Starting phenix.real_space_refine on Tue Jul 7 05:41:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lkt_63186/07_2026/9lkt_63186.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lkt_63186/07_2026/9lkt_63186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lkt_63186/07_2026/9lkt_63186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lkt_63186/07_2026/9lkt_63186.map" model { file = "/net/cci-nas-00/data/ceres_data/9lkt_63186/07_2026/9lkt_63186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lkt_63186/07_2026/9lkt_63186.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 117 5.49 5 Mg 1 5.21 5 S 285 5.16 5 C 27837 2.51 5 N 7754 2.21 5 O 8605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44609 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: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1050 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Y" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1041 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Z" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 6} Link IDs: {'rna3p': 8} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' ZN': 1, '3AT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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 56.901 112.225 87.338 1.00103.58 S ATOM 565 SG CYS A 72 57.413 115.700 88.871 1.00106.71 S ATOM 613 SG CYS A 79 60.703 113.829 87.459 1.00104.11 S ATOM 854 SG CYS A 109 69.831 84.464 124.548 1.00114.77 S ATOM 876 SG CYS A 112 67.681 86.569 126.831 1.00118.64 S ATOM 1245 SG CYS A 156 70.653 85.657 128.853 1.00130.18 S ATOM 1271 SG CYS A 159 67.768 82.976 128.198 1.00130.36 S ATOM 19137 SG CYS B1080 59.418 117.687 105.493 1.00102.14 S ATOM 19156 SG CYS B1083 60.821 113.974 105.546 1.00101.99 S ATOM 19222 SG CYS B1092 58.365 115.112 103.113 1.00 97.16 S ATOM 19250 SG CYS B1095 57.185 114.091 107.300 1.00100.21 S ATOM 28160 SG CYS I 5 119.705 47.135 103.784 1.00130.73 S ATOM 28177 SG CYS I 8 116.148 48.219 102.355 1.00130.05 S ATOM 28307 SG CYS I 25 115.532 49.784 105.931 1.00130.27 S ATOM 28328 SG CYS I 28 116.524 46.339 105.451 1.00128.16 S ATOM 28600 SG CYS J 7 113.104 127.613 45.652 1.00 75.41 S ATOM 28624 SG CYS J 10 114.337 131.119 44.752 1.00 75.83 S ATOM 28888 SG CYS J 44 116.851 128.892 45.879 1.00 81.33 S ATOM 28894 SG CYS J 45 115.969 128.419 42.352 1.00 82.39 S ATOM 29937 SG CYS L 19 80.880 101.112 36.041 1.00103.46 S ATOM 29956 SG CYS L 22 81.933 99.452 31.995 1.00109.30 S ATOM 30073 SG CYS L 36 77.900 101.058 33.682 1.00117.09 S ATOM 30099 SG CYS L 39 79.754 97.795 34.097 1.00117.30 S ATOM 41045 SG CYS P 290 46.425 91.650 109.377 1.00103.33 S ATOM 41169 SG CYS P 307 41.924 96.330 110.463 1.00108.29 S Time building chain proxies: 9.90, per 1000 atoms: 0.22 Number of scatterers: 44609 At special positions: 0 Unit cell: (169.232, 183.89, 177.228, 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 117 15.00 Mg 1 11.99 O 8605 8.00 N 7754 7.00 C 27837 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " Number of angles added : 6 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 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " 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 B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " 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 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " 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: 198 helices and 56 sheets defined 42.6% alpha, 16.8% beta 35 base pairs and 77 stacking pairs defined. Time for finding SS restraints: 5.78 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: 3.745A 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: 4.469A pdb=" N GLY A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 229 through 230 No H-bonds generated for 'chain 'A' and resid 229 through 230' Processing helix chain 'A' and resid 231 through 239 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: 3.771A 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 384 through 390 removed outlier: 3.511A pdb=" N ILE A 389 " --> pdb=" O HIS A 385 " (cutoff:3.500A) 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 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.793A 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 554 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: 3.671A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.802A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.607A 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: 3.881A 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 784 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 827 through 832 Processing helix chain 'A' and resid 843 through 880 removed outlier: 3.661A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 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: 3.536A 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 1188 through 1196 Processing helix chain 'A' and resid 1231 through 1238 removed outlier: 3.630A pdb=" N VAL A1235 " --> pdb=" O ASN A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1259 Processing helix chain 'A' and resid 1259 through 1278 removed outlier: 3.987A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.987A 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 Processing helix chain 'A' and resid 1355 through 1359 removed outlier: 3.664A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A1359 " --> pdb=" O GLY A1356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1355 through 1359' Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.279A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 35 removed outlier: 3.783A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.584A 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: 3.752A pdb=" N ALA B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 291 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: 3.620A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 3.552A pdb=" N LYS B 404 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 421 removed outlier: 4.275A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 removed outlier: 3.815A pdb=" N THR B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 508 through 518 Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.582A pdb=" N GLU B 530 " --> pdb=" O CYS B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 566 removed outlier: 3.747A 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 641 removed outlier: 3.846A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.629A pdb=" N THR B 663 " --> pdb=" O GLU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.917A pdb=" N LEU B 671 " --> pdb=" O VAL B 667 " (cutoff:3.500A) 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: 4.499A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.814A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 980 removed outlier: 3.670A 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 1069 through 1073 removed outlier: 3.630A pdb=" N ASP B1073 " --> pdb=" O MET B1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1069 through 1073' 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 112 Processing helix chain 'C' and resid 118 through 122 Processing helix 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: 3.775A 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: 3.858A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.620A 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 75 removed outlier: 4.063A pdb=" N SER D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) 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 122 removed outlier: 4.184A pdb=" N ALA D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.584A pdb=" N TYR E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) 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: 3.831A 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: 3.589A pdb=" N GLY K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.990A 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 192 Processing helix chain 'M' and resid 192 through 203 removed outlier: 3.952A pdb=" N GLU M 203 " --> pdb=" O LYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 222 removed outlier: 3.915A 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 290 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: 3.707A pdb=" N LEU M 332 " --> pdb=" O LYS M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 363 removed outlier: 3.559A 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: 4.114A 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: 4.132A 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: 3.998A 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 19 through 32 removed outlier: 4.053A pdb=" N ILE O 24 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 44 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.842A 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: 3.837A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 154 removed outlier: 4.182A 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: 4.468A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.292A 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 removed outlier: 3.513A pdb=" N ASP O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) 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: 4.215A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 3.628A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 491 through 530 removed outlier: 4.126A pdb=" N GLU O 495 " --> pdb=" O ILE O 491 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 4.012A 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 61 Processing helix chain 'P' and resid 88 through 103 removed outlier: 3.708A pdb=" N GLU P 92 " --> pdb=" O SER P 88 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 117 Processing helix chain 'P' and resid 119 through 133 Processing helix chain 'P' and resid 173 through 199 removed outlier: 3.604A 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 308 through 316 Processing helix chain 'Q' and resid 51 through 69 removed outlier: 3.930A 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: 3.740A 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: 7.382A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.571A 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: 6.627A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.766A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.447A 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: 3.751A pdb=" N SER A 268 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 4.424A 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: 3.707A 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: 3.623A pdb=" N ARG A 487 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE A 486 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 368 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N PHE A 488 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.990A 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: 4.243A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 617 through 620 removed outlier: 6.657A pdb=" N GLN A 641 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LEU A 645 " --> pdb=" O GLN A 641 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 883 through 884 removed outlier: 6.926A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1210 through 1215 removed outlier: 7.204A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A1088 " --> pdb=" O ARG A1245 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG A1245 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 3.946A pdb=" N GLN A1202 " --> pdb=" O THR A1108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1114 through 1122 removed outlier: 3.680A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1361 through 1364 Processing sheet with id=AB5, first strand: chain 'B' and resid 64 through 65 removed outlier: 7.382A pdb=" N LEU B 75 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR B 120 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR B 77 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLU B 118 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 79 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 111 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY B 134 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE B 113 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 115 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA B 130 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB7, first strand: chain 'B' and resid 360 through 363 removed outlier: 5.976A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 189 through 193 Processing sheet with id=AB9, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AC1, first strand: chain 'B' and resid 501 through 502 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 544 through 550 removed outlier: 6.610A pdb=" N VAL B 539 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL B 548 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE B 537 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL B 583 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.547A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.547A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 986 through 987 removed outlier: 7.273A pdb=" N LEU B 755 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 910 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU B 757 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 927 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 929 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'B' and resid 795 through 796 removed outlier: 3.543A pdb=" N LYS B 801 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 918 through 919 Processing sheet with id=AD1, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.226A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 13 through 15 removed outlier: 7.101A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 13 through 15 removed outlier: 6.743A pdb=" N HIS C 305 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.337A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 215 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 88 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.863A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.646A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 240 through 241 Processing sheet with id=AD8, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AD9, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.723A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA D 6 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU G 4 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N HIS G 67 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALA G 57 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LYS G 69 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU G 55 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE G 51 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL G 75 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE G 49 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N PHE G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N CYS G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 72 through 75 removed outlier: 6.584A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.879A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.550A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 105 through 108 removed outlier: 4.071A pdb=" N ASP G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU G 101 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE G 107 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL G 99 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.900A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AE7, first strand: chain 'K' and resid 26 through 30 Processing sheet with id=AE8, first strand: chain 'M' and resid 10 through 17 removed outlier: 3.538A pdb=" N ALA M 115 " --> pdb=" O LEU N 269 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY N 327 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 25 through 34 removed outlier: 6.913A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG M 33 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 11.669A pdb=" N GLU N 359 " --> pdb=" O PRO M 31 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N VAL N 361 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N GLN M 29 " --> pdb=" O VAL N 361 " (cutoff:3.500A) removed outlier: 10.051A pdb=" N VAL N 363 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N LEU M 27 " --> pdb=" O VAL N 363 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 318 through 321 Processing sheet with id=AF2, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AF3, first strand: chain 'O' and resid 34 through 35 removed outlier: 3.537A pdb=" N GLN O 34 " --> pdb=" O TYR O 75 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR O 75 " --> pdb=" O GLN O 34 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 157 through 159 Processing sheet with id=AF5, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AF6, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AF7, first strand: chain 'O' and resid 409 through 410 Processing sheet with id=AF8, first strand: chain 'P' and resid 63 through 68 Processing sheet with id=AF9, first strand: chain 'P' and resid 136 through 140 Processing sheet with id=AG1, first strand: chain 'P' and resid 211 through 212 Processing sheet with id=AG2, first strand: chain 'V' and resid 15 through 17 removed outlier: 6.577A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1908 hydrogen bonds defined for protein. 5388 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 77 stacking parallelities Total time for adding SS restraints: 13.47 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 18771 1.43 - 1.64: 26437 1.64 - 1.86: 443 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 45663 Sorted by residual: bond pdb=" O3' DG Y 1 " pdb=" P DG Y 2 " ideal model delta sigma weight residual 1.607 1.452 0.155 1.50e-02 4.44e+03 1.07e+02 bond pdb=" O3B 3AT B1202 " pdb=" PG 3AT B1202 " ideal model delta sigma weight residual 1.745 1.609 0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C1' DC Y 17 " pdb=" N1 DC Y 17 " ideal model delta sigma weight residual 1.468 1.552 -0.084 1.40e-02 5.10e+03 3.61e+01 bond pdb=" C1' DA Y -9 " pdb=" N9 DA Y -9 " ideal model delta sigma weight residual 1.468 1.392 0.076 1.40e-02 5.10e+03 2.96e+01 bond pdb=" C1' DG X -17 " pdb=" N9 DG X -17 " ideal model delta sigma weight residual 1.468 1.400 0.068 1.40e-02 5.10e+03 2.35e+01 ... (remaining 45658 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 61681 2.20 - 4.40: 446 4.40 - 6.61: 19 6.61 - 8.81: 2 8.81 - 11.01: 2 Bond angle restraints: 62150 Sorted by residual: angle pdb=" N VAL K 93 " pdb=" CA VAL K 93 " pdb=" C VAL K 93 " ideal model delta sigma weight residual 111.90 107.80 4.10 8.10e-01 1.52e+00 2.56e+01 angle pdb=" N3 DT Y -23 " pdb=" C4 DT Y -23 " pdb=" O4 DT Y -23 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.15e+01 angle pdb=" N3 DT X 22 " pdb=" C4 DT X 22 " pdb=" O4 DT X 22 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" O4 DT Y -23 " pdb=" C4 DT Y -23 " pdb=" C5 DT Y -23 " ideal model delta sigma weight residual 124.90 121.87 3.03 7.00e-01 2.04e+00 1.88e+01 angle pdb=" N3 DT Y -21 " pdb=" C4 DT Y -21 " pdb=" O4 DT Y -21 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 62145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 27294 35.95 - 71.90: 502 71.90 - 107.85: 27 107.85 - 143.80: 2 143.80 - 179.75: 7 Dihedral angle restraints: 27832 sinusoidal: 12353 harmonic: 15479 Sorted by residual: 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 -31.94 136.53 1 2.00e+01 2.50e-03 4.14e+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 -173.26 -117.47 1 2.00e+01 2.50e-03 3.51e+01 dihedral pdb=" O1A 3AT B1202 " pdb=" O3A 3AT B1202 " pdb=" PA 3AT B1202 " pdb=" PB 3AT B1202 " ideal model delta sinusoidal sigma weight residual 157.19 -20.10 177.29 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 27829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 5670 0.043 - 0.087: 888 0.087 - 0.130: 417 0.130 - 0.173: 21 0.173 - 0.217: 1 Chirality restraints: 6997 Sorted by residual: chirality pdb=" C1' 3AT B1202 " pdb=" C2' 3AT B1202 " pdb=" N9 3AT B1202 " pdb=" O4' 3AT B1202 " both_signs ideal model delta sigma weight residual False 2.32 2.53 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE G 148 " pdb=" N ILE G 148 " pdb=" C ILE G 148 " pdb=" CB ILE G 148 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE G 13 " pdb=" N ILE G 13 " pdb=" C ILE G 13 " pdb=" CB ILE G 13 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 6994 not shown) Planarity restraints: 7607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC Y 11 " 0.003 2.00e-02 2.50e+03 1.15e-02 2.98e+00 pdb=" N1 DC Y 11 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DC Y 11 " 0.028 2.00e-02 2.50e+03 pdb=" O2 DC Y 11 " -0.017 2.00e-02 2.50e+03 pdb=" N3 DC Y 11 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DC Y 11 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC Y 11 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC Y 11 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC Y 11 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 467 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 468 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 468 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 468 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA X -15 " -0.017 2.00e-02 2.50e+03 8.75e-03 2.11e+00 pdb=" N9 DA X -15 " -0.001 2.00e-02 2.50e+03 pdb=" C8 DA X -15 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA X -15 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DA X -15 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DA X -15 " -0.000 2.00e-02 2.50e+03 pdb=" N6 DA X -15 " -0.018 2.00e-02 2.50e+03 pdb=" N1 DA X -15 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA X -15 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA X -15 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA X -15 " 0.006 2.00e-02 2.50e+03 ... (remaining 7604 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 49 2.28 - 2.93: 18614 2.93 - 3.59: 65761 3.59 - 4.24: 104121 4.24 - 4.90: 173097 Nonbonded interactions: 361642 Sorted by model distance: nonbonded pdb=" OG1 THR A 303 " pdb=" NE2 GLN O 377 " model vdw 1.623 3.120 nonbonded pdb=" O ILE A 230 " pdb=" N THR O 2 " model vdw 1.987 3.120 nonbonded pdb=" NH2 ARG B 682 " pdb=" O2G 3AT B1202 " model vdw 2.003 2.496 nonbonded pdb=" OE1 GLN E 95 " pdb=" OH TYR E 125 " model vdw 2.031 3.040 nonbonded pdb=" OP1 U Z 2 " pdb=" O3' GTP Z 101 " model vdw 2.069 3.040 ... (remaining 361637 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: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.060 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 58.990 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.640 45691 Z= 0.360 Angle : 0.716 58.590 62189 Z= 0.323 Chirality : 0.039 0.217 6997 Planarity : 0.002 0.038 7607 Dihedral : 12.135 179.750 17828 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.45 % Allowed : 2.41 % Favored : 97.15 % 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 are not related in a simple way. whole: -1.23 (0.11), residues: 5269 helix: 0.48 (0.11), residues: 2087 sheet: -1.22 (0.18), residues: 708 loop : -1.84 (0.11), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1285 TYR 0.008 0.001 TYR A1116 PHE 0.006 0.001 PHE D 69 TRP 0.005 0.001 TRP P 313 HIS 0.002 0.000 HIS B 676 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.20 (45663) covalent geometry : angle 0.47104 / 0.31 (62150) hydrogen bonds : bond 0.10252 / 6.47 ( 1969) hydrogen bonds : angle 4.35478 / 3.07 ( 5556) metal coordination : bond 0.29466 / 15.11 ( 26) metal coordination : angle 21.51182 / 12.95 ( 39) Misc. bond : bond 0.28431 / 14.96 ( 2) *********************** 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 1445 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 1424 time to evaluate : 1.844 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: A 7 ARG cc_start: 0.7979 (ptm-80) cc_final: 0.7768 (ptm160) REVERT: A 51 LEU cc_start: 0.7676 (mt) cc_final: 0.7417 (mt) REVERT: A 75 ASN cc_start: 0.7803 (m-40) cc_final: 0.7365 (p0) REVERT: A 130 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7730 (pttt) REVERT: A 246 LYS cc_start: 0.6787 (mtmt) cc_final: 0.6367 (mppt) REVERT: A 422 GLN cc_start: 0.8028 (tt0) cc_final: 0.7528 (tt0) REVERT: A 439 LYS cc_start: 0.8147 (tmmt) cc_final: 0.7770 (pttp) REVERT: A 620 LYS cc_start: 0.6522 (mtmt) cc_final: 0.6063 (mptt) REVERT: A 650 MET cc_start: 0.8686 (mmm) cc_final: 0.7922 (mmt) REVERT: A 780 MET cc_start: 0.8172 (mtm) cc_final: 0.7399 (mtp) REVERT: A 905 ASP cc_start: 0.6904 (t0) cc_final: 0.6142 (t0) REVERT: A 1078 LYS cc_start: 0.7931 (mttp) cc_final: 0.7549 (mmtm) REVERT: A 1118 GLU cc_start: 0.6952 (pt0) cc_final: 0.5677 (pt0) REVERT: A 1121 PHE cc_start: 0.5979 (m-80) cc_final: 0.5194 (m-80) REVERT: A 1185 MET cc_start: 0.8623 (pmm) cc_final: 0.8365 (pmm) REVERT: A 1270 GLU cc_start: 0.7031 (tp30) cc_final: 0.6710 (mm-30) REVERT: A 1314 SER cc_start: 0.7421 (t) cc_final: 0.6531 (m) REVERT: B 184 LEU cc_start: 0.9312 (mt) cc_final: 0.8911 (mm) REVERT: B 285 LYS cc_start: 0.8368 (ttmm) cc_final: 0.8146 (tptt) REVERT: B 320 HIS cc_start: 0.7497 (p-80) cc_final: 0.6791 (p-80) REVERT: B 380 PHE cc_start: 0.4857 (t80) cc_final: 0.4431 (t80) REVERT: B 413 ASN cc_start: 0.7317 (m-40) cc_final: 0.6736 (m-40) REVERT: B 417 ASN cc_start: 0.8362 (m-40) cc_final: 0.8085 (m-40) REVERT: B 434 GLN cc_start: 0.8279 (mt0) cc_final: 0.8036 (mm-40) REVERT: B 460 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5764 (mm-30) REVERT: B 488 GLU cc_start: 0.7413 (pt0) cc_final: 0.7201 (pt0) REVERT: B 537 PHE cc_start: 0.7510 (m-80) cc_final: 0.7257 (m-80) REVERT: B 623 ASP cc_start: 0.8052 (m-30) cc_final: 0.7442 (m-30) REVERT: B 706 ASP cc_start: 0.8234 (m-30) cc_final: 0.8011 (m-30) REVERT: B 890 ARG cc_start: 0.8367 (ttt180) cc_final: 0.8139 (ttt-90) REVERT: B 895 ASP cc_start: 0.8322 (m-30) cc_final: 0.8043 (m-30) REVERT: B 1025 ARG cc_start: 0.6616 (mtt90) cc_final: 0.6138 (mtt-85) REVERT: B 1062 MET cc_start: 0.8318 (mmm) cc_final: 0.8042 (mmm) REVERT: B 1078 ASP cc_start: 0.8305 (m-30) cc_final: 0.8080 (m-30) REVERT: C 183 ASP cc_start: 0.7046 (m-30) cc_final: 0.6612 (m-30) REVERT: C 240 THR cc_start: 0.8092 (t) cc_final: 0.7888 (p) REVERT: D 76 HIS cc_start: 0.6825 (m170) cc_final: 0.6619 (m170) REVERT: D 85 GLN cc_start: 0.8464 (mt0) cc_final: 0.8226 (mt0) REVERT: D 100 MET cc_start: 0.6228 (mpp) cc_final: 0.5757 (mpt) REVERT: E 9 ARG cc_start: 0.6979 (mtt90) cc_final: 0.6625 (mtp-110) REVERT: E 70 ASP cc_start: 0.5117 (t0) cc_final: 0.4656 (t0) REVERT: E 88 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8046 (mmtt) REVERT: E 107 GLN cc_start: 0.7142 (tt0) cc_final: 0.6857 (tm-30) REVERT: E 140 THR cc_start: 0.7921 (m) cc_final: 0.7655 (m) REVERT: E 141 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7524 (mm-30) REVERT: E 167 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6997 (mp0) REVERT: F 87 THR cc_start: 0.8885 (p) cc_final: 0.8647 (p) REVERT: F 98 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8529 (tttp) REVERT: F 101 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8521 (mtpp) REVERT: F 114 SER cc_start: 0.8734 (t) cc_final: 0.8322 (p) REVERT: G 50 ASP cc_start: 0.5651 (p0) cc_final: 0.5380 (p0) REVERT: G 51 ILE cc_start: 0.7401 (mt) cc_final: 0.6863 (mt) REVERT: G 73 ARG cc_start: 0.7184 (mtm180) cc_final: 0.6873 (mtm180) REVERT: G 81 LEU cc_start: 0.8184 (mt) cc_final: 0.7807 (tt) REVERT: G 89 ILE cc_start: 0.6274 (mm) cc_final: 0.5859 (mm) REVERT: G 95 GLU cc_start: 0.7953 (pp20) cc_final: 0.7566 (pm20) REVERT: H 7 GLU cc_start: 0.8267 (tt0) cc_final: 0.8041 (tt0) REVERT: H 37 MET cc_start: 0.7519 (mmm) cc_final: 0.6963 (mmt) REVERT: H 128 ASP cc_start: 0.7381 (m-30) cc_final: 0.7167 (t70) REVERT: H 130 ASN cc_start: 0.8433 (m-40) cc_final: 0.8095 (m110) REVERT: K 78 SER cc_start: 0.8441 (m) cc_final: 0.8227 (t) REVERT: K 89 THR cc_start: 0.8659 (p) cc_final: 0.8386 (p) REVERT: M 16 TYR cc_start: 0.7481 (m-10) cc_final: 0.6929 (m-80) REVERT: M 19 LYS cc_start: 0.8489 (mmmm) cc_final: 0.7966 (mmmm) REVERT: M 99 LYS cc_start: 0.7527 (mtmt) cc_final: 0.6757 (mttp) REVERT: M 105 SER cc_start: 0.5976 (t) cc_final: 0.5317 (t) REVERT: M 114 TYR cc_start: 0.8319 (m-80) cc_final: 0.8083 (m-80) REVERT: M 119 TYR cc_start: 0.6929 (t80) cc_final: 0.6454 (t80) REVERT: M 193 TYR cc_start: 0.6646 (t80) cc_final: 0.6410 (t80) REVERT: M 238 LEU cc_start: 0.7249 (mt) cc_final: 0.7038 (mp) REVERT: M 244 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8585 (mt-10) REVERT: M 247 MET cc_start: 0.8177 (mmp) cc_final: 0.7852 (mmt) REVERT: M 249 LEU cc_start: 0.7276 (pp) cc_final: 0.6991 (pp) REVERT: M 270 MET cc_start: 0.5267 (tpp) cc_final: 0.2934 (ptt) REVERT: N 337 VAL cc_start: 0.7036 (t) cc_final: 0.6672 (t) REVERT: N 372 GLU cc_start: 0.5971 (mt-10) cc_final: 0.5594 (pt0) REVERT: O 31 THR cc_start: 0.6947 (p) cc_final: 0.6710 (p) REVERT: O 61 ASN cc_start: 0.8591 (t0) cc_final: 0.8268 (m-40) REVERT: O 259 MET cc_start: 0.8183 (mpp) cc_final: 0.7415 (mpp) REVERT: O 329 SER cc_start: 0.7373 (p) cc_final: 0.7131 (t) REVERT: O 355 GLN cc_start: 0.8942 (tt0) cc_final: 0.8577 (tt0) REVERT: O 401 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7809 (mm-30) REVERT: O 425 THR cc_start: 0.7752 (m) cc_final: 0.7542 (p) REVERT: O 474 MET cc_start: 0.3637 (ppp) cc_final: 0.1789 (tmm) REVERT: O 530 THR cc_start: 0.8320 (t) cc_final: 0.8015 (m) REVERT: O 531 MET cc_start: 0.6830 (mtm) cc_final: 0.6480 (mtm) REVERT: P 60 MET cc_start: -0.1486 (ptt) cc_final: -0.1718 (mtm) REVERT: P 189 GLN cc_start: 0.8991 (tt0) cc_final: 0.8710 (tm-30) REVERT: P 227 LYS cc_start: 0.6754 (mmtm) cc_final: 0.6191 (tptt) REVERT: P 271 ARG cc_start: 0.6748 (ptm-80) cc_final: 0.6516 (ttp80) REVERT: P 292 VAL cc_start: 0.8141 (p) cc_final: 0.7649 (t) REVERT: P 298 GLU cc_start: 0.8006 (tt0) cc_final: 0.7796 (tp30) REVERT: Q 54 GLU cc_start: 0.7675 (mp0) cc_final: 0.7317 (mp0) REVERT: Q 60 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8509 (tp) REVERT: Q 63 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7543 (mm-30) REVERT: Q 64 LEU cc_start: 0.8603 (mt) cc_final: 0.8364 (mp) REVERT: Q 76 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8125 (mt-10) outliers start: 21 outliers final: 4 residues processed: 1436 average time/residue: 0.2963 time to fit residues: 682.6345 Evaluate side-chains 853 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 847 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 MET Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain Q residue 60 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 0.0040 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 0.0980 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 154 ASN A 163 ASN A 203 HIS A 343 GLN A 528 ASN A 599 GLN A 739 GLN A 794 GLN ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 GLN B 215 ASN B 260 HIS B 552 HIS B 616 GLN B 692 GLN B1132 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN G 115 GLN H 29 HIS M 11 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 378 HIS O 34 GLN O 68 HIS O 168 ASN O 402 ASN O 457 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.197110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132531 restraints weight = 60198.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136557 restraints weight = 34630.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137405 restraints weight = 21629.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137794 restraints weight = 21584.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137888 restraints weight = 19815.223| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 45691 Z= 0.144 Angle : 0.620 21.941 62189 Z= 0.301 Chirality : 0.044 0.284 6997 Planarity : 0.004 0.055 7607 Dihedral : 15.972 179.745 7118 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.45 % Allowed : 9.94 % Favored : 87.61 % 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 are not related in a simple way. whole: -0.37 (0.11), residues: 5269 helix: 1.22 (0.11), residues: 2071 sheet: -0.75 (0.19), residues: 683 loop : -1.37 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 206 TYR 0.029 0.001 TYR E 90 PHE 0.025 0.002 PHE E 75 TRP 0.018 0.001 TRP M 205 HIS 0.013 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (45663) covalent geometry : angle 0.58660 / 0.30 (62150) hydrogen bonds : bond 0.03485 / 2.26 ( 1969) hydrogen bonds : angle 4.03025 / 2.84 ( 5556) metal coordination : bond 0.01502 / 0.82 ( 26) metal coordination : angle 7.98118 / 4.26 ( 39) Misc. bond : bond 0.00131 / 0.07 ( 2) *********************** 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 1017 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 902 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.7293 (m90) cc_final: 0.6892 (p-80) REVERT: A 51 LEU cc_start: 0.8124 (mt) cc_final: 0.7909 (mt) REVERT: A 246 LYS cc_start: 0.7333 (mtmt) cc_final: 0.6955 (mtmm) REVERT: A 468 LEU cc_start: 0.8471 (mt) cc_final: 0.8202 (mt) REVERT: A 620 LYS cc_start: 0.6563 (mtmt) cc_final: 0.6299 (mptt) REVERT: A 650 MET cc_start: 0.8867 (mmm) cc_final: 0.8235 (mmt) REVERT: A 680 MET cc_start: 0.8635 (mtp) cc_final: 0.8280 (mtp) REVERT: A 770 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7028 (mt-10) REVERT: A 780 MET cc_start: 0.9247 (mtm) cc_final: 0.8672 (mtp) REVERT: A 795 MET cc_start: 0.9027 (ptm) cc_final: 0.8708 (ptp) REVERT: A 867 GLU cc_start: 0.7682 (tp30) cc_final: 0.7459 (tp30) REVERT: A 941 SER cc_start: 0.8607 (p) cc_final: 0.8115 (t) REVERT: A 1118 GLU cc_start: 0.6823 (pt0) cc_final: 0.6326 (pt0) REVERT: A 1139 LEU cc_start: 0.8828 (tp) cc_final: 0.8626 (tt) REVERT: A 1142 LEU cc_start: 0.8257 (mp) cc_final: 0.8008 (mp) REVERT: A 1185 MET cc_start: 0.8592 (pmm) cc_final: 0.8342 (pmm) REVERT: A 1222 LYS cc_start: 0.7215 (pttt) cc_final: 0.6458 (pttp) REVERT: A 1270 GLU cc_start: 0.7274 (tp30) cc_final: 0.7057 (mm-30) REVERT: A 1311 MET cc_start: 0.8354 (ptp) cc_final: 0.8033 (ptp) REVERT: B 28 ARG cc_start: 0.7991 (mmt90) cc_final: 0.7530 (mmt180) REVERT: B 205 SER cc_start: 0.8348 (t) cc_final: 0.7712 (p) REVERT: B 285 LYS cc_start: 0.8315 (ttmm) cc_final: 0.8106 (tptt) REVERT: B 413 ASN cc_start: 0.7588 (m-40) cc_final: 0.7133 (m-40) REVERT: B 417 ASN cc_start: 0.8748 (m-40) cc_final: 0.8385 (m-40) REVERT: B 529 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 537 PHE cc_start: 0.7708 (m-80) cc_final: 0.7276 (m-80) REVERT: B 540 PHE cc_start: 0.8511 (m-80) cc_final: 0.8302 (m-80) REVERT: B 600 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7906 (mttp) REVERT: B 603 LYS cc_start: 0.8580 (pttm) cc_final: 0.8201 (pttt) REVERT: B 623 ASP cc_start: 0.8227 (m-30) cc_final: 0.7731 (m-30) REVERT: B 692 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7792 (pt0) REVERT: B 787 PHE cc_start: 0.7538 (p90) cc_final: 0.7145 (p90) REVERT: B 789 LYS cc_start: 0.5710 (ptpt) cc_final: 0.5492 (pttt) REVERT: B 859 LYS cc_start: 0.8350 (mptt) cc_final: 0.8023 (mtpp) REVERT: B 1015 MET cc_start: 0.8104 (mmm) cc_final: 0.7459 (mtp) REVERT: B 1062 MET cc_start: 0.8511 (mmm) cc_final: 0.8159 (mmm) REVERT: B 1078 ASP cc_start: 0.8076 (m-30) cc_final: 0.7843 (m-30) REVERT: B 1096 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8590 (mptt) REVERT: C 215 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8481 (m) REVERT: D 51 LYS cc_start: 0.6259 (tttp) cc_final: 0.6055 (tttp) REVERT: E 9 ARG cc_start: 0.7476 (mtt90) cc_final: 0.7120 (mtp-110) REVERT: E 47 LYS cc_start: 0.8001 (tmmt) cc_final: 0.7260 (ttpp) REVERT: E 115 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7890 (mtpt) REVERT: E 127 LEU cc_start: 0.7665 (mp) cc_final: 0.7442 (mp) REVERT: G 50 ASP cc_start: 0.6829 (p0) cc_final: 0.6411 (p0) REVERT: G 73 ARG cc_start: 0.8043 (mtm180) cc_final: 0.7639 (mtm180) REVERT: G 81 LEU cc_start: 0.8364 (mt) cc_final: 0.7982 (tt) REVERT: G 89 ILE cc_start: 0.6812 (mm) cc_final: 0.6572 (mm) REVERT: G 150 PHE cc_start: 0.5589 (OUTLIER) cc_final: 0.4076 (m-80) REVERT: H 130 ASN cc_start: 0.8635 (m-40) cc_final: 0.8378 (m110) REVERT: H 138 ASP cc_start: 0.7920 (t0) cc_final: 0.7627 (t0) REVERT: K 89 THR cc_start: 0.8035 (p) cc_final: 0.7757 (p) REVERT: M 92 TYR cc_start: 0.6520 (m-80) cc_final: 0.6315 (m-80) REVERT: M 99 LYS cc_start: 0.7413 (mtmt) cc_final: 0.6868 (mttp) REVERT: M 102 PHE cc_start: 0.6973 (m-10) cc_final: 0.6762 (m-10) REVERT: M 119 TYR cc_start: 0.6550 (t80) cc_final: 0.6225 (t80) REVERT: M 270 MET cc_start: 0.4821 (tpp) cc_final: 0.2625 (ptt) REVERT: M 298 MET cc_start: 0.3987 (mmm) cc_final: 0.3742 (mmm) REVERT: N 332 ARG cc_start: 0.6411 (mtt90) cc_final: 0.5989 (mtt90) REVERT: N 380 LYS cc_start: 0.8046 (mttp) cc_final: 0.7480 (mtmt) REVERT: O 259 MET cc_start: 0.8285 (mpp) cc_final: 0.7549 (mpp) REVERT: O 408 GLU cc_start: 0.7829 (tt0) cc_final: 0.7165 (tt0) REVERT: O 425 THR cc_start: 0.8006 (m) cc_final: 0.7770 (p) REVERT: O 474 MET cc_start: 0.3095 (ppp) cc_final: 0.1674 (tmm) REVERT: O 530 THR cc_start: 0.8293 (t) cc_final: 0.8007 (m) REVERT: P 85 MET cc_start: 0.1515 (mpp) cc_final: 0.1265 (mpp) REVERT: P 189 GLN cc_start: 0.8925 (tt0) cc_final: 0.8616 (tm-30) REVERT: P 227 LYS cc_start: 0.6651 (mmtm) cc_final: 0.6162 (tptt) REVERT: Q 54 GLU cc_start: 0.7843 (mp0) cc_final: 0.7537 (mp0) REVERT: Q 108 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7251 (mtp85) outliers start: 115 outliers final: 53 residues processed: 963 average time/residue: 0.2746 time to fit residues: 433.6569 Evaluate side-chains 783 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 726 time to evaluate : 1.717 ------------------------------------------------------------------------------- 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 155 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1096 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain M residue 24 LYS Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 269 LEU Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 357 LEU Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain Q residue 79 GLU Chi-restraints excluded: chain Q residue 83 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 155 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 431 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 326 optimal weight: 0.7980 chunk 470 optimal weight: 4.9990 chunk 376 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 528 optimal weight: 50.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN A 314 GLN A 423 GLN A 611 ASN A 836 ASN A1202 GLN A1336 GLN A1364 HIS B 215 ASN B 253 GLN B 610 HIS ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS D 88 ASN D 112 GLN I 40 ASN M 134 GLN O 34 GLN O 60 HIS O 158 GLN O 236 GLN O 245 HIS O 355 GLN O 415 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.184275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128747 restraints weight = 58127.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124402 restraints weight = 37785.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125027 restraints weight = 52741.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126334 restraints weight = 32167.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128227 restraints weight = 26515.348| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 45691 Z= 0.195 Angle : 0.640 15.712 62189 Z= 0.321 Chirality : 0.045 0.254 6997 Planarity : 0.005 0.047 7607 Dihedral : 16.007 179.054 7108 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.92 % Allowed : 11.71 % Favored : 85.37 % 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 are not related in a simple way. whole: -0.10 (0.11), residues: 5269 helix: 1.39 (0.11), residues: 2079 sheet: -0.66 (0.19), residues: 706 loop : -1.15 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 222 TYR 0.034 0.002 TYR O 188 PHE 0.023 0.002 PHE A 462 TRP 0.026 0.001 TRP P 217 HIS 0.010 0.001 HIS A 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (45663) covalent geometry : angle 0.62364 / 0.32 (62150) hydrogen bonds : bond 0.03800 / 2.50 ( 1969) hydrogen bonds : angle 4.13429 / 2.92 ( 5556) metal coordination : bond 0.00702 / 0.36 ( 26) metal coordination : angle 5.71807 / 3.18 ( 39) Misc. bond : bond 0.00560 / 0.29 ( 2) *********************** 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 944 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 807 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.7388 (m90) cc_final: 0.6880 (p-80) REVERT: A 51 LEU cc_start: 0.8351 (mt) cc_final: 0.8145 (mt) REVERT: A 78 ASP cc_start: 0.7910 (t0) cc_final: 0.7630 (t0) REVERT: A 144 LYS cc_start: 0.8199 (tppt) cc_final: 0.7977 (ttmm) REVERT: A 504 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7802 (mt-10) REVERT: A 770 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7199 (mt-10) REVERT: A 780 MET cc_start: 0.9309 (mtm) cc_final: 0.8946 (mtp) REVERT: A 867 GLU cc_start: 0.7707 (tp30) cc_final: 0.7506 (tp30) REVERT: A 941 SER cc_start: 0.8558 (p) cc_final: 0.8094 (t) REVERT: A 1139 LEU cc_start: 0.9013 (tp) cc_final: 0.8756 (tt) REVERT: A 1222 LYS cc_start: 0.7087 (pttt) cc_final: 0.6864 (pttp) REVERT: A 1314 SER cc_start: 0.7574 (t) cc_final: 0.7184 (m) REVERT: B 28 ARG cc_start: 0.8035 (mmt90) cc_final: 0.7734 (mmt180) REVERT: B 211 LYS cc_start: 0.7410 (mttt) cc_final: 0.6867 (ptmm) REVERT: B 340 ARG cc_start: 0.7630 (ttt90) cc_final: 0.7284 (ttt90) REVERT: B 529 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7324 (tm-30) REVERT: B 600 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7924 (mttt) REVERT: B 603 LYS cc_start: 0.8681 (pttm) cc_final: 0.8318 (pttt) REVERT: B 623 ASP cc_start: 0.8149 (m-30) cc_final: 0.7766 (m-30) REVERT: B 627 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8239 (mt-10) REVERT: B 787 PHE cc_start: 0.7569 (p90) cc_final: 0.7252 (p90) REVERT: B 789 LYS cc_start: 0.6602 (ptpt) cc_final: 0.5920 (pttt) REVERT: B 899 SER cc_start: 0.9141 (p) cc_final: 0.8847 (p) REVERT: B 1015 MET cc_start: 0.8891 (mmm) cc_final: 0.8142 (mtt) REVERT: B 1062 MET cc_start: 0.8514 (mmm) cc_final: 0.8260 (mmm) REVERT: D 43 ASN cc_start: 0.8761 (m-40) cc_final: 0.8352 (m-40) REVERT: E 9 ARG cc_start: 0.7958 (mtt90) cc_final: 0.7492 (mtp-110) REVERT: E 90 TYR cc_start: 0.8130 (m-80) cc_final: 0.7512 (m-80) REVERT: E 98 ASN cc_start: 0.8706 (t0) cc_final: 0.8286 (t0) REVERT: E 115 LYS cc_start: 0.8273 (mtmt) cc_final: 0.8020 (mtpt) REVERT: F 84 GLU cc_start: 0.7963 (pm20) cc_final: 0.7529 (pm20) REVERT: G 150 PHE cc_start: 0.4999 (OUTLIER) cc_final: 0.4122 (m-80) REVERT: H 28 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8071 (pp) REVERT: H 122 LEU cc_start: 0.8523 (mt) cc_final: 0.8157 (mt) REVERT: H 138 ASP cc_start: 0.8056 (t0) cc_final: 0.7697 (t0) REVERT: I 26 ASN cc_start: 0.8312 (t0) cc_final: 0.7987 (t0) REVERT: I 45 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8040 (tptp) REVERT: K 79 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8657 (ptpt) REVERT: K 89 THR cc_start: 0.8168 (p) cc_final: 0.7899 (p) REVERT: K 108 GLN cc_start: 0.8268 (tp40) cc_final: 0.7129 (tp-100) REVERT: M 14 ASP cc_start: 0.7634 (t0) cc_final: 0.7257 (t0) REVERT: M 16 TYR cc_start: 0.7831 (m-80) cc_final: 0.7366 (m-80) REVERT: M 92 TYR cc_start: 0.6425 (m-80) cc_final: 0.6042 (m-80) REVERT: M 99 LYS cc_start: 0.7396 (mtmt) cc_final: 0.6976 (mttp) REVERT: M 247 MET cc_start: 0.7986 (mmm) cc_final: 0.7740 (mmt) REVERT: M 270 MET cc_start: 0.4555 (tpp) cc_final: 0.2148 (ptt) REVERT: M 298 MET cc_start: 0.4168 (mmm) cc_final: 0.3769 (mmm) REVERT: N 380 LYS cc_start: 0.8019 (mttp) cc_final: 0.7527 (mtmt) REVERT: O 15 GLU cc_start: 0.7903 (tp30) cc_final: 0.7370 (tp30) REVERT: O 180 LEU cc_start: 0.8142 (mt) cc_final: 0.7929 (tp) REVERT: O 259 MET cc_start: 0.8186 (mpp) cc_final: 0.7523 (mpp) REVERT: O 415 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7614 (m-70) REVERT: O 474 MET cc_start: 0.2610 (ppp) cc_final: 0.1920 (tmm) REVERT: O 530 THR cc_start: 0.8469 (t) cc_final: 0.8227 (m) REVERT: P 189 GLN cc_start: 0.8524 (tt0) cc_final: 0.8323 (tm-30) REVERT: P 217 TRP cc_start: 0.6747 (t60) cc_final: 0.6482 (t60) REVERT: P 292 VAL cc_start: 0.8793 (p) cc_final: 0.8158 (t) REVERT: Q 64 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8567 (mp) REVERT: Q 111 MET cc_start: 0.8070 (mpp) cc_final: 0.7836 (mpp) outliers start: 137 outliers final: 81 residues processed: 893 average time/residue: 0.2477 time to fit residues: 365.3880 Evaluate side-chains 802 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 716 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 34 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 731 GLU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1061 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 30 CYS Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 261 THR Chi-restraints excluded: chain N residue 264 GLU Chi-restraints excluded: chain N residue 328 LYS Chi-restraints excluded: chain N residue 345 THR Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 415 HIS Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 79 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 146 optimal weight: 2.9990 chunk 460 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 341 optimal weight: 0.9990 chunk 310 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS A 163 ASN A 314 GLN A 343 GLN A1336 GLN B 129 ASN B 215 ASN B 253 GLN B 417 ASN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN D 61 GLN D 76 HIS I 40 ASN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 ASN O 158 GLN O 236 GLN O 415 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.185502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130575 restraints weight = 58159.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126175 restraints weight = 43364.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127219 restraints weight = 54810.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.128185 restraints weight = 34243.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.130122 restraints weight = 28497.764| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45691 Z= 0.133 Angle : 0.571 11.859 62189 Z= 0.287 Chirality : 0.043 0.266 6997 Planarity : 0.004 0.080 7607 Dihedral : 16.001 179.549 7108 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.21 % Allowed : 13.50 % Favored : 84.29 % 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 are not related in a simple way. whole: 0.12 (0.12), residues: 5269 helix: 1.58 (0.12), residues: 2079 sheet: -0.56 (0.19), residues: 692 loop : -1.03 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 213 TYR 0.031 0.001 TYR O 188 PHE 0.025 0.001 PHE G 80 TRP 0.017 0.001 TRP M 205 HIS 0.007 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (45663) covalent geometry : angle 0.55938 / 0.29 (62150) hydrogen bonds : bond 0.03362 / 2.20 ( 1969) hydrogen bonds : angle 4.05798 / 2.87 ( 5556) metal coordination : bond 0.00633 / 0.33 ( 26) metal coordination : angle 4.57699 / 2.63 ( 39) Misc. bond : bond 0.00345 / 0.18 ( 2) *********************** 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 867 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 763 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.7346 (m90) cc_final: 0.6731 (p-80) REVERT: A 761 ASP cc_start: 0.7600 (m-30) cc_final: 0.7366 (m-30) REVERT: A 770 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 780 MET cc_start: 0.9309 (mtm) cc_final: 0.8929 (mtp) REVERT: A 941 SER cc_start: 0.8624 (p) cc_final: 0.8170 (t) REVERT: A 1139 LEU cc_start: 0.8925 (tp) cc_final: 0.8666 (tt) REVERT: A 1222 LYS cc_start: 0.7116 (pttt) cc_final: 0.6840 (pttp) REVERT: A 1314 SER cc_start: 0.7543 (t) cc_final: 0.7225 (m) REVERT: A 1336 GLN cc_start: 0.7784 (tt0) cc_final: 0.7497 (tt0) REVERT: B 28 ARG cc_start: 0.8004 (mmt90) cc_final: 0.7774 (mmt180) REVERT: B 529 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 530 GLU cc_start: 0.8056 (mp0) cc_final: 0.7702 (mp0) REVERT: B 603 LYS cc_start: 0.8690 (pttm) cc_final: 0.8299 (pttt) REVERT: B 623 ASP cc_start: 0.8091 (m-30) cc_final: 0.7731 (m-30) REVERT: B 627 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 787 PHE cc_start: 0.7553 (p90) cc_final: 0.7283 (p90) REVERT: B 899 SER cc_start: 0.9066 (p) cc_final: 0.8776 (p) REVERT: B 1015 MET cc_start: 0.8833 (mmm) cc_final: 0.7948 (mtt) REVERT: B 1037 GLU cc_start: 0.7768 (tt0) cc_final: 0.7473 (tm-30) REVERT: B 1062 MET cc_start: 0.8635 (mmm) cc_final: 0.8267 (mmm) REVERT: C 125 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7472 (mtt180) REVERT: D 43 ASN cc_start: 0.8549 (m-40) cc_final: 0.8339 (m-40) REVERT: E 9 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7511 (mtp-110) REVERT: G 50 ASP cc_start: 0.7215 (p0) cc_final: 0.6898 (p0) REVERT: G 149 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7346 (mmm160) REVERT: G 150 PHE cc_start: 0.4824 (OUTLIER) cc_final: 0.4039 (m-80) REVERT: H 28 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8215 (pp) REVERT: H 138 ASP cc_start: 0.8182 (t0) cc_final: 0.7699 (t0) REVERT: I 26 ASN cc_start: 0.8234 (t0) cc_final: 0.7987 (t0) REVERT: I 45 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8090 (tptp) REVERT: K 46 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7490 (mm-30) REVERT: K 73 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8477 (p) REVERT: K 89 THR cc_start: 0.8153 (p) cc_final: 0.7896 (p) REVERT: K 108 GLN cc_start: 0.8258 (tp40) cc_final: 0.7050 (tp-100) REVERT: L 37 ARG cc_start: 0.8007 (mpp80) cc_final: 0.7784 (mtm180) REVERT: M 14 ASP cc_start: 0.7613 (t0) cc_final: 0.7119 (t0) REVERT: M 16 TYR cc_start: 0.7663 (m-80) cc_final: 0.7418 (m-80) REVERT: M 40 ASP cc_start: 0.7739 (m-30) cc_final: 0.7514 (m-30) REVERT: M 92 TYR cc_start: 0.6331 (m-80) cc_final: 0.6005 (m-80) REVERT: M 99 LYS cc_start: 0.7478 (mtmt) cc_final: 0.7044 (mttp) REVERT: M 247 MET cc_start: 0.8041 (mmm) cc_final: 0.7701 (mmt) REVERT: M 270 MET cc_start: 0.4592 (tpp) cc_final: 0.2165 (ptt) REVERT: M 298 MET cc_start: 0.4179 (mmm) cc_final: 0.3820 (mmm) REVERT: O 15 GLU cc_start: 0.7867 (tp30) cc_final: 0.7333 (tp30) REVERT: O 259 MET cc_start: 0.7968 (mpp) cc_final: 0.7274 (mpp) REVERT: O 474 MET cc_start: 0.2654 (ppp) cc_final: 0.2102 (tmm) REVERT: O 517 ASP cc_start: 0.7584 (t0) cc_final: 0.7111 (t0) REVERT: O 530 THR cc_start: 0.8480 (t) cc_final: 0.8276 (m) REVERT: P 189 GLN cc_start: 0.8456 (tt0) cc_final: 0.8248 (tm-30) REVERT: Q 32 LEU cc_start: 0.7727 (mt) cc_final: 0.7165 (tp) REVERT: Q 64 LEU cc_start: 0.8896 (mp) cc_final: 0.8665 (mp) REVERT: Q 111 MET cc_start: 0.8070 (mpp) cc_final: 0.7735 (mpp) outliers start: 104 outliers final: 69 residues processed: 829 average time/residue: 0.2432 time to fit residues: 334.9760 Evaluate side-chains 778 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 705 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 16 ILE Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 214 ARG Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 264 GLU Chi-restraints excluded: chain N residue 328 LYS Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 362 SER Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain Q residue 79 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 456 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 chunk 485 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 439 optimal weight: 7.9990 chunk 247 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 451 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN B 129 ASN B 215 ASN B 417 ASN B 692 GLN ** B 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 ASN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 341 HIS N 358 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.179155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124115 restraints weight = 57489.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.119243 restraints weight = 46451.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120268 restraints weight = 55752.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.121565 restraints weight = 34772.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122878 restraints weight = 29155.106| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 45691 Z= 0.231 Angle : 0.639 15.712 62189 Z= 0.322 Chirality : 0.045 0.254 6997 Planarity : 0.004 0.058 7607 Dihedral : 15.993 179.132 7108 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.90 % Allowed : 13.58 % Favored : 83.52 % 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 are not related in a simple way. whole: 0.08 (0.11), residues: 5269 helix: 1.51 (0.12), residues: 2080 sheet: -0.62 (0.19), residues: 668 loop : -1.00 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 51 TYR 0.027 0.002 TYR O 188 PHE 0.024 0.002 PHE G 80 TRP 0.013 0.001 TRP M 205 HIS 0.012 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.23 (45663) covalent geometry : angle 0.62393 / 0.32 (62150) hydrogen bonds : bond 0.03848 / 2.54 ( 1969) hydrogen bonds : angle 4.25595 / 3.00 ( 5556) metal coordination : bond 0.01322 / 0.70 ( 26) metal coordination : angle 5.63213 / 3.00 ( 39) Misc. bond : bond 0.00050 / 0.02 ( 2) *********************** 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 882 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 746 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.7496 (m90) cc_final: 0.6727 (p-80) REVERT: A 158 HIS cc_start: 0.7042 (t70) cc_final: 0.6188 (t70) REVERT: A 504 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 761 ASP cc_start: 0.7727 (m-30) cc_final: 0.7511 (m-30) REVERT: A 770 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7243 (mt-10) REVERT: A 780 MET cc_start: 0.9301 (mtm) cc_final: 0.9018 (mtp) REVERT: A 901 ILE cc_start: 0.8982 (tp) cc_final: 0.8706 (tt) REVERT: A 941 SER cc_start: 0.8616 (p) cc_final: 0.8107 (t) REVERT: A 1139 LEU cc_start: 0.9036 (tp) cc_final: 0.8801 (tt) REVERT: A 1140 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 1222 LYS cc_start: 0.7235 (pttt) cc_final: 0.6946 (pttp) REVERT: A 1288 MET cc_start: 0.7868 (mtp) cc_final: 0.7630 (mtp) REVERT: A 1314 SER cc_start: 0.7722 (t) cc_final: 0.7420 (m) REVERT: A 1326 ASP cc_start: 0.7082 (t0) cc_final: 0.6875 (t0) REVERT: A 1336 GLN cc_start: 0.8020 (tt0) cc_final: 0.7776 (tt0) REVERT: B 59 MET cc_start: 0.7565 (tmm) cc_final: 0.7359 (ttp) REVERT: B 211 LYS cc_start: 0.7655 (mttt) cc_final: 0.7014 (pttp) REVERT: B 340 ARG cc_start: 0.8004 (ttt90) cc_final: 0.7588 (ttt90) REVERT: B 529 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7690 (tm-30) REVERT: B 530 GLU cc_start: 0.8177 (mp0) cc_final: 0.7873 (mp0) REVERT: B 537 PHE cc_start: 0.8668 (m-80) cc_final: 0.8240 (m-80) REVERT: B 578 LEU cc_start: 0.9227 (mp) cc_final: 0.9014 (mt) REVERT: B 603 LYS cc_start: 0.8724 (pttm) cc_final: 0.8357 (pttt) REVERT: B 623 ASP cc_start: 0.8140 (m-30) cc_final: 0.7820 (m-30) REVERT: B 627 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8279 (mt-10) REVERT: B 899 SER cc_start: 0.9215 (p) cc_final: 0.8935 (p) REVERT: B 1015 MET cc_start: 0.8805 (mmm) cc_final: 0.8104 (mtt) REVERT: B 1037 GLU cc_start: 0.7925 (tt0) cc_final: 0.7652 (tm-30) REVERT: B 1062 MET cc_start: 0.8660 (mmm) cc_final: 0.8229 (mmm) REVERT: C 98 THR cc_start: 0.8996 (m) cc_final: 0.8788 (p) REVERT: C 125 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7626 (mtt180) REVERT: C 324 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7117 (tp30) REVERT: D 43 ASN cc_start: 0.8760 (m-40) cc_final: 0.8449 (m-40) REVERT: D 73 LEU cc_start: 0.8629 (mm) cc_final: 0.8337 (mm) REVERT: E 9 ARG cc_start: 0.8020 (mtt90) cc_final: 0.7690 (mtp-110) REVERT: E 73 PHE cc_start: 0.7255 (m-80) cc_final: 0.6769 (m-80) REVERT: E 98 ASN cc_start: 0.8633 (t0) cc_final: 0.8324 (t0) REVERT: G 9 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7173 (t0) REVERT: G 150 PHE cc_start: 0.4898 (OUTLIER) cc_final: 0.4230 (m-80) REVERT: H 28 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8530 (pp) REVERT: H 138 ASP cc_start: 0.8279 (t0) cc_final: 0.7749 (t0) REVERT: I 26 ASN cc_start: 0.8269 (t0) cc_final: 0.7987 (t0) REVERT: K 46 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7536 (mm-30) REVERT: K 73 THR cc_start: 0.8876 (OUTLIER) cc_final: 0.8635 (p) REVERT: K 89 THR cc_start: 0.8281 (p) cc_final: 0.8021 (p) REVERT: M 14 ASP cc_start: 0.7568 (t0) cc_final: 0.7221 (t0) REVERT: M 16 TYR cc_start: 0.7900 (m-80) cc_final: 0.7188 (m-80) REVERT: M 99 LYS cc_start: 0.7557 (mtmt) cc_final: 0.7183 (mttp) REVERT: M 247 MET cc_start: 0.8003 (mmm) cc_final: 0.7650 (mmt) REVERT: M 270 MET cc_start: 0.4627 (tpp) cc_final: 0.2282 (ptt) REVERT: M 298 MET cc_start: 0.4039 (mmm) cc_final: 0.3703 (mmm) REVERT: N 332 ARG cc_start: 0.6562 (mtt90) cc_final: 0.6335 (mtt90) REVERT: N 347 ASP cc_start: 0.7317 (t0) cc_final: 0.7056 (t0) REVERT: N 350 MET cc_start: 0.8279 (tpp) cc_final: 0.7852 (ttm) REVERT: N 386 SER cc_start: 0.8390 (m) cc_final: 0.8090 (p) REVERT: O 15 GLU cc_start: 0.7812 (tp30) cc_final: 0.7270 (tp30) REVERT: O 259 MET cc_start: 0.7948 (mpp) cc_final: 0.7343 (mpp) REVERT: O 474 MET cc_start: 0.2608 (ppp) cc_final: 0.2161 (tmm) REVERT: O 517 ASP cc_start: 0.7615 (t0) cc_final: 0.7186 (t0) REVERT: O 531 MET cc_start: 0.7339 (mtm) cc_final: 0.7029 (mtp) REVERT: P 189 GLN cc_start: 0.8426 (tt0) cc_final: 0.8193 (tm-30) REVERT: Q 44 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8624 (mmtm) REVERT: Q 64 LEU cc_start: 0.8940 (mp) cc_final: 0.8659 (mp) outliers start: 136 outliers final: 94 residues processed: 830 average time/residue: 0.2432 time to fit residues: 334.6062 Evaluate side-chains 773 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 673 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 742 CYS 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 1140 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1061 SER Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 127 TRP Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 214 ARG Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 261 THR Chi-restraints excluded: chain N residue 264 GLU Chi-restraints excluded: chain N residue 328 LYS Chi-restraints excluded: chain N residue 354 CYS Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 97 THR Chi-restraints excluded: chain O residue 255 VAL Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 79 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 492 optimal weight: 10.0000 chunk 261 optimal weight: 0.6980 chunk 420 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 293 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 chunk 263 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 382 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A1202 GLN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN C 277 ASN E 71 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 355 GLN O 415 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125864 restraints weight = 57430.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120965 restraints weight = 42716.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.122043 restraints weight = 51658.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122614 restraints weight = 31015.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122808 restraints weight = 26459.716| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45691 Z= 0.129 Angle : 0.572 15.249 62189 Z= 0.286 Chirality : 0.043 0.259 6997 Planarity : 0.004 0.057 7607 Dihedral : 15.911 179.580 7108 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.32 % Allowed : 14.99 % 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 are not related in a simple way. whole: 0.28 (0.12), residues: 5269 helix: 1.69 (0.12), residues: 2074 sheet: -0.51 (0.19), residues: 659 loop : -0.89 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 206 TYR 0.038 0.001 TYR O 188 PHE 0.024 0.001 PHE G 80 TRP 0.015 0.001 TRP M 205 HIS 0.006 0.001 HIS L 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (45663) covalent geometry : angle 0.55769 / 0.29 (62150) hydrogen bonds : bond 0.03409 / 2.23 ( 1969) hydrogen bonds : angle 4.13939 / 2.92 ( 5556) metal coordination : bond 0.00721 / 0.37 ( 26) metal coordination : angle 5.17331 / 2.79 ( 39) Misc. bond : bond 0.00048 / 0.02 ( 2) *********************** 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 828 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 719 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.7525 (m90) cc_final: 0.6659 (p-80) REVERT: A 119 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7203 (pt0) REVERT: A 158 HIS cc_start: 0.7086 (t70) cc_final: 0.6264 (t70) REVERT: A 718 ASN cc_start: 0.8214 (m-40) cc_final: 0.7972 (m110) REVERT: A 761 ASP cc_start: 0.7767 (m-30) cc_final: 0.7559 (m-30) REVERT: A 770 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 780 MET cc_start: 0.9327 (mtm) cc_final: 0.8885 (mtp) REVERT: A 901 ILE cc_start: 0.8892 (tp) cc_final: 0.8621 (tt) REVERT: A 941 SER cc_start: 0.8662 (p) cc_final: 0.8174 (t) REVERT: A 1116 TYR cc_start: 0.8202 (p90) cc_final: 0.7548 (p90) REVERT: A 1139 LEU cc_start: 0.9051 (tp) cc_final: 0.8756 (tt) REVERT: A 1222 LYS cc_start: 0.7227 (pttt) cc_final: 0.6913 (pttp) REVERT: A 1282 ILE cc_start: 0.9031 (mt) cc_final: 0.8807 (tt) REVERT: A 1288 MET cc_start: 0.8055 (mtp) cc_final: 0.7733 (mtp) REVERT: A 1314 SER cc_start: 0.7584 (t) cc_final: 0.7315 (m) REVERT: A 1326 ASP cc_start: 0.7149 (t0) cc_final: 0.6837 (t0) REVERT: B 59 MET cc_start: 0.7624 (tmm) cc_final: 0.7354 (ttp) REVERT: B 211 LYS cc_start: 0.7699 (mttt) cc_final: 0.6976 (ptmm) REVERT: B 340 ARG cc_start: 0.7930 (ttt90) cc_final: 0.7452 (ttt90) REVERT: B 529 GLU cc_start: 0.8473 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 530 GLU cc_start: 0.8107 (mp0) cc_final: 0.7685 (mp0) REVERT: B 603 LYS cc_start: 0.8715 (pttm) cc_final: 0.8374 (pttt) REVERT: B 623 ASP cc_start: 0.8108 (m-30) cc_final: 0.7845 (m-30) REVERT: B 627 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8288 (mt-10) REVERT: B 787 PHE cc_start: 0.7556 (p90) cc_final: 0.7280 (p90) REVERT: B 889 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8285 (mtt180) REVERT: B 899 SER cc_start: 0.9123 (p) cc_final: 0.8805 (p) REVERT: B 955 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8008 (m-30) REVERT: B 1015 MET cc_start: 0.8829 (mmm) cc_final: 0.8023 (mtt) REVERT: B 1037 GLU cc_start: 0.7740 (tt0) cc_final: 0.7505 (tm-30) REVERT: B 1062 MET cc_start: 0.8641 (mmm) cc_final: 0.8162 (mmm) REVERT: C 98 THR cc_start: 0.9062 (m) cc_final: 0.8820 (p) REVERT: C 125 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7643 (mtt180) REVERT: D 5 ASP cc_start: 0.7978 (p0) cc_final: 0.7365 (p0) REVERT: D 43 ASN cc_start: 0.8749 (m-40) cc_final: 0.8474 (m-40) REVERT: D 73 LEU cc_start: 0.8679 (mm) cc_final: 0.8395 (mm) REVERT: E 9 ARG cc_start: 0.7925 (mtt90) cc_final: 0.7639 (mtp-110) REVERT: E 98 ASN cc_start: 0.8651 (t0) cc_final: 0.8331 (t0) REVERT: E 103 LEU cc_start: 0.8575 (mp) cc_final: 0.8240 (mp) REVERT: G 6 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7281 (mt-10) REVERT: G 150 PHE cc_start: 0.4889 (OUTLIER) cc_final: 0.4230 (m-80) REVERT: H 28 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8463 (pp) REVERT: H 138 ASP cc_start: 0.8325 (t0) cc_final: 0.7752 (t0) REVERT: K 46 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7525 (mm-30) REVERT: K 73 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8557 (p) REVERT: K 79 LYS cc_start: 0.8960 (ptpt) cc_final: 0.8697 (pttt) REVERT: K 108 GLN cc_start: 0.8428 (tp40) cc_final: 0.7781 (tp-100) REVERT: M 14 ASP cc_start: 0.7476 (t0) cc_final: 0.6997 (t0) REVERT: M 16 TYR cc_start: 0.7828 (m-80) cc_final: 0.7122 (m-80) REVERT: M 40 ASP cc_start: 0.7833 (m-30) cc_final: 0.7588 (m-30) REVERT: M 65 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6358 (pp) REVERT: M 99 LYS cc_start: 0.7585 (mtmt) cc_final: 0.7214 (mttp) REVERT: M 111 THR cc_start: 0.7957 (p) cc_final: 0.7649 (p) REVERT: M 205 TRP cc_start: 0.8307 (OUTLIER) cc_final: 0.7697 (m-90) REVERT: M 270 MET cc_start: 0.4547 (tpp) cc_final: 0.2267 (ptt) REVERT: M 298 MET cc_start: 0.3787 (mmm) cc_final: 0.3522 (mmm) REVERT: N 157 MET cc_start: 0.4536 (mmm) cc_final: 0.4297 (mpp) REVERT: N 332 ARG cc_start: 0.6544 (mtt90) cc_final: 0.6192 (mtt90) REVERT: N 347 ASP cc_start: 0.7328 (t0) cc_final: 0.7074 (t0) REVERT: N 350 MET cc_start: 0.8269 (tpp) cc_final: 0.7868 (ttm) REVERT: N 386 SER cc_start: 0.8437 (m) cc_final: 0.8093 (p) REVERT: O 474 MET cc_start: 0.2683 (ppp) cc_final: 0.2108 (tmm) REVERT: O 517 ASP cc_start: 0.7666 (t0) cc_final: 0.7219 (t0) REVERT: O 531 MET cc_start: 0.7316 (mtm) cc_final: 0.6988 (mtp) REVERT: P 189 GLN cc_start: 0.8490 (tt0) cc_final: 0.8173 (tm-30) REVERT: Q 44 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8638 (mmtm) REVERT: Q 64 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8568 (mp) outliers start: 109 outliers final: 75 residues processed: 790 average time/residue: 0.2520 time to fit residues: 328.0671 Evaluate side-chains 762 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 678 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 36 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 889 ARG Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 955 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 214 ARG Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 264 GLU Chi-restraints excluded: chain N residue 328 LYS Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 79 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 267 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 419 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 435 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 463 optimal weight: 5.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN A1277 ASN A1336 GLN B 215 ASN D 18 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.179123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.123974 restraints weight = 57422.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117864 restraints weight = 46537.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.120579 restraints weight = 45956.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.120192 restraints weight = 32371.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121260 restraints weight = 27639.342| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 45691 Z= 0.192 Angle : 0.609 15.680 62189 Z= 0.305 Chirality : 0.044 0.253 6997 Planarity : 0.004 0.063 7607 Dihedral : 15.890 179.456 7108 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.73 % Allowed : 15.22 % Favored : 82.05 % 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 are not related in a simple way. whole: 0.26 (0.12), residues: 5269 helix: 1.65 (0.12), residues: 2080 sheet: -0.57 (0.19), residues: 661 loop : -0.87 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1041 TYR 0.028 0.002 TYR O 188 PHE 0.024 0.002 PHE G 80 TRP 0.013 0.001 TRP M 205 HIS 0.010 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (45663) covalent geometry : angle 0.59494 / 0.30 (62150) hydrogen bonds : bond 0.03673 / 2.43 ( 1969) hydrogen bonds : angle 4.21220 / 2.97 ( 5556) metal coordination : bond 0.01004 / 0.55 ( 26) metal coordination : angle 5.25811 / 2.83 ( 39) Misc. bond : bond 0.00055 / 0.03 ( 2) *********************** 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 804 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 676 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.7592 (m90) cc_final: 0.6671 (p-80) REVERT: A 89 GLU cc_start: 0.6508 (mm-30) cc_final: 0.6148 (mm-30) REVERT: A 99 ARG cc_start: 0.7672 (mmt180) cc_final: 0.7462 (mmt180) REVERT: A 158 HIS cc_start: 0.7446 (t70) cc_final: 0.6571 (t70) REVERT: A 760 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7685 (ttt180) REVERT: A 770 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 780 MET cc_start: 0.9228 (mtm) cc_final: 0.9016 (mtp) REVERT: A 901 ILE cc_start: 0.9000 (tp) cc_final: 0.8727 (tt) REVERT: A 1116 TYR cc_start: 0.8206 (p90) cc_final: 0.7585 (p90) REVERT: A 1139 LEU cc_start: 0.9091 (tp) cc_final: 0.8843 (tt) REVERT: A 1222 LYS cc_start: 0.7395 (pttt) cc_final: 0.7019 (pttp) REVERT: A 1288 MET cc_start: 0.8126 (mtp) cc_final: 0.7874 (mtp) REVERT: A 1314 SER cc_start: 0.7613 (t) cc_final: 0.7366 (m) REVERT: A 1326 ASP cc_start: 0.7435 (t0) cc_final: 0.7146 (t0) REVERT: B 211 LYS cc_start: 0.8002 (mttt) cc_final: 0.7220 (ptmm) REVERT: B 278 PHE cc_start: 0.8582 (m-80) cc_final: 0.8366 (m-80) REVERT: B 340 ARG cc_start: 0.8094 (ttt90) cc_final: 0.7635 (ttt90) REVERT: B 529 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 530 GLU cc_start: 0.8053 (mp0) cc_final: 0.7757 (mp0) REVERT: B 537 PHE cc_start: 0.8867 (m-80) cc_final: 0.8592 (m-80) REVERT: B 562 MET cc_start: 0.8462 (mmm) cc_final: 0.8237 (mmm) REVERT: B 603 LYS cc_start: 0.8706 (pttm) cc_final: 0.8386 (pttt) REVERT: B 623 ASP cc_start: 0.8106 (m-30) cc_final: 0.7859 (m-30) REVERT: B 627 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8316 (mt-10) REVERT: B 787 PHE cc_start: 0.7662 (p90) cc_final: 0.7346 (p90) REVERT: B 889 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8400 (mtt180) REVERT: B 899 SER cc_start: 0.9175 (p) cc_final: 0.8889 (p) REVERT: B 1015 MET cc_start: 0.8770 (mmm) cc_final: 0.8089 (mtt) REVERT: B 1037 GLU cc_start: 0.7733 (tt0) cc_final: 0.7522 (tm-30) REVERT: B 1062 MET cc_start: 0.8705 (mmm) cc_final: 0.8265 (mmm) REVERT: C 98 THR cc_start: 0.9069 (m) cc_final: 0.8665 (p) REVERT: C 125 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7612 (mtt180) REVERT: D 5 ASP cc_start: 0.8216 (p0) cc_final: 0.7755 (p0) REVERT: D 40 GLN cc_start: 0.7115 (tp-100) cc_final: 0.6892 (tp-100) REVERT: D 43 ASN cc_start: 0.8752 (m-40) cc_final: 0.8439 (m-40) REVERT: E 98 ASN cc_start: 0.8669 (t0) cc_final: 0.8269 (t0) REVERT: G 6 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7466 (mt-10) REVERT: G 150 PHE cc_start: 0.4874 (OUTLIER) cc_final: 0.4238 (m-80) REVERT: H 18 GLU cc_start: 0.8351 (mp0) cc_final: 0.8032 (mp0) REVERT: H 28 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8490 (pp) REVERT: H 138 ASP cc_start: 0.8336 (t0) cc_final: 0.7775 (t0) REVERT: K 46 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7460 (mm-30) REVERT: K 73 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8611 (p) REVERT: K 79 LYS cc_start: 0.9030 (ptpt) cc_final: 0.8712 (pttt) REVERT: L 51 ARG cc_start: 0.8409 (ttp-110) cc_final: 0.8073 (ptp-110) REVERT: M 16 TYR cc_start: 0.7905 (m-80) cc_final: 0.7434 (m-80) REVERT: M 65 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6450 (pp) REVERT: M 99 LYS cc_start: 0.7639 (mtmt) cc_final: 0.7259 (mttp) REVERT: M 111 THR cc_start: 0.8110 (p) cc_final: 0.7821 (p) REVERT: M 205 TRP cc_start: 0.8429 (OUTLIER) cc_final: 0.7747 (m-90) REVERT: M 270 MET cc_start: 0.4649 (tpp) cc_final: 0.2507 (ptt) REVERT: M 298 MET cc_start: 0.3581 (mmm) cc_final: 0.3349 (mmm) REVERT: N 157 MET cc_start: 0.4716 (mmm) cc_final: 0.4423 (mpp) REVERT: N 347 ASP cc_start: 0.7541 (t0) cc_final: 0.7324 (t0) REVERT: N 350 MET cc_start: 0.8351 (tpp) cc_final: 0.8095 (ttp) REVERT: N 386 SER cc_start: 0.8601 (m) cc_final: 0.8302 (p) REVERT: O 474 MET cc_start: 0.2614 (ppp) cc_final: 0.2157 (tmm) REVERT: O 517 ASP cc_start: 0.7852 (t0) cc_final: 0.7381 (t0) REVERT: O 531 MET cc_start: 0.7532 (mtm) cc_final: 0.7223 (mtp) REVERT: P 189 GLN cc_start: 0.8403 (tt0) cc_final: 0.8162 (tm-30) REVERT: Q 64 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8558 (mp) outliers start: 128 outliers final: 92 residues processed: 765 average time/residue: 0.2601 time to fit residues: 328.0840 Evaluate side-chains 741 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 640 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 889 ARG Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 309 SER Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 214 ARG Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 261 THR Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 255 VAL Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 68 MET Chi-restraints excluded: chain Q residue 79 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 455 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 388 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 370 optimal weight: 0.9980 chunk 449 optimal weight: 0.0030 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A1202 GLN B 129 ASN B 215 ASN D 18 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 244 GLN P 201 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.180903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.124876 restraints weight = 57696.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.120261 restraints weight = 41692.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121410 restraints weight = 50198.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.122092 restraints weight = 29960.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.125112 restraints weight = 25674.721| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45691 Z= 0.122 Angle : 0.575 15.584 62189 Z= 0.287 Chirality : 0.043 0.257 6997 Planarity : 0.004 0.063 7607 Dihedral : 15.856 179.770 7108 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.24 % Allowed : 15.71 % Favored : 82.05 % 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 are not related in a simple way. whole: 0.38 (0.12), residues: 5269 helix: 1.77 (0.12), residues: 2075 sheet: -0.53 (0.19), residues: 661 loop : -0.81 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 213 TYR 0.026 0.001 TYR O 188 PHE 0.023 0.001 PHE G 80 TRP 0.014 0.001 TRP M 205 HIS 0.007 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (45663) covalent geometry : angle 0.56202 / 0.29 (62150) hydrogen bonds : bond 0.03379 / 2.22 ( 1969) hydrogen bonds : angle 4.13930 / 2.92 ( 5556) metal coordination : bond 0.00687 / 0.35 ( 26) metal coordination : angle 4.91255 / 2.69 ( 39) Misc. bond : bond 0.00049 / 0.02 ( 2) *********************** 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 779 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 674 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.7536 (m90) cc_final: 0.6650 (p-80) REVERT: A 130 LYS cc_start: 0.8028 (ptpt) cc_final: 0.7792 (pttt) REVERT: A 136 TYR cc_start: 0.8298 (t80) cc_final: 0.7919 (t80) REVERT: A 760 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7669 (ttt180) REVERT: A 770 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7088 (mt-10) REVERT: A 780 MET cc_start: 0.9222 (mtm) cc_final: 0.8991 (mtp) REVERT: A 901 ILE cc_start: 0.8983 (tp) cc_final: 0.8653 (tt) REVERT: A 1116 TYR cc_start: 0.8160 (p90) cc_final: 0.7634 (p90) REVERT: A 1139 LEU cc_start: 0.9069 (tp) cc_final: 0.8811 (tt) REVERT: A 1222 LYS cc_start: 0.7338 (pttt) cc_final: 0.6994 (pttp) REVERT: A 1288 MET cc_start: 0.8078 (mtp) cc_final: 0.7784 (mtp) REVERT: A 1314 SER cc_start: 0.7458 (t) cc_final: 0.7194 (m) REVERT: A 1326 ASP cc_start: 0.7161 (t0) cc_final: 0.6917 (t0) REVERT: B 211 LYS cc_start: 0.7902 (mttt) cc_final: 0.7278 (ptmm) REVERT: B 340 ARG cc_start: 0.8064 (ttt90) cc_final: 0.7636 (ttt90) REVERT: B 529 GLU cc_start: 0.8484 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 530 GLU cc_start: 0.7944 (mp0) cc_final: 0.7695 (mp0) REVERT: B 603 LYS cc_start: 0.8693 (pttm) cc_final: 0.8411 (pttt) REVERT: B 787 PHE cc_start: 0.7567 (p90) cc_final: 0.7252 (p90) REVERT: B 899 SER cc_start: 0.9097 (p) cc_final: 0.8794 (p) REVERT: B 955 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: B 1015 MET cc_start: 0.8774 (mmm) cc_final: 0.8056 (mtt) REVERT: B 1037 GLU cc_start: 0.7705 (tt0) cc_final: 0.7453 (tm-30) REVERT: B 1062 MET cc_start: 0.8583 (mmm) cc_final: 0.8149 (mmm) REVERT: B 1116 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7915 (mt-10) REVERT: C 98 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8792 (p) REVERT: C 125 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7610 (mtt180) REVERT: D 5 ASP cc_start: 0.8173 (p0) cc_final: 0.7740 (p0) REVERT: D 40 GLN cc_start: 0.7083 (tp-100) cc_final: 0.6872 (tp-100) REVERT: D 43 ASN cc_start: 0.8741 (m-40) cc_final: 0.8418 (m-40) REVERT: E 98 ASN cc_start: 0.8636 (t0) cc_final: 0.8171 (t0) REVERT: G 150 PHE cc_start: 0.4690 (OUTLIER) cc_final: 0.4189 (m-80) REVERT: H 18 GLU cc_start: 0.8310 (mp0) cc_final: 0.8013 (mp0) REVERT: H 28 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8565 (pp) REVERT: H 138 ASP cc_start: 0.8275 (t0) cc_final: 0.7735 (t0) REVERT: K 46 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7384 (mm-30) REVERT: K 73 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8587 (p) REVERT: K 79 LYS cc_start: 0.8956 (ptpt) cc_final: 0.8665 (pttt) REVERT: L 51 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.8002 (mtm110) REVERT: M 14 ASP cc_start: 0.7277 (t0) cc_final: 0.6664 (t0) REVERT: M 16 TYR cc_start: 0.7889 (m-80) cc_final: 0.7237 (m-80) REVERT: M 24 LYS cc_start: 0.7648 (mmmm) cc_final: 0.7185 (mmmm) REVERT: M 40 ASP cc_start: 0.7754 (m-30) cc_final: 0.7524 (m-30) REVERT: M 65 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6440 (pp) REVERT: M 99 LYS cc_start: 0.7457 (mtmt) cc_final: 0.7107 (mttp) REVERT: M 140 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8603 (t) REVERT: M 205 TRP cc_start: 0.8373 (OUTLIER) cc_final: 0.7669 (m-90) REVERT: M 270 MET cc_start: 0.4473 (tpp) cc_final: 0.2450 (ptt) REVERT: M 298 MET cc_start: 0.3558 (mmm) cc_final: 0.3353 (mmm) REVERT: N 332 ARG cc_start: 0.7029 (mtt90) cc_final: 0.6476 (mtt90) REVERT: N 347 ASP cc_start: 0.7511 (t0) cc_final: 0.7288 (t0) REVERT: N 350 MET cc_start: 0.8404 (tpp) cc_final: 0.8100 (ttp) REVERT: N 386 SER cc_start: 0.8614 (m) cc_final: 0.8308 (p) REVERT: O 187 MET cc_start: 0.7215 (ttm) cc_final: 0.7009 (ttm) REVERT: O 474 MET cc_start: 0.2561 (ppp) cc_final: 0.2139 (tmm) REVERT: O 517 ASP cc_start: 0.7818 (t0) cc_final: 0.7363 (t0) REVERT: O 531 MET cc_start: 0.7366 (mtm) cc_final: 0.7082 (mtp) REVERT: P 189 GLN cc_start: 0.8460 (tt0) cc_final: 0.8222 (tm-30) REVERT: Q 64 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8519 (mp) outliers start: 105 outliers final: 76 residues processed: 737 average time/residue: 0.2464 time to fit residues: 301.2464 Evaluate side-chains 729 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 642 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 36 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 955 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 127 TRP Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 140 SER Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 214 ARG Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 264 GLU Chi-restraints excluded: chain N residue 328 LYS Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 244 GLN Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 404 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 525 optimal weight: 50.0000 chunk 336 optimal weight: 0.0070 chunk 398 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 450 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 366 optimal weight: 4.9990 chunk 503 optimal weight: 20.0000 overall best weight: 1.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN D 18 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.179391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124019 restraints weight = 57340.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117811 restraints weight = 45241.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.120590 restraints weight = 45690.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.120154 restraints weight = 32073.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.121227 restraints weight = 28549.260| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 45691 Z= 0.161 Angle : 0.590 15.530 62189 Z= 0.295 Chirality : 0.043 0.265 6997 Planarity : 0.004 0.063 7607 Dihedral : 15.849 179.850 7108 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.17 % Allowed : 15.95 % Favored : 81.88 % 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 are not related in a simple way. whole: 0.35 (0.12), residues: 5269 helix: 1.73 (0.12), residues: 2080 sheet: -0.54 (0.19), residues: 661 loop : -0.82 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 206 TYR 0.040 0.001 TYR O 188 PHE 0.028 0.001 PHE G 80 TRP 0.013 0.001 TRP M 205 HIS 0.008 0.001 HIS O 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (45663) covalent geometry : angle 0.57721 / 0.29 (62150) hydrogen bonds : bond 0.03463 / 2.27 ( 1969) hydrogen bonds : angle 4.16912 / 2.94 ( 5556) metal coordination : bond 0.00812 / 0.43 ( 26) metal coordination : angle 4.83544 / 2.67 ( 39) Misc. bond : bond 0.00040 / 0.02 ( 2) *********************** 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 757 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 655 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.7674 (m90) cc_final: 0.6721 (p-80) REVERT: A 760 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7669 (ttt180) REVERT: A 780 MET cc_start: 0.9214 (mtm) cc_final: 0.9004 (mtp) REVERT: A 901 ILE cc_start: 0.9011 (tp) cc_final: 0.8700 (tt) REVERT: A 1116 TYR cc_start: 0.8179 (p90) cc_final: 0.7535 (p90) REVERT: A 1139 LEU cc_start: 0.9054 (tp) cc_final: 0.8812 (tt) REVERT: A 1222 LYS cc_start: 0.7382 (pttt) cc_final: 0.6920 (pttp) REVERT: A 1288 MET cc_start: 0.8134 (mtp) cc_final: 0.7859 (mtp) REVERT: A 1311 MET cc_start: 0.9040 (ptp) cc_final: 0.8690 (ptp) REVERT: A 1314 SER cc_start: 0.7478 (t) cc_final: 0.7242 (m) REVERT: A 1326 ASP cc_start: 0.7256 (t0) cc_final: 0.7039 (t0) REVERT: B 106 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8466 (m-30) REVERT: B 211 LYS cc_start: 0.8006 (mttt) cc_final: 0.7336 (ptmm) REVERT: B 340 ARG cc_start: 0.8136 (ttt90) cc_final: 0.7675 (ttt90) REVERT: B 529 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7656 (tm-30) REVERT: B 530 GLU cc_start: 0.7993 (mp0) cc_final: 0.7669 (mp0) REVERT: B 603 LYS cc_start: 0.8719 (pttm) cc_final: 0.8434 (pttt) REVERT: B 787 PHE cc_start: 0.7673 (p90) cc_final: 0.7340 (p90) REVERT: B 889 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8348 (mtt180) REVERT: B 899 SER cc_start: 0.9160 (p) cc_final: 0.8868 (p) REVERT: B 955 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: B 1015 MET cc_start: 0.8801 (mmm) cc_final: 0.8175 (mtt) REVERT: B 1037 GLU cc_start: 0.7725 (tt0) cc_final: 0.7491 (tm-30) REVERT: B 1062 MET cc_start: 0.8735 (mmm) cc_final: 0.8335 (mmm) REVERT: C 56 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7816 (ttt) REVERT: C 98 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8763 (p) REVERT: C 125 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7660 (mtt180) REVERT: D 5 ASP cc_start: 0.8087 (p0) cc_final: 0.7877 (p0) REVERT: D 40 GLN cc_start: 0.7184 (tp-100) cc_final: 0.6919 (tp-100) REVERT: D 43 ASN cc_start: 0.8651 (m-40) cc_final: 0.8340 (m-40) REVERT: E 98 ASN cc_start: 0.8670 (t0) cc_final: 0.8208 (t0) REVERT: G 83 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7074 (mp0) REVERT: G 150 PHE cc_start: 0.4852 (OUTLIER) cc_final: 0.4543 (m-80) REVERT: H 18 GLU cc_start: 0.8427 (mp0) cc_final: 0.8097 (mp0) REVERT: H 28 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8572 (pp) REVERT: H 138 ASP cc_start: 0.8383 (t0) cc_final: 0.7822 (t0) REVERT: K 46 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7430 (mm-30) REVERT: K 73 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8614 (p) REVERT: K 79 LYS cc_start: 0.9035 (ptpt) cc_final: 0.8711 (pttt) REVERT: L 51 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.8059 (mtm110) REVERT: M 14 ASP cc_start: 0.7298 (t0) cc_final: 0.6664 (t0) REVERT: M 16 TYR cc_start: 0.7862 (m-80) cc_final: 0.7275 (m-80) REVERT: M 24 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7240 (mmmm) REVERT: M 65 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6526 (pp) REVERT: M 99 LYS cc_start: 0.7494 (mtmt) cc_final: 0.7136 (mttp) REVERT: M 205 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.7705 (m-90) REVERT: M 270 MET cc_start: 0.4132 (tpp) cc_final: 0.2329 (ptt) REVERT: M 298 MET cc_start: 0.3560 (mmm) cc_final: 0.3336 (mmm) REVERT: N 347 ASP cc_start: 0.7587 (t0) cc_final: 0.7377 (t0) REVERT: N 350 MET cc_start: 0.8416 (tpp) cc_final: 0.8139 (ttp) REVERT: N 386 SER cc_start: 0.8705 (m) cc_final: 0.8407 (p) REVERT: O 474 MET cc_start: 0.2578 (ppp) cc_final: 0.2158 (tmm) REVERT: O 517 ASP cc_start: 0.7889 (t0) cc_final: 0.7445 (t0) REVERT: O 531 MET cc_start: 0.7556 (mtm) cc_final: 0.7285 (mtp) REVERT: P 189 GLN cc_start: 0.8477 (tt0) cc_final: 0.8234 (tm-30) REVERT: Q 64 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8591 (mp) outliers start: 102 outliers final: 80 residues processed: 715 average time/residue: 0.2622 time to fit residues: 308.5841 Evaluate side-chains 726 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 633 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 36 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 155 ILE Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 889 ARG Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 955 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1040 SER Chi-restraints excluded: chain B residue 1061 SER Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 127 TRP Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 214 ARG Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 328 LYS Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 378 optimal weight: 0.0170 chunk 472 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 287 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 228 optimal weight: 0.5980 chunk 129 optimal weight: 0.0870 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.181807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125544 restraints weight = 57595.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120591 restraints weight = 41318.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121958 restraints weight = 49712.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.122708 restraints weight = 30480.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124846 restraints weight = 26014.588| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 45691 Z= 0.112 Angle : 0.571 15.371 62189 Z= 0.287 Chirality : 0.042 0.267 6997 Planarity : 0.004 0.063 7607 Dihedral : 15.807 179.660 7108 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.77 % Allowed : 16.48 % Favored : 81.75 % 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 are not related in a simple way. whole: 0.49 (0.12), residues: 5269 helix: 1.87 (0.12), residues: 2074 sheet: -0.47 (0.20), residues: 661 loop : -0.76 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 206 TYR 0.036 0.001 TYR O 188 PHE 0.022 0.001 PHE G 80 TRP 0.015 0.001 TRP M 205 HIS 0.015 0.001 HIS N 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (45663) covalent geometry : angle 0.56148 / 0.29 (62150) hydrogen bonds : bond 0.03199 / 2.09 ( 1969) hydrogen bonds : angle 4.10114 / 2.89 ( 5556) metal coordination : bond 0.00618 / 0.31 ( 26) metal coordination : angle 4.27832 / 2.46 ( 39) Misc. bond : bond 0.00048 / 0.02 ( 2) ********************** 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 769 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 686 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 HIS cc_start: 0.7577 (m90) cc_final: 0.6613 (p-80) REVERT: A 136 TYR cc_start: 0.8310 (t80) cc_final: 0.8039 (t80) REVERT: A 224 LEU cc_start: 0.8965 (tp) cc_final: 0.8744 (tt) REVERT: A 643 SER cc_start: 0.9036 (m) cc_final: 0.8681 (p) REVERT: A 760 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7956 (ttp80) REVERT: A 780 MET cc_start: 0.9241 (mtm) cc_final: 0.8928 (mtp) REVERT: A 901 ILE cc_start: 0.8962 (tp) cc_final: 0.8675 (tt) REVERT: A 912 MET cc_start: 0.8977 (mmp) cc_final: 0.8496 (mmp) REVERT: A 1116 TYR cc_start: 0.8163 (p90) cc_final: 0.7550 (p90) REVERT: A 1139 LEU cc_start: 0.9056 (tp) cc_final: 0.8836 (tt) REVERT: A 1222 LYS cc_start: 0.7335 (pttt) cc_final: 0.6898 (pttp) REVERT: A 1288 MET cc_start: 0.8057 (mtp) cc_final: 0.7730 (mtp) REVERT: A 1311 MET cc_start: 0.8930 (ptp) cc_final: 0.8630 (ptp) REVERT: A 1326 ASP cc_start: 0.7265 (t0) cc_final: 0.7007 (t0) REVERT: B 211 LYS cc_start: 0.7900 (mttt) cc_final: 0.7244 (ptmm) REVERT: B 246 GLU cc_start: 0.8231 (mp0) cc_final: 0.7825 (mp0) REVERT: B 340 ARG cc_start: 0.8095 (ttt90) cc_final: 0.7662 (ttt90) REVERT: B 529 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7631 (tm-30) REVERT: B 530 GLU cc_start: 0.7868 (mp0) cc_final: 0.7584 (mp0) REVERT: B 578 LEU cc_start: 0.9218 (mp) cc_final: 0.9013 (mt) REVERT: B 603 LYS cc_start: 0.8692 (pttm) cc_final: 0.8415 (pttt) REVERT: B 609 LYS cc_start: 0.8302 (ttpt) cc_final: 0.8030 (tppt) REVERT: B 787 PHE cc_start: 0.7608 (p90) cc_final: 0.7286 (p90) REVERT: B 899 SER cc_start: 0.9060 (p) cc_final: 0.8766 (p) REVERT: B 955 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: B 1015 MET cc_start: 0.8732 (mmm) cc_final: 0.8075 (mtt) REVERT: B 1062 MET cc_start: 0.8699 (mmm) cc_final: 0.8272 (mmm) REVERT: B 1116 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7862 (mt-10) REVERT: C 56 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7817 (ttt) REVERT: C 98 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8781 (p) REVERT: C 125 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7589 (mtt180) REVERT: D 5 ASP cc_start: 0.8041 (p0) cc_final: 0.7838 (p0) REVERT: D 43 ASN cc_start: 0.8637 (m-40) cc_final: 0.8358 (m-40) REVERT: E 73 PHE cc_start: 0.7246 (m-80) cc_final: 0.6785 (m-80) REVERT: E 98 ASN cc_start: 0.8662 (t0) cc_final: 0.8213 (t0) REVERT: G 150 PHE cc_start: 0.4522 (OUTLIER) cc_final: 0.4290 (m-80) REVERT: H 18 GLU cc_start: 0.8356 (mp0) cc_final: 0.8074 (mp0) REVERT: H 28 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8647 (pp) REVERT: H 138 ASP cc_start: 0.8335 (t0) cc_final: 0.7814 (t0) REVERT: J 26 GLN cc_start: 0.7971 (mt0) cc_final: 0.7582 (tt0) REVERT: J 48 MET cc_start: 0.8161 (tpp) cc_final: 0.7465 (tpp) REVERT: K 46 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7389 (mm-30) REVERT: K 73 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8553 (p) REVERT: K 79 LYS cc_start: 0.8967 (ptpt) cc_final: 0.8688 (pttt) REVERT: K 108 GLN cc_start: 0.8460 (tp40) cc_final: 0.7853 (tp-100) REVERT: L 51 ARG cc_start: 0.8324 (ttp-110) cc_final: 0.7962 (mtm110) REVERT: M 16 TYR cc_start: 0.7802 (m-80) cc_final: 0.7420 (m-80) REVERT: M 65 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6451 (pp) REVERT: M 99 LYS cc_start: 0.7465 (mtmt) cc_final: 0.7154 (mttp) REVERT: M 205 TRP cc_start: 0.8405 (OUTLIER) cc_final: 0.7716 (m-90) REVERT: M 270 MET cc_start: 0.4041 (tpp) cc_final: 0.2044 (ptt) REVERT: M 298 MET cc_start: 0.3548 (mmm) cc_final: 0.3330 (mmm) REVERT: N 347 ASP cc_start: 0.7535 (t0) cc_final: 0.7328 (t0) REVERT: N 350 MET cc_start: 0.8383 (tpp) cc_final: 0.8143 (ttp) REVERT: N 386 SER cc_start: 0.8696 (m) cc_final: 0.8393 (p) REVERT: O 474 MET cc_start: 0.2512 (ppp) cc_final: 0.2125 (tmm) REVERT: O 517 ASP cc_start: 0.7890 (t0) cc_final: 0.7421 (t0) REVERT: P 189 GLN cc_start: 0.8483 (tt0) cc_final: 0.8253 (tm-30) REVERT: Q 64 LEU cc_start: 0.8955 (mp) cc_final: 0.8613 (mp) outliers start: 83 outliers final: 64 residues processed: 739 average time/residue: 0.2491 time to fit residues: 305.1988 Evaluate side-chains 720 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 646 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 36 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 742 CYS Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 1313 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 357 TYR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 777 CYS Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 955 ASP Chi-restraints excluded: chain B residue 1032 THR Chi-restraints excluded: chain B residue 1061 SER Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 125 ARG Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 118 HIS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain G residue 150 PHE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 7 ASP Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 205 TRP Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 214 ARG Chi-restraints excluded: chain M residue 220 HIS Chi-restraints excluded: chain M residue 231 SER Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain N residue 264 GLU Chi-restraints excluded: chain N residue 328 LYS Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 370 THR Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 523 LEU Chi-restraints excluded: chain P residue 98 ILE Chi-restraints excluded: chain Q residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 38 optimal weight: 1.9990 chunk 454 optimal weight: 8.9990 chunk 470 optimal weight: 0.9990 chunk 150 optimal weight: 0.1980 chunk 526 optimal weight: 20.0000 chunk 417 optimal weight: 8.9990 chunk 494 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 480 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 HIS A 343 GLN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** D 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 HIS O 158 GLN O 236 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.181883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.128716 restraints weight = 58124.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123423 restraints weight = 46643.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124818 restraints weight = 56437.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125425 restraints weight = 35828.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.128241 restraints weight = 30212.542| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.167 45691 Z= 0.160 Angle : 0.645 59.196 62189 Z= 0.345 Chirality : 0.043 0.892 6997 Planarity : 0.004 0.063 7607 Dihedral : 15.809 179.655 7108 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 1.81 % Allowed : 16.63 % Favored : 81.56 % 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 are not related in a simple way. whole: 0.48 (0.12), residues: 5269 helix: 1.86 (0.12), residues: 2074 sheet: -0.46 (0.20), residues: 661 loop : -0.76 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG O 449 TYR 0.031 0.001 TYR O 188 PHE 0.018 0.001 PHE G 80 TRP 0.015 0.001 TRP G 127 HIS 0.013 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (45663) covalent geometry : angle 0.63629 / 0.34 (62150) hydrogen bonds : bond 0.03214 / 2.10 ( 1969) hydrogen bonds : angle 4.10334 / 2.89 ( 5556) metal coordination : bond 0.00598 / 0.31 ( 26) metal coordination : angle 4.27486 / 2.46 ( 39) Misc. bond : bond 0.00045 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8904.88 seconds wall clock time: 154 minutes 33.84 seconds (9273.84 seconds total)