7179 (ttm170) REVERT: Q 70 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7325 (mtm110) REVERT: Q 73 TYR cc_start: 0.8106 (m-80) cc_final: 0.7825 (m-80) REVERT: Q 105 ARG cc_start: 0.7756 (ptp90) cc_final: 0.6913 (ptp90) REVERT: Q 111 MET cc_start: 0.7165 (mmm) cc_final: 0.6832 (mmm) outliers start: 126 outliers final: 108 residues processed: 811 average time/residue: 0.2659 time to fit residues: 358.6126 Evaluate side-chains 820 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 705 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 820 LYS Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 98 HIS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain M residue 171 LYS Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 144 LYS Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain N residue 381 HIS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 385 MET Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 250 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 108 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 446 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 330 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 412 optimal weight: 50.0000 chunk 256 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 83 optimal weight: 0.1980 chunk 397 optimal weight: 0.0770 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 HIS ** M 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 381 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 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 = 0.4275 r_free = 0.4275 target = 0.192016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132921 restraints weight = 61639.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127642 restraints weight = 44440.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.129337 restraints weight = 43149.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128842 restraints weight = 35697.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131399 restraints weight = 29045.992| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 45566 Z= 0.151 Angle : 0.688 27.875 61999 Z= 0.338 Chirality : 0.044 0.324 6974 Planarity : 0.004 0.062 7602 Dihedral : 15.410 179.045 7008 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.66 % Allowed : 19.59 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.00 (0.12), residues: 5269 helix: 1.32 (0.12), residues: 2056 sheet: -0.57 (0.19), residues: 692 loop : -0.93 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG P 196 TYR 0.037 0.001 TYR B1058 PHE 0.041 0.002 PHE E 75 TRP 0.018 0.001 TRP Q 103 HIS 0.010 0.001 HIS N 381 Details of bonding type rmsd covalent geometry : bond 0.00361 (45539) covalent geometry : angle 0.66547 (61957) hydrogen bonds : bond 0.03510 ( 1957) hydrogen bonds : angle 4.42510 ( 5538) metal coordination : bond 0.00778 ( 27) metal coordination : angle 6.72359 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 718 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7263 (p-80) REVERT: A 34 ILE cc_start: 0.8994 (pp) cc_final: 0.8590 (pt) REVERT: A 131 ARG cc_start: 0.7992 (ptp90) cc_final: 0.7250 (ptp90) REVERT: A 243 GLU cc_start: 0.8168 (mp0) cc_final: 0.7681 (pm20) REVERT: A 332 MET cc_start: 0.7524 (mmm) cc_final: 0.7257 (tpt) REVERT: A 428 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8201 (ppp) REVERT: A 511 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7378 (mm110) REVERT: A 780 MET cc_start: 0.8305 (ptp) cc_final: 0.7988 (mtp) REVERT: A 831 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8097 (tptm) REVERT: A 915 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7902 (ptpt) REVERT: A 947 LEU cc_start: 0.9174 (tt) cc_final: 0.8934 (mm) REVERT: A 1061 MET cc_start: 0.7042 (tpt) cc_final: 0.5933 (tpp) REVERT: A 1091 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8536 (mmmm) REVERT: A 1105 ILE cc_start: 0.8670 (pt) cc_final: 0.8455 (pt) REVERT: A 1112 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7648 (mp0) REVERT: A 1138 ARG cc_start: 0.8461 (mtm110) cc_final: 0.7977 (mtm110) REVERT: A 1194 GLU cc_start: 0.7572 (pp20) cc_final: 0.7296 (pp20) REVERT: A 1198 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8054 (ptpp) REVERT: A 1215 ASP cc_start: 0.8115 (t0) cc_final: 0.7634 (t0) REVERT: A 1273 TYR cc_start: 0.8352 (t80) cc_final: 0.7220 (t80) REVERT: A 1337 LYS cc_start: 0.8717 (ptpt) cc_final: 0.8248 (mttt) REVERT: B 59 MET cc_start: 0.7665 (tmm) cc_final: 0.7259 (tmm) REVERT: B 64 LYS cc_start: 0.5897 (ttmt) cc_final: 0.5199 (tttm) REVERT: B 86 ASP cc_start: 0.7765 (m-30) cc_final: 0.7537 (m-30) REVERT: B 243 MET cc_start: 0.8072 (mtp) cc_final: 0.7746 (mtp) REVERT: B 262 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8565 (mpp) REVERT: B 281 MET cc_start: 0.8937 (tpp) cc_final: 0.8664 (tpp) REVERT: B 488 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7681 (tp30) REVERT: B 525 LEU cc_start: 0.8316 (tp) cc_final: 0.8096 (tt) REVERT: B 526 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7541 (pp) REVERT: B 529 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 562 MET cc_start: 0.8937 (mmm) cc_final: 0.8640 (tpt) REVERT: B 719 MET cc_start: 0.8020 (mmm) cc_final: 0.7588 (mmm) REVERT: B 801 LYS cc_start: 0.8398 (tppt) cc_final: 0.7922 (mmmm) REVERT: B 999 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: B 1025 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7593 (mtm-85) REVERT: D 69 PHE cc_start: 0.9222 (t80) cc_final: 0.8824 (t80) REVERT: D 86 LEU cc_start: 0.9170 (mm) cc_final: 0.8759 (pp) REVERT: E 18 MET cc_start: 0.8955 (mmt) cc_final: 0.8723 (mmp) REVERT: E 19 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8245 (tp40) REVERT: E 53 PRO cc_start: 0.8292 (Cg_endo) cc_final: 0.7824 (Cg_exo) REVERT: E 94 MET cc_start: 0.7923 (mmt) cc_final: 0.7711 (mmt) REVERT: E 105 VAL cc_start: 0.9055 (t) cc_final: 0.8771 (p) REVERT: E 108 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7754 (tt0) REVERT: F 107 ARG cc_start: 0.8317 (ttt90) cc_final: 0.7911 (ttm-80) REVERT: G 121 ASP cc_start: 0.5176 (m-30) cc_final: 0.4477 (m-30) REVERT: G 149 ARG cc_start: 0.7636 (mmm160) cc_final: 0.6809 (mmm160) REVERT: H 42 ASP cc_start: 0.8464 (m-30) cc_final: 0.7917 (m-30) REVERT: J 60 LEU cc_start: 0.8818 (mt) cc_final: 0.8559 (mm) REVERT: K 60 MET cc_start: 0.8907 (tpp) cc_final: 0.8606 (mmm) REVERT: K 77 GLU cc_start: 0.7507 (pt0) cc_final: 0.7275 (pt0) REVERT: K 78 SER cc_start: 0.8598 (m) cc_final: 0.8258 (p) REVERT: K 108 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7498 (tt0) REVERT: L 18 ILE cc_start: 0.9101 (mt) cc_final: 0.8799 (mm) REVERT: L 44 MET cc_start: 0.8845 (mmm) cc_final: 0.8140 (mmm) REVERT: M 11 GLN cc_start: 0.7432 (tp40) cc_final: 0.7217 (tp40) REVERT: M 38 THR cc_start: 0.7568 (m) cc_final: 0.7244 (p) REVERT: M 41 ASP cc_start: 0.8780 (p0) cc_final: 0.8467 (p0) REVERT: M 121 GLN cc_start: 0.8454 (pm20) cc_final: 0.7511 (mm110) REVERT: M 205 TRP cc_start: 0.7092 (m-90) cc_final: 0.6788 (m-90) REVERT: M 214 ARG cc_start: 0.8425 (pmt-80) cc_final: 0.7564 (mtt180) REVERT: M 286 MET cc_start: 0.6917 (mmm) cc_final: 0.6381 (mmm) REVERT: M 298 MET cc_start: 0.7635 (mmm) cc_final: 0.7050 (mmm) REVERT: O 321 GLU cc_start: 0.8011 (mp0) cc_final: 0.7711 (mp0) REVERT: O 394 MET cc_start: 0.7990 (ttp) cc_final: 0.7740 (ttm) REVERT: P 151 MET cc_start: 0.7778 (mtt) cc_final: 0.7176 (mmp) REVERT: P 187 PHE cc_start: 0.9128 (t80) cc_final: 0.8331 (t80) REVERT: P 214 HIS cc_start: 0.9229 (t-90) cc_final: 0.8897 (t70) REVERT: P 217 TRP cc_start: 0.9031 (t60) cc_final: 0.8551 (t60) REVERT: Q 33 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8159 (tptp) REVERT: Q 71 MET cc_start: 0.8450 (tpp) cc_final: 0.8142 (tpp) REVERT: Q 73 TYR cc_start: 0.8144 (m-80) cc_final: 0.7655 (m-80) REVERT: Q 105 ARG cc_start: 0.7745 (ptp90) cc_final: 0.6877 (ptp90) outliers start: 125 outliers final: 105 residues processed: 800 average time/residue: 0.2669 time to fit residues: 353.8465 Evaluate side-chains 812 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 701 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 793 SER Chi-restraints excluded: chain A residue 831 LYS Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1096 ASP Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1175 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 27 TRP Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 999 GLU Chi-restraints excluded: chain B residue 1036 THR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 212 MET Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 57 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 184 TYR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 2 LEU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 230 SER Chi-restraints excluded: chain N residue 144 LYS Chi-restraints excluded: chain N residue 151 THR Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 381 HIS Chi-restraints excluded: chain N residue 396 LYS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 55 CYS Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 140 ASP Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 193 LEU Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 385 MET Chi-restraints excluded: chain O residue 461 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 502 LEU Chi-restraints excluded: chain O residue 520 ILE Chi-restraints excluded: chain O residue 529 CYS Chi-restraints excluded: chain P residue 250 MET Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 108 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 161 optimal weight: 4.9990 chunk 209 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 437 optimal weight: 7.9990 chunk 361 optimal weight: 0.7980 chunk 330 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 465 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 381 HIS ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.191589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.132645 restraints weight = 61777.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127470 restraints weight = 44085.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.129144 restraints weight = 44938.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129109 restraints weight = 33414.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130501 restraints weight = 29237.617| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 45566 Z= 0.168 Angle : 0.698 27.407 61999 Z= 0.344 Chirality : 0.045 0.342 6974 Planarity : 0.004 0.060 7602 Dihedral : 15.406 178.898 7008 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.66 % Allowed : 19.82 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.01 (0.12), residues: 5269 helix: 1.30 (0.12), residues: 2060 sheet: -0.60 (0.19), residues: 707 loop : -0.91 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG P 196 TYR 0.039 0.001 TYR B1058 PHE 0.042 0.002 PHE E 75 TRP 0.018 0.001 TRP Q 103 HIS 0.015 0.001 HIS M 44 Details of bonding type rmsd covalent geometry : bond 0.00405 (45539) covalent geometry : angle 0.67654 (61957) hydrogen bonds : bond 0.03564 ( 1957) hydrogen bonds : angle 4.45894 ( 5538) metal coordination : bond 0.00844 ( 27) metal coordination : angle 6.67881 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9265.04 seconds wall clock time: 160 minutes 51.76 seconds (9651.76 seconds total)