Starting phenix.real_space_refine on Tue Jul 7 05:33:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k39_62010/07_2026/9k39_62010.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k39_62010/07_2026/9k39_62010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k39_62010/07_2026/9k39_62010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k39_62010/07_2026/9k39_62010.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k39_62010/07_2026/9k39_62010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k39_62010/07_2026/9k39_62010.map" } resolution = 2.8 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= 0.007 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 113 5.49 5 Mg 1 5.21 5 S 285 5.16 5 C 27795 2.51 5 N 7745 2.21 5 O 8577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.06s 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: 44526 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: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 424 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 50} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1031 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "Y" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1019 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "Z" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 5} Link IDs: {'rna3p': 6} 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 57.793 112.239 83.296 1.00103.58 S ATOM 565 SG CYS A 72 58.337 115.829 84.795 1.00106.71 S ATOM 613 SG CYS A 79 61.536 113.796 83.425 1.00104.11 S ATOM 854 SG CYS A 109 68.197 86.176 122.638 1.00114.77 S ATOM 876 SG CYS A 112 65.685 88.738 124.577 1.00118.64 S ATOM 1245 SG CYS A 156 68.396 87.504 126.670 1.00130.18 S ATOM 1271 SG CYS A 159 65.513 85.346 125.884 1.00130.36 S ATOM 19137 SG CYS B1080 59.672 118.901 101.143 1.00102.14 S ATOM 19156 SG CYS B1083 60.937 115.094 101.456 1.00101.99 S ATOM 19222 SG CYS B1092 58.581 116.088 98.802 1.00 97.16 S ATOM 19250 SG CYS B1095 57.441 115.464 102.883 1.00100.21 S ATOM 28160 SG CYS I 5 116.924 45.996 106.073 1.00130.73 S ATOM 28177 SG CYS I 8 113.219 47.026 104.189 1.00130.05 S ATOM 28307 SG CYS I 25 113.028 48.859 107.509 1.00130.27 S ATOM 28328 SG CYS I 28 113.770 45.272 107.485 1.00128.16 S ATOM 28598 SG CYS J 7 116.237 123.332 43.227 1.00 75.41 S ATOM 28622 SG CYS J 10 117.638 126.584 42.049 1.00 75.83 S ATOM 28886 SG CYS J 44 119.935 124.257 43.744 1.00 81.33 S ATOM 28892 SG CYS J 45 118.925 123.557 39.928 1.00 82.39 S ATOM 29935 SG CYS L 19 83.190 97.459 33.766 1.00103.46 S ATOM 29954 SG CYS L 22 84.412 95.638 29.590 1.00109.30 S ATOM 30071 SG CYS L 36 80.312 97.395 31.214 1.00117.09 S ATOM 30097 SG CYS L 39 82.037 94.250 31.721 1.00117.30 S ATOM 41043 SG CYS P 290 45.621 93.534 106.018 1.00103.33 S ATOM 41167 SG CYS P 307 41.132 98.308 106.692 1.00108.29 S Time building chain proxies: 7.72, per 1000 atoms: 0.17 Number of scatterers: 44526 At special positions: 0 Unit cell: (173.23, 181.225, 171.897, 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 113 15.00 Mg 1 11.99 O 8577 8.00 N 7745 7.00 C 27795 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: 3.45 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=" NE2 HIS A 82 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 69 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 109 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 159 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 156 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " 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 I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 7 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 45 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 44 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 10 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " Number of angles added : 33 10538 Ramachandran restraints generated. 5269 Oldfield, 0 Emsley, 5269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10004 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 59 sheets defined 42.5% alpha, 17.3% beta 33 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 5.21 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.524A pdb=" N GLY A 61 " --> pdb=" O HIS A 58 " (cutoff:3.500A) 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: 3.806A 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: 4.379A pdb=" N GLY A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.569A pdb=" N ARG A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 277 through 300 removed outlier: 3.743A pdb=" N MET A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.632A 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 492 through 497 removed outlier: 3.744A pdb=" N TYR A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 572 No H-bonds generated for 'chain 'A' and resid 571 through 572' Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.750A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.768A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.889A 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: 3.893A pdb=" N ALA A 676 " --> pdb=" O GLY A 672 " (cutoff:3.500A) Proline residue: A 688 - end of helix Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 733 Processing helix chain 'A' and resid 743 through 771 Processing helix chain 'A' and resid 775 through 783 Processing helix chain 'A' and resid 788 through 797 Processing helix chain 'A' and resid 843 through 880 removed outlier: 3.783A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 removed outlier: 3.524A pdb=" N ASP A 905 " --> pdb=" O TYR A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 941 through 954 removed outlier: 3.535A 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: 3.574A 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: 3.875A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.961A 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: 3.741A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.632A 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: 4.249A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.834A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.668A 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: 3.669A pdb=" N ALA B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 Processing helix chain 'B' and resid 304 through 315 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 364 through 392 removed outlier: 3.687A pdb=" N LEU B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 Processing helix chain 'B' and resid 408 through 422 removed outlier: 4.144A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 removed outlier: 3.913A 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 removed outlier: 3.635A pdb=" N VAL B 512 " --> pdb=" O ASP B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.518A pdb=" N LEU B 526 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.608A 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: 3.950A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.565A pdb=" N LEU B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 691 Processing helix chain 'B' and resid 722 through 729 Processing helix chain 'B' and resid 730 through 733 Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 932 through 938 removed outlier: 4.309A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.790A pdb=" N LEU B 943 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 979 removed outlier: 3.573A pdb=" N VAL B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1048 through 1059 Processing helix chain 'B' and resid 1060 through 1069 Processing helix chain 'B' and resid 1108 through 1120 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 82 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 removed outlier: 3.508A pdb=" N LEU C 162 " --> pdb=" O ASP C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 158 through 162' Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 247 through 257 removed outlier: 3.784A pdb=" N GLU C 251 " --> pdb=" O GLY C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 317 through 344 Processing helix chain 'D' and resid 12 through 30 removed outlier: 3.771A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.646A pdb=" N GLN D 39 " --> pdb=" O HIS D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 56 Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 111 through 121 removed outlier: 4.069A pdb=" N ALA D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.524A pdb=" N ALA J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.785A 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: 3.522A pdb=" N GLY K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS K 61 " --> pdb=" O TYR K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 126 Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 140 through 159 Processing helix chain 'M' and resid 182 through 191 Processing helix chain 'M' and resid 192 through 203 removed outlier: 3.984A pdb=" N GLU M 203 " --> pdb=" O LYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 223 removed outlier: 3.842A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN M 223 " --> pdb=" O GLU M 219 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 226 No H-bonds generated for 'chain 'M' and resid 224 through 226' Processing helix chain 'M' and resid 241 through 250 Processing helix chain 'M' and resid 264 through 268 removed outlier: 3.688A pdb=" N VAL M 267 " --> pdb=" O PRO M 264 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU M 268 " --> pdb=" O SER M 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 264 through 268' 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 317 removed outlier: 3.707A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL M 317 " --> pdb=" O GLY M 313 " (cutoff:3.500A) 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: 3.572A 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: 4.006A 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: 4.057A 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: 3.875A 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: 4.062A 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: 3.776A pdb=" N HIS O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 71 No H-bonds generated for 'chain 'O' and resid 69 through 71' Processing helix chain 'O' and resid 78 through 85 Processing helix chain 'O' and resid 87 through 99 Processing helix chain 'O' and resid 100 through 114 Processing helix chain 'O' and resid 117 through 133 removed outlier: 4.033A pdb=" N GLU O 131 " --> pdb=" O ASP O 127 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR O 132 " --> pdb=" O ARG O 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 154 removed outlier: 4.083A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 removed outlier: 3.509A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 278 removed outlier: 4.509A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.265A 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: 3.521A 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: 4.138A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 3.622A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 491 through 530 removed outlier: 4.002A pdb=" N GLU O 495 " --> pdb=" O ILE O 491 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP O 517 " --> pdb=" O GLU O 513 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR O 519 " --> pdb=" O GLN O 515 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 29 Processing helix chain 'P' and resid 34 through 42 Processing helix chain 'P' and resid 46 through 60 Processing helix chain 'P' and resid 88 through 103 removed outlier: 3.639A pdb=" N GLU P 92 " --> pdb=" O SER P 88 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'P' and resid 108 through 117 Processing helix chain 'P' and resid 119 through 133 Processing helix chain 'P' and resid 173 through 199 removed outlier: 3.638A pdb=" N LYS P 199 " --> pdb=" O ALA P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 210 Processing helix chain 'P' and resid 213 through 224 Processing helix chain 'P' and resid 231 through 245 Processing helix chain 'P' and resid 281 through 285 Processing helix chain 'P' and resid 292 through 296 Processing helix chain 'P' and resid 307 through 316 Processing helix chain 'Q' and resid 51 through 69 removed outlier: 3.921A 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: 3.608A 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: 7.351A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.631A 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: 6.768A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.819A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.502A 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: 3.784A pdb=" N SER A 268 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 4.508A 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 Processing sheet with id=AA6, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 7.965A pdb=" N PHE A 486 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 6.700A 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: 6.932A 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: 4.140A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA A 418 " --> pdb=" O HIS A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AA9, first strand: chain 'A' and resid 617 through 620 Processing sheet with id=AB1, first strand: chain 'A' and resid 883 through 884 removed outlier: 6.905A pdb=" N VAL A 890 " --> pdb=" O ILE A 898 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1210 through 1216 removed outlier: 7.097A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 11.057A pdb=" N THR A1086 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR A1244 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN A1088 " --> pdb=" O LYS A1242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1108 through 1109 removed outlier: 3.919A pdb=" N GLN A1202 " --> pdb=" O THR A1108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1114 through 1121 removed outlier: 3.719A pdb=" N TYR A1116 " --> pdb=" O LYS A1131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1361 through 1364 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 65 removed outlier: 6.751A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA B 111 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG B 135 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 113 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 117 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASN B 129 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 119 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE B 127 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 86 through 87 removed outlier: 3.660A pdb=" N ARG B 95 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'B' and resid 360 through 363 removed outlier: 6.472A pdb=" N ILE B 180 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 189 through 193 Processing sheet with id=AC2, first strand: chain 'B' and resid 424 through 426 Processing sheet with id=AC3, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC4, first strand: chain 'B' and resid 501 through 502 Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 550 removed outlier: 5.414A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL B 583 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE B 540 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.608A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 712 removed outlier: 6.608A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL B 869 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 986 through 987 removed outlier: 7.320A pdb=" N LEU B 755 " --> pdb=" O GLY B 908 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 910 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 757 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE B 927 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 929 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR B1003 " --> pdb=" O VAL B 743 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AD1, first strand: chain 'B' and resid 795 through 796 removed outlier: 3.553A pdb=" N LYS B 801 " --> pdb=" O ASP B 796 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 826 through 828 removed outlier: 6.811A pdb=" N ILE B 856 " --> pdb=" O LEU B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 918 through 919 Processing sheet with id=AD4, first strand: chain 'B' and resid 1086 through 1087 removed outlier: 4.049A pdb=" N ASP B1078 " --> pdb=" O GLY B1087 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 21 through 22 removed outlier: 7.203A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 21 through 22 removed outlier: 6.701A pdb=" N HIS C 305 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 174 through 176 removed outlier: 4.313A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.699A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 167 through 169 removed outlier: 6.899A pdb=" N VAL C 168 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 240 through 241 removed outlier: 3.669A pdb=" N THR C 240 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 262 through 266 Processing sheet with id=AE3, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.598A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA D 6 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU G 4 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N HIS G 67 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA G 57 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LYS G 69 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU G 55 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.341A 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: 6.626A pdb=" N PHE G 49 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N PHE G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N CYS G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 58 through 63 removed outlier: 5.985A pdb=" N THR E 59 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N VAL E 74 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU E 61 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 63 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ASP E 70 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.648A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.652A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 105 through 108 removed outlier: 3.791A pdb=" N ASP G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 101 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE G 107 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N VAL G 99 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N HIS G 98 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 14 removed outlier: 6.910A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 13 through 16 Processing sheet with id=AF1, first strand: chain 'K' and resid 26 through 30 Processing sheet with id=AF2, first strand: chain 'M' and resid 10 through 17 removed outlier: 8.500A pdb=" N LEU M 124 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP M 14 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU M 126 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR M 16 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY N 327 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN M 11 " --> pdb=" O ILE N 331 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 25 through 34 removed outlier: 6.919A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG M 33 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 11.791A pdb=" N GLU N 359 " --> pdb=" O PRO M 31 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N VAL N 361 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 9.773A pdb=" N GLN M 29 " --> pdb=" O VAL N 361 " (cutoff:3.500A) removed outlier: 9.882A pdb=" N VAL N 363 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N LEU M 27 " --> pdb=" O VAL N 363 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 291 through 292 Processing sheet with id=AF5, first strand: chain 'M' and resid 365 through 366 Processing sheet with id=AF6, first strand: chain 'O' and resid 34 through 35 Processing sheet with id=AF7, first strand: chain 'O' and resid 157 through 159 Processing sheet with id=AF8, first strand: chain 'O' and resid 288 through 289 Processing sheet with id=AF9, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AG1, first strand: chain 'O' and resid 409 through 410 Processing sheet with id=AG2, first strand: chain 'P' and resid 63 through 68 Processing sheet with id=AG3, first strand: chain 'P' and resid 136 through 140 Processing sheet with id=AG4, first strand: chain 'P' and resid 211 through 212 Processing sheet with id=AG5, first strand: chain 'V' and resid 15 through 17 removed outlier: 6.472A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1906 hydrogen bonds defined for protein. 5397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 12.83 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 18633 1.42 - 1.64: 26482 1.64 - 1.85: 444 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 45571 Sorted by residual: bond pdb=" O3' DT Y -9 " pdb=" P DT Y -8 " ideal model delta sigma weight residual 1.607 1.424 0.183 1.50e-02 4.44e+03 1.49e+02 bond pdb=" P DT Y -8 " pdb=" OP1 DT Y -8 " ideal model delta sigma weight residual 1.480 1.268 0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C1' DG Y 1 " pdb=" N9 DG Y 1 " ideal model delta sigma weight residual 1.468 1.338 0.130 1.40e-02 5.10e+03 8.57e+01 bond pdb=" O3' DG Y -7 " pdb=" P DC Y -6 " ideal model delta sigma weight residual 1.607 1.729 -0.122 1.50e-02 4.44e+03 6.63e+01 bond pdb=" P DC Y -6 " pdb=" OP1 DC Y -6 " ideal model delta sigma weight residual 1.480 1.323 0.157 2.00e-02 2.50e+03 6.13e+01 ... (remaining 45566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.17: 61936 5.17 - 10.34: 53 10.34 - 15.51: 13 15.51 - 20.68: 5 20.68 - 25.85: 1 Bond angle restraints: 62008 Sorted by residual: angle pdb=" O2' C Z 4 " pdb=" C2' C Z 4 " pdb=" C1' C Z 4 " ideal model delta sigma weight residual 108.40 82.55 25.85 1.50e+00 4.44e-01 2.97e+02 angle pdb=" O4' DC Y -6 " pdb=" C4' DC Y -6 " pdb=" C3' DC Y -6 " ideal model delta sigma weight residual 106.00 97.41 8.59 6.00e-01 2.78e+00 2.05e+02 angle pdb=" O3' DC Y -6 " pdb=" P DG Y -5 " pdb=" O5' DG Y -5 " ideal model delta sigma weight residual 104.00 123.14 -19.14 1.50e+00 4.44e-01 1.63e+02 angle pdb=" O4' DG Y -5 " pdb=" C4' DG Y -5 " pdb=" C3' DG Y -5 " ideal model delta sigma weight residual 106.00 99.65 6.35 6.00e-01 2.78e+00 1.12e+02 angle pdb=" C4' DG Y -7 " pdb=" C3' DG Y -7 " pdb=" C2' DG Y -7 " ideal model delta sigma weight residual 103.10 94.07 9.03 9.00e-01 1.23e+00 1.01e+02 ... (remaining 62003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 27140 35.87 - 71.74: 588 71.74 - 107.61: 28 107.61 - 143.49: 3 143.49 - 179.36: 8 Dihedral angle restraints: 27767 sinusoidal: 12288 harmonic: 15479 Sorted by residual: dihedral pdb=" O3A GTP Z 101 " pdb=" O3B GTP Z 101 " pdb=" PB GTP Z 101 " pdb=" PG GTP Z 101 " ideal model delta sinusoidal sigma weight residual -56.21 -176.72 120.51 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" C8 GTP Z 101 " pdb=" C1' GTP Z 101 " pdb=" N9 GTP Z 101 " pdb=" O4' GTP Z 101 " ideal model delta sinusoidal sigma weight residual 104.59 -15.25 119.84 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" O3B GTP Z 101 " pdb=" O3A GTP Z 101 " pdb=" PB GTP Z 101 " pdb=" PA GTP Z 101 " ideal model delta sinusoidal sigma weight residual -68.92 -171.38 102.46 1 2.00e+01 2.50e-03 2.92e+01 ... (remaining 27764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 6671 0.100 - 0.199: 289 0.199 - 0.299: 10 0.299 - 0.399: 4 0.399 - 0.498: 4 Chirality restraints: 6978 Sorted by residual: chirality pdb=" P DC Y -6 " pdb=" OP1 DC Y -6 " pdb=" OP2 DC Y -6 " pdb=" O5' DC Y -6 " both_signs ideal model delta sigma weight residual True 2.34 -1.84 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" P DT Y -8 " pdb=" OP1 DT Y -8 " pdb=" OP2 DT Y -8 " pdb=" O5' DT Y -8 " both_signs ideal model delta sigma weight residual True 2.34 -1.87 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" C3' DC Y -6 " pdb=" C4' DC Y -6 " pdb=" O3' DC Y -6 " pdb=" C2' DC Y -6 " both_signs ideal model delta sigma weight residual False -2.73 -2.28 -0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 6975 not shown) Planarity restraints: 7603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG Y 1 " -0.080 2.00e-02 2.50e+03 2.98e-02 2.66e+01 pdb=" N9 DG Y 1 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DG Y 1 " 0.027 2.00e-02 2.50e+03 pdb=" N7 DG Y 1 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DG Y 1 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DG Y 1 " -0.013 2.00e-02 2.50e+03 pdb=" O6 DG Y 1 " -0.029 2.00e-02 2.50e+03 pdb=" N1 DG Y 1 " -0.011 2.00e-02 2.50e+03 pdb=" C2 DG Y 1 " 0.007 2.00e-02 2.50e+03 pdb=" N2 DG Y 1 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG Y 1 " 0.024 2.00e-02 2.50e+03 pdb=" C4 DG Y 1 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U Z 2 " -0.061 2.00e-02 2.50e+03 3.35e-02 2.53e+01 pdb=" N1 U Z 2 " 0.059 2.00e-02 2.50e+03 pdb=" C2 U Z 2 " -0.016 2.00e-02 2.50e+03 pdb=" O2 U Z 2 " 0.029 2.00e-02 2.50e+03 pdb=" N3 U Z 2 " -0.022 2.00e-02 2.50e+03 pdb=" C4 U Z 2 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U Z 2 " -0.004 2.00e-02 2.50e+03 pdb=" C5 U Z 2 " -0.015 2.00e-02 2.50e+03 pdb=" C6 U Z 2 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG Y -5 " -0.062 2.00e-02 2.50e+03 2.34e-02 1.64e+01 pdb=" N9 DG Y -5 " 0.029 2.00e-02 2.50e+03 pdb=" C8 DG Y -5 " 0.021 2.00e-02 2.50e+03 pdb=" N7 DG Y -5 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG Y -5 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG Y -5 " -0.011 2.00e-02 2.50e+03 pdb=" O6 DG Y -5 " -0.023 2.00e-02 2.50e+03 pdb=" N1 DG Y -5 " -0.009 2.00e-02 2.50e+03 pdb=" C2 DG Y -5 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG Y -5 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG Y -5 " 0.018 2.00e-02 2.50e+03 pdb=" C4 DG Y -5 " 0.016 2.00e-02 2.50e+03 ... (remaining 7600 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 61 2.32 - 2.97: 20206 2.97 - 3.61: 66173 3.61 - 4.26: 104083 4.26 - 4.90: 171169 Nonbonded interactions: 361692 Sorted by model distance: nonbonded pdb=" OG1 THR A 303 " pdb=" NE2 GLN O 377 " model vdw 1.680 3.120 nonbonded pdb=" NH2 ARG B 682 " pdb=" O1G 3AT B1202 " model vdw 1.852 2.496 nonbonded pdb=" O2' C Z 8 " pdb=" O4' 3AT B1202 " model vdw 1.960 3.040 nonbonded pdb=" O2 DT X 25 " pdb=" N2 DG Y -24 " model vdw 2.019 3.120 nonbonded pdb=" CE MET B 689 " pdb=" OP1 C Z 8 " model vdw 2.036 3.460 ... (remaining 361687 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 54.000 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 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:7.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 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 0.705 45599 Z= 0.456 Angle : 0.789 55.675 62047 Z= 0.411 Chirality : 0.045 0.498 6978 Planarity : 0.003 0.060 7603 Dihedral : 13.139 179.357 17763 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.96 % Allowed : 3.41 % Favored : 95.63 % 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: -1.04 (0.11), residues: 5269 helix: 0.34 (0.11), residues: 2046 sheet: -1.00 (0.18), residues: 698 loop : -1.43 (0.11), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 87 TYR 0.010 0.001 TYR A1116 PHE 0.007 0.001 PHE B1004 TRP 0.007 0.001 TRP P 313 HIS 0.002 0.000 HIS M 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.33 (45571) covalent geometry : angle 0.60682 / 0.40 (62008) hydrogen bonds : bond 0.14670 / 9.53 ( 1962) hydrogen bonds : angle 5.70118 / 4.02 ( 5559) metal coordination : bond 0.25549 / 14.08 ( 26) metal coordination : angle 20.11569 / 11.37 ( 39) Misc. bond : bond 0.36531 / 18.96 ( 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 1402 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 1357 time to evaluate : 1.890 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: A 39 LYS cc_start: 0.7639 (pttp) cc_final: 0.7393 (ptpt) REVERT: A 42 TYR cc_start: 0.6797 (m-80) cc_final: 0.6428 (m-80) REVERT: A 89 GLU cc_start: 0.6230 (mm-30) cc_final: 0.5538 (mt-10) REVERT: A 128 TYR cc_start: 0.7546 (t80) cc_final: 0.7266 (t80) REVERT: A 246 LYS cc_start: 0.5217 (mtmt) cc_final: 0.4762 (mtmm) REVERT: A 249 ASP cc_start: 0.6944 (m-30) cc_final: 0.6434 (m-30) REVERT: A 284 THR cc_start: 0.7541 (m) cc_final: 0.7057 (p) REVERT: A 308 GLU cc_start: 0.7633 (tp30) cc_final: 0.7425 (tt0) REVERT: A 379 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7129 (mt-10) REVERT: A 647 SER cc_start: 0.8120 (t) cc_final: 0.7129 (p) REVERT: A 722 LYS cc_start: 0.6622 (mtmt) cc_final: 0.6386 (ptmm) REVERT: A 755 GLU cc_start: 0.6473 (mm-30) cc_final: 0.5368 (tp30) REVERT: A 852 MET cc_start: 0.7353 (mtp) cc_final: 0.6453 (mtp) REVERT: A 896 ASP cc_start: 0.7534 (m-30) cc_final: 0.7267 (m-30) REVERT: A 915 LYS cc_start: 0.6940 (tptp) cc_final: 0.6559 (tptp) REVERT: A 917 GLU cc_start: 0.5561 (mm-30) cc_final: 0.5314 (mm-30) REVERT: A 947 LEU cc_start: 0.7833 (tt) cc_final: 0.7427 (mp) REVERT: A 954 LYS cc_start: 0.7489 (ptpt) cc_final: 0.7049 (mmtt) REVERT: A 962 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6810 (tt0) REVERT: A 1016 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6481 (tp30) REVERT: A 1026 GLN cc_start: 0.7595 (mt0) cc_final: 0.6938 (pp30) REVERT: A 1096 ASP cc_start: 0.7290 (t0) cc_final: 0.6997 (t70) REVERT: A 1115 GLU cc_start: 0.7162 (pt0) cc_final: 0.6914 (tm-30) REVERT: A 1135 GLU cc_start: 0.7407 (tp30) cc_final: 0.7188 (tp30) REVERT: A 1141 ARG cc_start: 0.7302 (mtt90) cc_final: 0.6918 (mtp85) REVERT: A 1185 MET cc_start: 0.7940 (pmm) cc_final: 0.7513 (pmt) REVERT: A 1215 ASP cc_start: 0.6412 (m-30) cc_final: 0.6197 (m-30) REVERT: A 1222 LYS cc_start: 0.7306 (pttt) cc_final: 0.6820 (ptpp) REVERT: A 1299 GLU cc_start: 0.7372 (tt0) cc_final: 0.7170 (pt0) REVERT: A 1334 PHE cc_start: 0.7857 (m-80) cc_final: 0.7517 (m-80) REVERT: A 1367 ASP cc_start: 0.7775 (t0) cc_final: 0.7409 (t70) REVERT: B 55 ILE cc_start: 0.7581 (tt) cc_final: 0.7097 (OUTLIER) REVERT: B 64 LYS cc_start: 0.6812 (ttmt) cc_final: 0.5949 (ttmm) REVERT: B 107 MET cc_start: 0.7663 (ptp) cc_final: 0.7415 (ptt) REVERT: B 139 MET cc_start: 0.8423 (ttm) cc_final: 0.8125 (ttm) REVERT: B 222 ARG cc_start: 0.7071 (ptp90) cc_final: 0.6784 (pmm-80) REVERT: B 413 ASN cc_start: 0.7621 (m-40) cc_final: 0.7261 (m-40) REVERT: B 417 ASN cc_start: 0.8231 (m-40) cc_final: 0.7970 (m-40) REVERT: B 423 ASN cc_start: 0.6529 (p0) cc_final: 0.6205 (m-40) REVERT: B 506 MET cc_start: 0.8592 (mpp) cc_final: 0.8087 (mmt) REVERT: B 557 ASN cc_start: 0.7858 (m-40) cc_final: 0.7587 (m-40) REVERT: B 581 ARG cc_start: 0.6518 (mtm110) cc_final: 0.6245 (mtp-110) REVERT: B 586 SER cc_start: 0.8221 (m) cc_final: 0.7888 (t) REVERT: B 609 LYS cc_start: 0.8360 (tmmt) cc_final: 0.7935 (tmmt) REVERT: B 623 ASP cc_start: 0.8687 (m-30) cc_final: 0.8428 (m-30) REVERT: B 729 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7531 (mm-30) REVERT: B 819 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7079 (mt-10) REVERT: B 822 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7811 (mm-30) REVERT: B 870 MET cc_start: 0.8122 (ttp) cc_final: 0.7794 (ttp) REVERT: B 904 LYS cc_start: 0.8005 (pttt) cc_final: 0.7772 (pttm) REVERT: B 1030 VAL cc_start: 0.8665 (t) cc_final: 0.8425 (p) REVERT: B 1037 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6667 (mt-10) REVERT: B 1105 ARG cc_start: 0.7335 (mmm160) cc_final: 0.6919 (ttt-90) REVERT: C 98 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7716 (p) REVERT: C 296 VAL cc_start: 0.9004 (m) cc_final: 0.8792 (p) REVERT: C 311 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6513 (mt-10) REVERT: C 316 LEU cc_start: 0.8040 (pt) cc_final: 0.7200 (mt) REVERT: D 1 MET cc_start: 0.4986 (mmp) cc_final: 0.4527 (mmm) REVERT: D 24 LYS cc_start: 0.6344 (tttt) cc_final: 0.5763 (tptm) REVERT: D 47 TYR cc_start: 0.7185 (t80) cc_final: 0.6955 (t80) REVERT: D 68 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7742 (tp30) REVERT: D 82 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6644 (mm-30) REVERT: E 19 GLN cc_start: 0.7339 (mt0) cc_final: 0.6771 (mm-40) REVERT: E 49 SER cc_start: 0.7551 (p) cc_final: 0.7336 (m) REVERT: E 52 ARG cc_start: 0.4899 (mtp85) cc_final: 0.4663 (ttm170) REVERT: E 73 PHE cc_start: 0.6068 (t80) cc_final: 0.4918 (t80) REVERT: E 74 VAL cc_start: 0.6861 (t) cc_final: 0.6350 (p) REVERT: E 78 GLU cc_start: 0.7453 (tt0) cc_final: 0.7237 (mm-30) REVERT: E 88 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7313 (mmmm) REVERT: E 92 GLN cc_start: 0.7527 (pp30) cc_final: 0.7292 (pt0) REVERT: E 104 ILE cc_start: 0.6932 (mt) cc_final: 0.6626 (mp) REVERT: E 124 LYS cc_start: 0.7860 (ptpp) cc_final: 0.7620 (pmtt) REVERT: E 139 ILE cc_start: 0.7729 (mt) cc_final: 0.7388 (tt) REVERT: E 189 GLN cc_start: 0.7873 (mt0) cc_final: 0.7626 (mt0) REVERT: E 192 LYS cc_start: 0.7391 (ttpt) cc_final: 0.7029 (tttt) REVERT: F 94 MET cc_start: 0.8051 (mtt) cc_final: 0.7652 (mtp) REVERT: F 98 LYS cc_start: 0.8092 (ttpp) cc_final: 0.7614 (ttmm) REVERT: F 124 ILE cc_start: 0.7965 (mt) cc_final: 0.7741 (mt) REVERT: G 17 GLN cc_start: 0.8067 (mt0) cc_final: 0.7733 (mt0) REVERT: G 28 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7107 (tt0) REVERT: G 53 LYS cc_start: 0.6936 (tptt) cc_final: 0.6522 (tptm) REVERT: G 69 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7823 (tttp) REVERT: G 89 ILE cc_start: 0.7045 (mm) cc_final: 0.6715 (OUTLIER) REVERT: H 7 GLU cc_start: 0.8146 (tt0) cc_final: 0.7939 (tt0) REVERT: H 55 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7605 (ttmm) REVERT: H 89 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7602 (mt-10) REVERT: H 136 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6768 (mt-10) REVERT: H 147 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8382 (mtmt) REVERT: J 41 LYS cc_start: 0.7733 (mttp) cc_final: 0.7058 (tmmt) REVERT: J 54 ASP cc_start: 0.7195 (t0) cc_final: 0.6985 (t0) REVERT: K 50 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7382 (t) REVERT: K 112 ASP cc_start: 0.7584 (m-30) cc_final: 0.7253 (m-30) REVERT: K 119 LYS cc_start: 0.6674 (ttpp) cc_final: 0.6463 (tttt) REVERT: L 22 CYS cc_start: 0.7198 (m) cc_final: 0.6032 (t) REVERT: M 105 SER cc_start: 0.6435 (t) cc_final: 0.6076 (p) REVERT: M 111 THR cc_start: 0.6925 (p) cc_final: 0.6644 (p) REVERT: M 190 VAL cc_start: 0.4789 (t) cc_final: 0.4426 (m) REVERT: M 210 TYR cc_start: 0.5943 (t80) cc_final: 0.5708 (t80) REVERT: M 220 HIS cc_start: 0.6331 (t-90) cc_final: 0.6117 (t-90) REVERT: M 286 MET cc_start: 0.5077 (mmm) cc_final: 0.4757 (mmm) REVERT: M 389 MET cc_start: 0.4139 (ptp) cc_final: 0.3480 (ptt) REVERT: N 152 LYS cc_start: 0.5447 (ptpt) cc_final: 0.5108 (ptpt) REVERT: N 271 LEU cc_start: 0.8133 (mt) cc_final: 0.7876 (pp) REVERT: N 328 LYS cc_start: 0.6908 (mtpp) cc_final: 0.6146 (mmtm) REVERT: N 372 GLU cc_start: 0.5343 (mt-10) cc_final: 0.4739 (mt-10) REVERT: O 61 ASN cc_start: 0.8023 (t0) cc_final: 0.7654 (t0) REVERT: O 85 MET cc_start: 0.7017 (ttm) cc_final: 0.6812 (ttt) REVERT: O 146 ASN cc_start: 0.8034 (m-40) cc_final: 0.7745 (m110) REVERT: O 186 ASP cc_start: 0.5320 (p0) cc_final: 0.4243 (m-30) REVERT: O 245 HIS cc_start: 0.7917 (t70) cc_final: 0.7673 (t70) REVERT: O 268 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6619 (ttp80) REVERT: O 273 MET cc_start: 0.7485 (mmp) cc_final: 0.7241 (mtp) REVERT: O 294 PHE cc_start: 0.7246 (t80) cc_final: 0.6926 (t80) REVERT: O 336 ILE cc_start: 0.5146 (mp) cc_final: 0.4874 (mt) REVERT: O 340 LYS cc_start: 0.6883 (mmmt) cc_final: 0.6581 (mtmm) REVERT: O 362 CYS cc_start: 0.7556 (t) cc_final: 0.7209 (t) REVERT: O 422 TYR cc_start: 0.7566 (m-80) cc_final: 0.6774 (m-80) REVERT: O 456 GLU cc_start: 0.7301 (pt0) cc_final: 0.6985 (pp20) REVERT: O 503 LYS cc_start: 0.7630 (ttmm) cc_final: 0.7343 (tmtp) REVERT: O 524 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6745 (tm-30) REVERT: O 531 MET cc_start: 0.5059 (mtm) cc_final: 0.4808 (mtm) REVERT: P 292 VAL cc_start: 0.7055 (p) cc_final: 0.6393 (t) REVERT: P 297 HIS cc_start: 0.6923 (t70) cc_final: 0.6483 (t-170) REVERT: Q 43 TYR cc_start: 0.6695 (m-80) cc_final: 0.6168 (m-80) REVERT: Q 64 LEU cc_start: 0.8654 (mt) cc_final: 0.8345 (mt) REVERT: Q 77 THR cc_start: 0.6804 (OUTLIER) cc_final: 0.6221 (m) outliers start: 45 outliers final: 18 residues processed: 1388 average time/residue: 0.7906 time to fit residues: 1350.3124 Evaluate side-chains 826 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 807 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 40.0000 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN A 119 GLN A 217 ASN A 225 ASN A 419 ASN A 423 GLN A 469 HIS A 599 GLN A 732 ASN A 739 GLN A 872 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN A1213 HIS A1239 HIS A1278 HIS B 43 HIS B 100 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 GLN B 260 HIS B 390 GLN B 472 GLN B 959 HIS B 982 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 GLN B1132 ASN C 139 GLN C 201 GLN C 277 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN E 168 ASN G 41 ASN G 115 GLN H 29 HIS H 46 GLN I 40 ASN K 81 ASN M 68 ASN M 134 GLN M 197 GLN M 341 HIS O 60 HIS O 158 GLN O 261 GLN O 475 GLN O 497 GLN O 507 ASN P 182 GLN P 201 ASN P 205 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.203288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126734 restraints weight = 53982.922| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.44 r_work: 0.3155 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 45599 Z= 0.309 Angle : 0.783 26.507 62047 Z= 0.390 Chirality : 0.051 0.287 6978 Planarity : 0.006 0.079 7603 Dihedral : 16.352 176.780 7074 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.62 % Favored : 96.36 % Rotamer: Outliers : 4.79 % Allowed : 12.97 % Favored : 82.24 % 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: 0.94 (0.11), residues: 2040 sheet: -0.65 (0.18), residues: 724 loop : -1.10 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A1136 TYR 0.039 0.003 TYR O 99 PHE 0.034 0.003 PHE A 462 TRP 0.021 0.002 TRP C 175 HIS 0.023 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.31 (45571) covalent geometry : angle 0.75070 / 0.39 (62008) hydrogen bonds : bond 0.04811 / 3.19 ( 1962) hydrogen bonds : angle 4.77353 / 3.38 ( 5559) metal coordination : bond 0.02647 / 1.52 ( 26) metal coordination : angle 8.89556 / 4.80 ( 39) Misc. bond : bond 0.03250 / 1.66 ( 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 1039 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 814 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8404 (pttp) cc_final: 0.8027 (ptpt) REVERT: A 65 LYS cc_start: 0.7968 (tptp) cc_final: 0.7621 (tttm) REVERT: A 75 ASN cc_start: 0.8131 (p0) cc_final: 0.7647 (OUTLIER) REVERT: A 76 LEU cc_start: 0.8771 (tp) cc_final: 0.8489 (tm) REVERT: A 78 ASP cc_start: 0.8288 (m-30) cc_final: 0.7848 (m-30) REVERT: A 85 TYR cc_start: 0.8399 (p90) cc_final: 0.7642 (p90) REVERT: A 107 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7152 (mpp) REVERT: A 124 GLN cc_start: 0.6811 (tt0) cc_final: 0.6536 (tm-30) REVERT: A 128 TYR cc_start: 0.7643 (t80) cc_final: 0.7407 (t80) REVERT: A 146 ILE cc_start: 0.8722 (mt) cc_final: 0.8459 (mt) REVERT: A 216 GLU cc_start: 0.8129 (tt0) cc_final: 0.7718 (tt0) REVERT: A 246 LYS cc_start: 0.6708 (mtmt) cc_final: 0.6159 (mtmm) REVERT: A 249 ASP cc_start: 0.8411 (m-30) cc_final: 0.8025 (m-30) REVERT: A 284 THR cc_start: 0.8575 (m) cc_final: 0.8066 (p) REVERT: A 428 MET cc_start: 0.8192 (ppp) cc_final: 0.7740 (ppp) REVERT: A 445 LYS cc_start: 0.8286 (mmpt) cc_final: 0.7742 (mtpt) REVERT: A 544 ASP cc_start: 0.8462 (t70) cc_final: 0.8235 (t0) REVERT: A 722 LYS cc_start: 0.7735 (mtmt) cc_final: 0.7454 (mtpm) REVERT: A 755 GLU cc_start: 0.7618 (mm-30) cc_final: 0.6930 (tp30) REVERT: A 770 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: A 852 MET cc_start: 0.9195 (mtp) cc_final: 0.8682 (mtp) REVERT: A 856 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7473 (mm-30) REVERT: A 867 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7626 (tp30) REVERT: A 947 LEU cc_start: 0.8611 (tt) cc_final: 0.8243 (mm) REVERT: A 954 LYS cc_start: 0.7731 (ptpt) cc_final: 0.7152 (mmtt) REVERT: A 978 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7832 (mm-30) REVERT: A 979 LYS cc_start: 0.8091 (mptt) cc_final: 0.7781 (mtmm) REVERT: A 996 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7290 (tp30) REVERT: A 1026 GLN cc_start: 0.8516 (mt0) cc_final: 0.8248 (pp30) REVERT: A 1094 ASP cc_start: 0.8061 (t70) cc_final: 0.7556 (t0) REVERT: A 1115 GLU cc_start: 0.7341 (pt0) cc_final: 0.7076 (tm-30) REVERT: A 1135 GLU cc_start: 0.7534 (tp30) cc_final: 0.7278 (tp30) REVERT: A 1141 ARG cc_start: 0.7750 (mtt90) cc_final: 0.7318 (mtp85) REVERT: A 1222 LYS cc_start: 0.7490 (pttt) cc_final: 0.7094 (ptpp) REVERT: A 1245 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8110 (mpt180) REVERT: A 1288 MET cc_start: 0.9247 (mtp) cc_final: 0.9038 (mtp) REVERT: A 1294 MET cc_start: 0.9239 (mtm) cc_final: 0.8976 (mtm) REVERT: A 1323 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7709 (mtmm) REVERT: A 1374 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7732 (mttm) REVERT: B 28 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8396 (mpt90) REVERT: B 39 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8533 (mm) REVERT: B 60 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8131 (ptpp) REVERT: B 64 LYS cc_start: 0.6844 (ttmt) cc_final: 0.5944 (ttmm) REVERT: B 84 LEU cc_start: 0.8343 (mt) cc_final: 0.8124 (mm) REVERT: B 136 MET cc_start: 0.9077 (tpp) cc_final: 0.8630 (tpp) REVERT: B 139 MET cc_start: 0.9447 (ttm) cc_final: 0.8826 (ttm) REVERT: B 171 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9076 (t) REVERT: B 183 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: B 223 PHE cc_start: 0.8402 (m-80) cc_final: 0.8154 (m-80) REVERT: B 232 GLU cc_start: 0.7563 (tt0) cc_final: 0.7306 (tt0) REVERT: B 282 GLN cc_start: 0.8409 (mt0) cc_final: 0.8203 (mt0) REVERT: B 328 PHE cc_start: 0.8212 (m-80) cc_final: 0.7303 (m-80) REVERT: B 332 CYS cc_start: 0.8832 (m) cc_final: 0.8602 (m) REVERT: B 409 ASP cc_start: 0.8232 (m-30) cc_final: 0.7866 (m-30) REVERT: B 413 ASN cc_start: 0.8299 (m-40) cc_final: 0.7876 (m-40) REVERT: B 431 MET cc_start: 0.7453 (ptm) cc_final: 0.6478 (ppp) REVERT: B 451 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.7913 (ttp) REVERT: B 506 MET cc_start: 0.9213 (mpp) cc_final: 0.8475 (mmt) REVERT: B 526 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7505 (pt) REVERT: B 719 MET cc_start: 0.9437 (mmm) cc_final: 0.9191 (mmm) REVERT: B 729 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8773 (mm-30) REVERT: B 753 ASP cc_start: 0.8571 (m-30) cc_final: 0.8295 (m-30) REVERT: B 857 THR cc_start: 0.8496 (t) cc_final: 0.8232 (t) REVERT: B 859 LYS cc_start: 0.8972 (mptt) cc_final: 0.8543 (mmtm) REVERT: B 870 MET cc_start: 0.9222 (ttp) cc_final: 0.8857 (ttp) REVERT: B 929 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8230 (ptm) REVERT: B 957 ARG cc_start: 0.8261 (mtm110) cc_final: 0.7936 (mtm110) REVERT: B 960 TYR cc_start: 0.9119 (m-80) cc_final: 0.8821 (m-80) REVERT: B 1015 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.8911 (mtp) REVERT: C 56 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8313 (ttm) REVERT: C 64 ASP cc_start: 0.8794 (m-30) cc_final: 0.8583 (m-30) REVERT: C 271 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7756 (mtmm) REVERT: D 22 ASP cc_start: 0.7927 (m-30) cc_final: 0.7584 (m-30) REVERT: D 47 TYR cc_start: 0.7479 (t80) cc_final: 0.7190 (t80) REVERT: D 68 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7735 (tp30) REVERT: D 82 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6922 (mm-30) REVERT: D 100 MET cc_start: 0.4242 (mmm) cc_final: 0.3402 (mtt) REVERT: E 70 ASP cc_start: 0.5316 (t0) cc_final: 0.4678 (p0) REVERT: E 71 GLN cc_start: 0.6950 (OUTLIER) cc_final: 0.6680 (mm-40) REVERT: E 72 MET cc_start: 0.7399 (ttt) cc_final: 0.7069 (ttt) REVERT: E 85 LYS cc_start: 0.8340 (pmtt) cc_final: 0.8025 (ptpp) REVERT: E 88 LYS cc_start: 0.8070 (mmtt) cc_final: 0.7851 (mmmm) REVERT: E 104 ILE cc_start: 0.8160 (mt) cc_final: 0.7870 (mp) REVERT: E 124 LYS cc_start: 0.8009 (ptpp) cc_final: 0.7809 (pmtt) REVERT: E 168 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8517 (p0) REVERT: E 172 ARG cc_start: 0.8872 (mmt90) cc_final: 0.8509 (mmt90) REVERT: F 51 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.4805 (mmp-170) REVERT: F 68 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8900 (m) REVERT: F 86 GLU cc_start: 0.8059 (tp30) cc_final: 0.7845 (tp30) REVERT: F 98 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8534 (ttmm) REVERT: G 28 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8023 (tt0) REVERT: G 33 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8531 (ttpp) REVERT: G 53 LYS cc_start: 0.7890 (tptt) cc_final: 0.7597 (tptm) REVERT: G 89 ILE cc_start: 0.7115 (mm) cc_final: 0.6640 (OUTLIER) REVERT: H 75 TYR cc_start: 0.6694 (t80) cc_final: 0.5893 (t80) REVERT: H 124 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.7417 (ttp80) REVERT: I 51 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6820 (m-30) REVERT: J 54 ASP cc_start: 0.8480 (t0) cc_final: 0.7961 (t70) REVERT: K 98 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8670 (ttp80) REVERT: K 102 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8513 (mt-10) REVERT: K 112 ASP cc_start: 0.8626 (m-30) cc_final: 0.8421 (m-30) REVERT: K 119 LYS cc_start: 0.8300 (ttpp) cc_final: 0.8091 (ttpp) REVERT: K 123 ASP cc_start: 0.8156 (m-30) cc_final: 0.7848 (m-30) REVERT: L 51 ARG cc_start: 0.8722 (mtm180) cc_final: 0.8453 (mtm110) REVERT: M 105 SER cc_start: 0.7165 (t) cc_final: 0.6850 (p) REVERT: M 189 ARG cc_start: 0.5648 (ttp80) cc_final: 0.5414 (ttp80) REVERT: M 286 MET cc_start: 0.4079 (mmm) cc_final: 0.3812 (mmm) REVERT: M 389 MET cc_start: 0.2645 (ptp) cc_final: 0.2223 (ptt) REVERT: N 152 LYS cc_start: 0.5604 (ptpt) cc_final: 0.5264 (ptpt) REVERT: N 253 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5589 (tt0) REVERT: N 328 LYS cc_start: 0.7432 (mtpp) cc_final: 0.7085 (mmtm) REVERT: N 333 LYS cc_start: 0.6624 (mmmt) cc_final: 0.6286 (mttm) REVERT: N 343 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6121 (mmmm) REVERT: O 61 ASN cc_start: 0.8029 (t0) cc_final: 0.7549 (t0) REVERT: O 68 HIS cc_start: 0.4935 (m-70) cc_final: 0.4616 (m90) REVERT: O 73 VAL cc_start: 0.7390 (OUTLIER) cc_final: 0.7071 (t) REVERT: O 85 MET cc_start: 0.7164 (ttm) cc_final: 0.6937 (ttt) REVERT: O 146 ASN cc_start: 0.7911 (m-40) cc_final: 0.7694 (m110) REVERT: O 186 ASP cc_start: 0.5518 (p0) cc_final: 0.4660 (m-30) REVERT: O 273 MET cc_start: 0.7390 (mmp) cc_final: 0.7003 (mtp) REVERT: O 275 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7113 (pt0) REVERT: O 340 LYS cc_start: 0.7265 (mmmt) cc_final: 0.6749 (mtmm) REVERT: O 422 TYR cc_start: 0.7343 (m-80) cc_final: 0.6920 (m-80) REVERT: O 456 GLU cc_start: 0.7282 (pt0) cc_final: 0.6971 (pp20) REVERT: O 503 LYS cc_start: 0.7318 (ttmm) cc_final: 0.7109 (tmtp) REVERT: P 230 LEU cc_start: 0.4824 (OUTLIER) cc_final: 0.4331 (tt) REVERT: Q 43 TYR cc_start: 0.7131 (m-80) cc_final: 0.6483 (m-80) REVERT: Q 54 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: Q 73 TYR cc_start: 0.7508 (m-10) cc_final: 0.7035 (m-10) REVERT: Q 76 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.5520 (pp20) REVERT: Q 110 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6156 (mpp) REVERT: Q 111 MET cc_start: 0.5663 (tpp) cc_final: 0.5388 (tpp) outliers start: 225 outliers final: 84 residues processed: 947 average time/residue: 0.7452 time to fit residues: 870.6317 Evaluate side-chains 798 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 689 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1015 MET Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 24 LYS Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 77 ILE Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 247 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain Q residue 33 LYS Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 380 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 284 optimal weight: 5.9990 chunk 496 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 337 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 398 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN A 219 ASN A 314 GLN A 528 ASN A 732 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN A1213 HIS B 784 ASN B 930 ASN C 96 ASN C 290 ASN D 76 HIS D 112 GLN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN M 68 ASN N 378 HIS O 168 ASN ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.203612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124887 restraints weight = 53436.470| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.47 r_work: 0.3149 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45599 Z= 0.146 Angle : 0.602 20.040 62047 Z= 0.300 Chirality : 0.044 0.300 6978 Planarity : 0.004 0.064 7603 Dihedral : 16.142 177.811 7052 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.05 % Allowed : 15.52 % Favored : 80.43 % 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: 0.04 (0.11), residues: 5269 helix: 1.34 (0.11), residues: 2060 sheet: -0.42 (0.19), residues: 690 loop : -0.95 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG L 42 TYR 0.019 0.001 TYR B 988 PHE 0.018 0.001 PHE A1191 TRP 0.013 0.001 TRP P 108 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (45571) covalent geometry : angle 0.57753 / 0.30 (62008) hydrogen bonds : bond 0.03950 / 2.59 ( 1962) hydrogen bonds : angle 4.49563 / 3.19 ( 5559) metal coordination : bond 0.00703 / 0.35 ( 26) metal coordination : angle 6.73190 / 3.83 ( 39) Misc. bond : bond 0.00759 / 0.36 ( 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 914 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 724 time to evaluate : 1.784 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: A 39 LYS cc_start: 0.8487 (pttp) cc_final: 0.8062 (ptpt) REVERT: A 65 LYS cc_start: 0.8092 (tptp) cc_final: 0.7591 (ttpt) REVERT: A 75 ASN cc_start: 0.8170 (p0) cc_final: 0.7681 (p0) REVERT: A 76 LEU cc_start: 0.8812 (tp) cc_final: 0.8579 (tm) REVERT: A 78 ASP cc_start: 0.8301 (m-30) cc_final: 0.7879 (m-30) REVERT: A 107 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.6998 (mpp) REVERT: A 111 THR cc_start: 0.7835 (m) cc_final: 0.7580 (p) REVERT: A 124 GLN cc_start: 0.6840 (tt0) cc_final: 0.6580 (tm-30) REVERT: A 128 TYR cc_start: 0.7619 (t80) cc_final: 0.7414 (t80) REVERT: A 216 GLU cc_start: 0.7900 (tt0) cc_final: 0.7539 (tt0) REVERT: A 270 LEU cc_start: 0.1890 (OUTLIER) cc_final: 0.1580 (pp) REVERT: A 284 THR cc_start: 0.8609 (m) cc_final: 0.8140 (p) REVERT: A 339 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7007 (ttm-80) REVERT: A 348 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8073 (tppt) REVERT: A 398 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8350 (mtmm) REVERT: A 428 MET cc_start: 0.8123 (ppp) cc_final: 0.7620 (pp-130) REVERT: A 544 ASP cc_start: 0.8114 (t70) cc_final: 0.7886 (t0) REVERT: A 722 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7628 (mtpm) REVERT: A 755 GLU cc_start: 0.7572 (mm-30) cc_final: 0.6874 (tp30) REVERT: A 760 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7129 (ttt-90) REVERT: A 770 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8142 (tp30) REVERT: A 852 MET cc_start: 0.9182 (mtp) cc_final: 0.8616 (mtp) REVERT: A 856 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 947 LEU cc_start: 0.8654 (tt) cc_final: 0.8259 (mm) REVERT: A 954 LYS cc_start: 0.7809 (ptpt) cc_final: 0.7173 (mmtt) REVERT: A 978 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7845 (mm-30) REVERT: A 979 LYS cc_start: 0.8091 (mptt) cc_final: 0.7722 (mtmt) REVERT: A 1026 GLN cc_start: 0.8521 (mt0) cc_final: 0.8119 (pp30) REVERT: A 1061 MET cc_start: 0.6908 (ptp) cc_final: 0.6352 (ptp) REVERT: A 1115 GLU cc_start: 0.7301 (pt0) cc_final: 0.6827 (tm-30) REVERT: A 1118 GLU cc_start: 0.7061 (pt0) cc_final: 0.6844 (pt0) REVERT: A 1135 GLU cc_start: 0.7636 (tp30) cc_final: 0.7376 (tp30) REVERT: A 1141 ARG cc_start: 0.7779 (mtt90) cc_final: 0.7367 (mtp85) REVERT: A 1189 LEU cc_start: 0.8015 (tp) cc_final: 0.7741 (tm) REVERT: A 1245 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8079 (mpt180) REVERT: A 1323 LYS cc_start: 0.7972 (mtpt) cc_final: 0.7633 (mtmm) REVERT: B 25 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8033 (tp30) REVERT: B 28 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8288 (mpt90) REVERT: B 64 LYS cc_start: 0.6843 (ttmt) cc_final: 0.6001 (ttmm) REVERT: B 136 MET cc_start: 0.9094 (tpp) cc_final: 0.8616 (tpt) REVERT: B 139 MET cc_start: 0.9481 (ttm) cc_final: 0.8880 (ttm) REVERT: B 232 GLU cc_start: 0.7641 (tt0) cc_final: 0.7379 (tt0) REVERT: B 282 GLN cc_start: 0.8425 (mt0) cc_final: 0.8214 (mt0) REVERT: B 328 PHE cc_start: 0.8394 (m-80) cc_final: 0.7505 (m-80) REVERT: B 409 ASP cc_start: 0.8250 (m-30) cc_final: 0.7909 (m-30) REVERT: B 413 ASN cc_start: 0.8238 (m-40) cc_final: 0.7951 (m-40) REVERT: B 451 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.7641 (ttp) REVERT: B 506 MET cc_start: 0.9248 (mpp) cc_final: 0.8456 (mmt) REVERT: B 613 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7997 (mt-10) REVERT: B 697 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9122 (mm) REVERT: B 719 MET cc_start: 0.9428 (mmm) cc_final: 0.9146 (mmm) REVERT: B 729 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8753 (mm-30) REVERT: B 753 ASP cc_start: 0.8593 (m-30) cc_final: 0.8288 (m-30) REVERT: B 781 ARG cc_start: 0.7476 (mmt90) cc_final: 0.6726 (mmt180) REVERT: B 859 LYS cc_start: 0.8975 (mptt) cc_final: 0.8436 (mmtm) REVERT: B 870 MET cc_start: 0.9157 (ttp) cc_final: 0.8866 (ttp) REVERT: B 930 ASN cc_start: 0.9040 (t0) cc_final: 0.8599 (t0) REVERT: B 957 ARG cc_start: 0.8323 (mtm110) cc_final: 0.8100 (mtm-85) REVERT: C 11 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.7954 (ptp-170) REVERT: C 56 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8400 (ttm) REVERT: C 64 ASP cc_start: 0.8762 (m-30) cc_final: 0.8521 (m-30) REVERT: D 10 LEU cc_start: 0.8031 (mt) cc_final: 0.7783 (mm) REVERT: D 47 TYR cc_start: 0.7451 (t80) cc_final: 0.7156 (t80) REVERT: D 68 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7730 (tp30) REVERT: D 82 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6898 (mm-30) REVERT: D 100 MET cc_start: 0.4216 (mmm) cc_final: 0.3227 (mtt) REVERT: D 116 LEU cc_start: 0.7238 (mt) cc_final: 0.6874 (pp) REVERT: E 70 ASP cc_start: 0.5465 (t0) cc_final: 0.5067 (p0) REVERT: E 71 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6677 (mm-40) REVERT: E 120 ASP cc_start: 0.7753 (p0) cc_final: 0.7534 (p0) REVERT: E 124 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7729 (pmtt) REVERT: E 202 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7229 (mtm180) REVERT: F 51 ARG cc_start: 0.7265 (mtm-85) cc_final: 0.4819 (mmp-170) REVERT: F 86 GLU cc_start: 0.8143 (tp30) cc_final: 0.7863 (tp30) REVERT: F 98 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8513 (ttmm) REVERT: G 28 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7902 (tt0) REVERT: G 29 GLU cc_start: 0.8398 (tp30) cc_final: 0.7997 (mp0) REVERT: G 33 LYS cc_start: 0.8719 (ttmm) cc_final: 0.8484 (ttpp) REVERT: G 53 LYS cc_start: 0.7815 (tptt) cc_final: 0.7431 (tptm) REVERT: G 89 ILE cc_start: 0.7271 (mm) cc_final: 0.6760 (OUTLIER) REVERT: H 75 TYR cc_start: 0.6485 (t80) cc_final: 0.5924 (t80) REVERT: H 81 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.6522 (ttt180) REVERT: H 124 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.7237 (ttp80) REVERT: I 48 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7627 (mm-30) REVERT: I 51 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6678 (m-30) REVERT: J 54 ASP cc_start: 0.8552 (t0) cc_final: 0.8348 (t70) REVERT: K 98 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8659 (ttp80) REVERT: K 119 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8139 (ttpp) REVERT: K 123 ASP cc_start: 0.8188 (m-30) cc_final: 0.7850 (m-30) REVERT: L 44 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8566 (mmt) REVERT: M 24 LYS cc_start: 0.6703 (mttp) cc_final: 0.6296 (mtpt) REVERT: M 42 ILE cc_start: 0.7917 (mt) cc_final: 0.7686 (mp) REVERT: M 97 MET cc_start: 0.6497 (ttt) cc_final: 0.5985 (ttp) REVERT: M 105 SER cc_start: 0.6999 (t) cc_final: 0.6684 (p) REVERT: M 189 ARG cc_start: 0.5441 (ttp80) cc_final: 0.5183 (ttp80) REVERT: M 286 MET cc_start: 0.3965 (mmm) cc_final: 0.3642 (mmm) REVERT: M 389 MET cc_start: 0.2399 (ptp) cc_final: 0.2014 (ptt) REVERT: N 142 LYS cc_start: 0.3128 (OUTLIER) cc_final: 0.2179 (ttpp) REVERT: N 152 LYS cc_start: 0.5568 (ptpt) cc_final: 0.5249 (ptpt) REVERT: N 328 LYS cc_start: 0.7304 (mtpp) cc_final: 0.7040 (mmtm) REVERT: N 333 LYS cc_start: 0.6727 (mmmt) cc_final: 0.6401 (mttt) REVERT: N 343 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6204 (mmmm) REVERT: N 347 ASP cc_start: 0.6455 (p0) cc_final: 0.6111 (t0) REVERT: N 390 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7060 (tp30) REVERT: O 61 ASN cc_start: 0.7944 (t0) cc_final: 0.7456 (t0) REVERT: O 85 MET cc_start: 0.7099 (ttm) cc_final: 0.6864 (ttt) REVERT: O 146 ASN cc_start: 0.7870 (m-40) cc_final: 0.7662 (m110) REVERT: O 186 ASP cc_start: 0.5542 (p0) cc_final: 0.4756 (m-30) REVERT: O 258 ARG cc_start: 0.6726 (OUTLIER) cc_final: 0.4858 (tpp-160) REVERT: O 273 MET cc_start: 0.7458 (mmp) cc_final: 0.7104 (mtp) REVERT: O 275 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7101 (pt0) REVERT: O 340 LYS cc_start: 0.7252 (mmmt) cc_final: 0.6715 (mtmm) REVERT: O 422 TYR cc_start: 0.7536 (m-80) cc_final: 0.7031 (m-80) REVERT: O 456 GLU cc_start: 0.7399 (pt0) cc_final: 0.7071 (pp20) REVERT: O 459 ARG cc_start: 0.7030 (tpp-160) cc_final: 0.6527 (mtm110) REVERT: O 503 LYS cc_start: 0.7326 (ttmm) cc_final: 0.7126 (tmtp) REVERT: O 524 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7163 (tm-30) REVERT: P 85 MET cc_start: 0.0610 (mpp) cc_final: -0.0983 (ppp) REVERT: P 230 LEU cc_start: 0.4803 (OUTLIER) cc_final: 0.4459 (tt) REVERT: P 267 MET cc_start: 0.4868 (mmm) cc_final: 0.4653 (mmp) REVERT: P 276 ILE cc_start: 0.7306 (mt) cc_final: 0.6935 (mt) REVERT: P 292 VAL cc_start: 0.7235 (p) cc_final: 0.6652 (t) REVERT: Q 43 TYR cc_start: 0.7193 (m-80) cc_final: 0.6524 (m-80) REVERT: Q 54 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.5932 (mp0) REVERT: Q 70 ARG cc_start: 0.7147 (ptp-110) cc_final: 0.6917 (ptp-110) REVERT: Q 73 TYR cc_start: 0.7578 (m-10) cc_final: 0.7199 (m-10) REVERT: Q 76 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5606 (pp20) REVERT: Q 109 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7054 (mt-10) REVERT: Q 111 MET cc_start: 0.5735 (tpp) cc_final: 0.5422 (tpp) outliers start: 190 outliers final: 74 residues processed: 840 average time/residue: 0.7539 time to fit residues: 780.6461 Evaluate side-chains 758 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 659 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 55 GLU Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 49 ILE Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 247 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 284 ILE Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 258 ARG Chi-restraints excluded: chain O residue 262 THR Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 418 SER Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 235 ILE Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 76 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 325 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 524 optimal weight: 50.0000 chunk 179 optimal weight: 0.7980 chunk 364 optimal weight: 3.9990 chunk 362 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 387 optimal weight: 10.0000 chunk 434 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 163 ASN A 219 ASN A 314 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN A1213 HIS C 96 ASN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN M 68 ASN ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 181 ASN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.200666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123282 restraints weight = 53059.969| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.48 r_work: 0.3113 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 45599 Z= 0.199 Angle : 0.620 12.921 62047 Z= 0.314 Chirality : 0.045 0.262 6978 Planarity : 0.005 0.057 7603 Dihedral : 16.048 176.787 7052 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.68 % Allowed : 15.65 % Favored : 79.66 % 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: 0.16 (0.11), residues: 5269 helix: 1.43 (0.11), residues: 2057 sheet: -0.30 (0.19), residues: 682 loop : -0.88 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 172 TYR 0.018 0.002 TYR B 357 PHE 0.018 0.002 PHE C 225 TRP 0.009 0.001 TRP P 313 HIS 0.017 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (45571) covalent geometry : angle 0.60564 / 0.31 (62008) hydrogen bonds : bond 0.04113 / 2.71 ( 1962) hydrogen bonds : angle 4.47034 / 3.17 ( 5559) metal coordination : bond 0.01035 / 0.55 ( 26) metal coordination : angle 5.33348 / 3.34 ( 39) Misc. bond : bond 0.00039 / 0.02 ( 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 893 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 673 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8664 (pttp) cc_final: 0.8204 (ptpt) REVERT: A 76 LEU cc_start: 0.8986 (tp) cc_final: 0.8750 (tm) REVERT: A 107 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7264 (mpp) REVERT: A 111 THR cc_start: 0.8241 (m) cc_final: 0.7953 (p) REVERT: A 124 GLN cc_start: 0.6890 (tt0) cc_final: 0.6623 (tm-30) REVERT: A 128 TYR cc_start: 0.7735 (t80) cc_final: 0.7485 (t80) REVERT: A 216 GLU cc_start: 0.8283 (tt0) cc_final: 0.7987 (tt0) REVERT: A 270 LEU cc_start: 0.2056 (OUTLIER) cc_final: 0.1745 (pp) REVERT: A 284 THR cc_start: 0.8653 (m) cc_final: 0.8337 (p) REVERT: A 307 MET cc_start: 0.8024 (tpp) cc_final: 0.7537 (mmm) REVERT: A 398 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8399 (mtmm) REVERT: A 428 MET cc_start: 0.8001 (ppp) cc_final: 0.7605 (pp-130) REVERT: A 722 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7888 (mtpm) REVERT: A 755 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7219 (tp30) REVERT: A 760 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7484 (ttt-90) REVERT: A 770 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8216 (tp30) REVERT: A 852 MET cc_start: 0.9206 (mtp) cc_final: 0.8753 (mtp) REVERT: A 856 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 947 LEU cc_start: 0.8774 (tt) cc_final: 0.8427 (mm) REVERT: A 954 LYS cc_start: 0.7882 (ptpt) cc_final: 0.7370 (mmtt) REVERT: A 978 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8004 (mm-30) REVERT: A 979 LYS cc_start: 0.8315 (mptt) cc_final: 0.7969 (mtmm) REVERT: A 989 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7825 (mm) REVERT: A 990 ASN cc_start: 0.7950 (m110) cc_final: 0.7746 (p0) REVERT: A 1026 GLN cc_start: 0.8588 (mt0) cc_final: 0.8323 (pp30) REVERT: A 1061 MET cc_start: 0.6880 (ptp) cc_final: 0.6576 (ptp) REVERT: A 1115 GLU cc_start: 0.7317 (pt0) cc_final: 0.6878 (tm-30) REVERT: A 1135 GLU cc_start: 0.7592 (tp30) cc_final: 0.7389 (tp30) REVERT: A 1141 ARG cc_start: 0.7812 (mtt90) cc_final: 0.7416 (mtp85) REVERT: A 1161 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7925 (mmtp) REVERT: A 1222 LYS cc_start: 0.7949 (mttp) cc_final: 0.7420 (mptt) REVERT: A 1245 ARG cc_start: 0.8603 (mmm-85) cc_final: 0.8297 (mpt180) REVERT: B 39 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8515 (mt) REVERT: B 136 MET cc_start: 0.9170 (tpp) cc_final: 0.8793 (tpt) REVERT: B 139 MET cc_start: 0.9456 (ttm) cc_final: 0.8877 (ttm) REVERT: B 183 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: B 328 PHE cc_start: 0.8488 (m-80) cc_final: 0.7691 (m-80) REVERT: B 374 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7908 (pp20) REVERT: B 409 ASP cc_start: 0.8323 (m-30) cc_final: 0.8032 (m-30) REVERT: B 413 ASN cc_start: 0.8367 (m-40) cc_final: 0.8079 (m-40) REVERT: B 451 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.7743 (ttp) REVERT: B 506 MET cc_start: 0.9260 (mpp) cc_final: 0.8506 (mmt) REVERT: B 507 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 508 ASP cc_start: 0.8218 (p0) cc_final: 0.7889 (p0) REVERT: B 529 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: B 719 MET cc_start: 0.9415 (mmm) cc_final: 0.9109 (mmm) REVERT: B 729 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8758 (mm-30) REVERT: B 752 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7604 (mm-30) REVERT: B 781 ARG cc_start: 0.7555 (mmt90) cc_final: 0.6819 (mmt180) REVERT: B 784 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7244 (p0) REVERT: B 859 LYS cc_start: 0.8867 (mptt) cc_final: 0.8353 (mmtm) REVERT: B 870 MET cc_start: 0.9158 (ttp) cc_final: 0.8722 (ttp) REVERT: B 938 MET cc_start: 0.9024 (mtm) cc_final: 0.8556 (mtm) REVERT: C 11 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8137 (ptp-170) REVERT: C 56 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8350 (ttm) REVERT: C 64 ASP cc_start: 0.8757 (m-30) cc_final: 0.8484 (m-30) REVERT: C 334 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7837 (tpm-80) REVERT: D 10 LEU cc_start: 0.8079 (mt) cc_final: 0.7833 (mm) REVERT: D 47 TYR cc_start: 0.7473 (t80) cc_final: 0.7199 (t80) REVERT: D 68 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7721 (tp30) REVERT: D 82 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6908 (mm-30) REVERT: D 100 MET cc_start: 0.4219 (mmm) cc_final: 0.3248 (mtt) REVERT: D 116 LEU cc_start: 0.7144 (mt) cc_final: 0.6793 (pp) REVERT: E 46 ASP cc_start: 0.7784 (t70) cc_final: 0.7332 (t70) REVERT: E 49 SER cc_start: 0.7436 (p) cc_final: 0.7065 (m) REVERT: E 70 ASP cc_start: 0.5627 (t0) cc_final: 0.5212 (p0) REVERT: E 71 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6952 (mm-40) REVERT: E 72 MET cc_start: 0.7481 (ttt) cc_final: 0.6489 (ttt) REVERT: E 85 LYS cc_start: 0.8380 (pmtt) cc_final: 0.8120 (ptpp) REVERT: E 202 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7181 (mtm180) REVERT: F 51 ARG cc_start: 0.7412 (mtm-85) cc_final: 0.5046 (mmp-170) REVERT: F 86 GLU cc_start: 0.8129 (tp30) cc_final: 0.7860 (tp30) REVERT: G 50 ASP cc_start: 0.8569 (p0) cc_final: 0.8310 (p0) REVERT: G 53 LYS cc_start: 0.7902 (tptt) cc_final: 0.7529 (tptt) REVERT: G 89 ILE cc_start: 0.7284 (mm) cc_final: 0.6767 (OUTLIER) REVERT: H 20 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8311 (tptp) REVERT: H 75 TYR cc_start: 0.6632 (t80) cc_final: 0.6100 (t80) REVERT: H 81 ARG cc_start: 0.7452 (ttp-110) cc_final: 0.6732 (mtp180) REVERT: H 124 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.7550 (ttp80) REVERT: I 51 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6735 (m-30) REVERT: K 59 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8476 (pt) REVERT: K 98 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8689 (ttp80) REVERT: K 119 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8514 (ttpp) REVERT: K 123 ASP cc_start: 0.8280 (m-30) cc_final: 0.7953 (m-30) REVERT: L 44 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8649 (mmt) REVERT: L 51 ARG cc_start: 0.8690 (mtp180) cc_final: 0.8417 (mtm110) REVERT: M 105 SER cc_start: 0.7304 (t) cc_final: 0.6944 (p) REVERT: M 120 ARG cc_start: 0.5268 (mtp85) cc_final: 0.4868 (mtp180) REVERT: M 286 MET cc_start: 0.4080 (mmm) cc_final: 0.3728 (mmm) REVERT: M 389 MET cc_start: 0.2596 (ptp) cc_final: 0.2177 (ptt) REVERT: N 142 LYS cc_start: 0.3116 (tmtt) cc_final: 0.2342 (tttp) REVERT: N 152 LYS cc_start: 0.5761 (ptpt) cc_final: 0.5377 (ptpt) REVERT: N 253 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6195 (tt0) REVERT: N 328 LYS cc_start: 0.7481 (mtpp) cc_final: 0.7160 (mmtm) REVERT: N 333 LYS cc_start: 0.6908 (mmmt) cc_final: 0.6599 (mttt) REVERT: N 343 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6398 (mmmm) REVERT: N 347 ASP cc_start: 0.6610 (p0) cc_final: 0.6397 (t0) REVERT: N 375 VAL cc_start: 0.7282 (t) cc_final: 0.6982 (m) REVERT: N 390 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7206 (tm-30) REVERT: N 396 LYS cc_start: 0.6382 (OUTLIER) cc_final: 0.6181 (pptt) REVERT: O 146 ASN cc_start: 0.7791 (m-40) cc_final: 0.7583 (m110) REVERT: O 186 ASP cc_start: 0.5544 (p0) cc_final: 0.4786 (m-30) REVERT: O 258 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6518 (tpp80) REVERT: O 273 MET cc_start: 0.7429 (mmp) cc_final: 0.6905 (mtp) REVERT: O 275 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7079 (pt0) REVERT: O 340 LYS cc_start: 0.7354 (mmmt) cc_final: 0.6775 (mtmm) REVERT: O 373 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5514 (mmtm) REVERT: O 419 ARG cc_start: 0.6890 (mmm160) cc_final: 0.6516 (mtp85) REVERT: O 422 TYR cc_start: 0.7311 (m-80) cc_final: 0.6830 (m-80) REVERT: O 456 GLU cc_start: 0.7183 (pt0) cc_final: 0.6862 (pp20) REVERT: O 503 LYS cc_start: 0.7418 (ttmm) cc_final: 0.7127 (tmtp) REVERT: P 85 MET cc_start: 0.0632 (mpp) cc_final: -0.0948 (ppp) REVERT: P 230 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4505 (tt) REVERT: P 292 VAL cc_start: 0.7546 (p) cc_final: 0.6980 (t) REVERT: Q 43 TYR cc_start: 0.7214 (m-80) cc_final: 0.6573 (m-80) REVERT: Q 54 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.5939 (mp0) REVERT: Q 67 THR cc_start: 0.8038 (t) cc_final: 0.7740 (p) REVERT: Q 73 TYR cc_start: 0.7506 (m-10) cc_final: 0.7145 (m-10) REVERT: Q 76 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5666 (pp20) REVERT: Q 109 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7072 (mt-10) outliers start: 220 outliers final: 105 residues processed: 819 average time/residue: 0.7149 time to fit residues: 721.0238 Evaluate side-chains 775 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 638 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 529 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 334 ARG Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 24 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 247 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 396 LYS Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 258 ARG Chi-restraints excluded: chain O residue 262 THR Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 418 SER Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 235 ILE Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 76 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 154 optimal weight: 0.9990 chunk 415 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 305 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 327 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 272 optimal weight: 2.9990 chunk 506 optimal weight: 8.9990 chunk 461 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 163 ASN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN A 314 GLN A 732 ASN A 872 GLN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN J 52 HIS K 97 GLN M 68 ASN O 244 GLN ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN P 181 ASN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.199795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122570 restraints weight = 52786.002| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.29 r_work: 0.3088 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 45599 Z= 0.180 Angle : 0.596 9.765 62047 Z= 0.304 Chirality : 0.044 0.265 6978 Planarity : 0.004 0.052 7603 Dihedral : 15.974 176.834 7050 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.41 % Allowed : 16.59 % Favored : 79.00 % 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 (0.11), residues: 5269 helix: 1.51 (0.11), residues: 2060 sheet: -0.28 (0.19), residues: 680 loop : -0.81 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 459 TYR 0.017 0.001 TYR D 14 PHE 0.032 0.002 PHE P 187 TRP 0.010 0.001 TRP A 595 HIS 0.013 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (45571) covalent geometry : angle 0.58406 / 0.30 (62008) hydrogen bonds : bond 0.03995 / 2.62 ( 1962) hydrogen bonds : angle 4.42815 / 3.15 ( 5559) metal coordination : bond 0.00907 / 0.46 ( 26) metal coordination : angle 4.70627 / 2.95 ( 39) Misc. bond : bond 0.00036 / 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 869 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 662 time to evaluate : 1.342 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 39 LYS cc_start: 0.8723 (pttp) cc_final: 0.8260 (ptpt) REVERT: A 65 LYS cc_start: 0.8261 (tptp) cc_final: 0.7825 (ttpt) REVERT: A 76 LEU cc_start: 0.9080 (tp) cc_final: 0.8853 (tm) REVERT: A 107 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7417 (mpp) REVERT: A 111 THR cc_start: 0.8280 (m) cc_final: 0.7904 (p) REVERT: A 124 GLN cc_start: 0.6930 (tt0) cc_final: 0.6569 (tm-30) REVERT: A 216 GLU cc_start: 0.8367 (tt0) cc_final: 0.8100 (tt0) REVERT: A 225 ASN cc_start: 0.8229 (t0) cc_final: 0.7981 (t0) REVERT: A 270 LEU cc_start: 0.2340 (OUTLIER) cc_final: 0.1977 (pp) REVERT: A 284 THR cc_start: 0.8570 (m) cc_final: 0.8239 (p) REVERT: A 307 MET cc_start: 0.8058 (tpp) cc_final: 0.7503 (mmt) REVERT: A 311 ASP cc_start: 0.8043 (t0) cc_final: 0.7818 (t0) REVERT: A 339 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7162 (ttm-80) REVERT: A 398 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8385 (mtmm) REVERT: A 428 MET cc_start: 0.7915 (ppp) cc_final: 0.7508 (pp-130) REVERT: A 544 ASP cc_start: 0.8252 (t70) cc_final: 0.7955 (t0) REVERT: A 755 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7204 (tp30) REVERT: A 760 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7390 (ttp-110) REVERT: A 770 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8203 (tp30) REVERT: A 804 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8281 (mp) REVERT: A 852 MET cc_start: 0.9214 (mtp) cc_final: 0.8761 (mtp) REVERT: A 856 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 947 LEU cc_start: 0.8595 (tt) cc_final: 0.8227 (mm) REVERT: A 954 LYS cc_start: 0.7872 (ptpt) cc_final: 0.7379 (mmtt) REVERT: A 978 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8083 (pt0) REVERT: A 979 LYS cc_start: 0.8265 (mptt) cc_final: 0.7851 (mtmm) REVERT: A 989 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7896 (mm) REVERT: A 1061 MET cc_start: 0.7006 (ptp) cc_final: 0.6703 (ptp) REVERT: A 1112 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: A 1115 GLU cc_start: 0.7440 (pt0) cc_final: 0.6939 (tm-30) REVERT: A 1135 GLU cc_start: 0.7603 (tp30) cc_final: 0.7396 (tp30) REVERT: A 1141 ARG cc_start: 0.7855 (mtt90) cc_final: 0.7375 (mtp85) REVERT: A 1161 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7968 (mmtp) REVERT: A 1222 LYS cc_start: 0.7957 (mttp) cc_final: 0.7481 (mptt) REVERT: A 1245 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8287 (mpt180) REVERT: B 39 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8567 (mt) REVERT: B 95 ARG cc_start: 0.7976 (ttp-110) cc_final: 0.7763 (ttt-90) REVERT: B 136 MET cc_start: 0.9177 (tpp) cc_final: 0.8824 (tpt) REVERT: B 139 MET cc_start: 0.9459 (ttm) cc_final: 0.8878 (ttm) REVERT: B 183 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: B 328 PHE cc_start: 0.8468 (m-80) cc_final: 0.7970 (m-80) REVERT: B 374 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7940 (pp20) REVERT: B 409 ASP cc_start: 0.8314 (m-30) cc_final: 0.8022 (m-30) REVERT: B 413 ASN cc_start: 0.8379 (m-40) cc_final: 0.8100 (m-40) REVERT: B 451 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.7694 (ttp) REVERT: B 506 MET cc_start: 0.9236 (mpp) cc_final: 0.8500 (mmt) REVERT: B 507 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7647 (mm-30) REVERT: B 508 ASP cc_start: 0.8250 (p0) cc_final: 0.7902 (p0) REVERT: B 707 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8851 (t) REVERT: B 719 MET cc_start: 0.9433 (mmm) cc_final: 0.9130 (mmm) REVERT: B 729 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8725 (mm-30) REVERT: B 752 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7397 (mm-30) REVERT: B 781 ARG cc_start: 0.7423 (mmt90) cc_final: 0.6767 (mmt180) REVERT: B 784 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7105 (p0) REVERT: B 859 LYS cc_start: 0.8767 (mptt) cc_final: 0.8375 (mmtm) REVERT: B 870 MET cc_start: 0.9190 (ttp) cc_final: 0.8982 (ttp) REVERT: B 938 MET cc_start: 0.9078 (mtm) cc_final: 0.8610 (mtm) REVERT: B 1020 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8918 (ttt) REVERT: C 11 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8122 (ptp-170) REVERT: C 64 ASP cc_start: 0.8739 (m-30) cc_final: 0.8516 (m-30) REVERT: C 212 MET cc_start: 0.9235 (mtt) cc_final: 0.8868 (mtp) REVERT: D 10 LEU cc_start: 0.8210 (mt) cc_final: 0.7969 (mm) REVERT: D 68 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7686 (tp30) REVERT: D 82 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6731 (mm-30) REVERT: D 100 MET cc_start: 0.4228 (mmm) cc_final: 0.3143 (mtt) REVERT: D 113 ILE cc_start: 0.6951 (mm) cc_final: 0.6548 (mm) REVERT: D 116 LEU cc_start: 0.7187 (mt) cc_final: 0.6836 (pp) REVERT: E 12 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7160 (tppp) REVERT: E 49 SER cc_start: 0.7430 (p) cc_final: 0.7047 (m) REVERT: E 202 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7125 (mtm180) REVERT: F 51 ARG cc_start: 0.7397 (mtm-85) cc_final: 0.4994 (mmp-170) REVERT: F 86 GLU cc_start: 0.8157 (tp30) cc_final: 0.7897 (tp30) REVERT: G 50 ASP cc_start: 0.8706 (p0) cc_final: 0.8351 (p0) REVERT: G 53 LYS cc_start: 0.7896 (tptt) cc_final: 0.7560 (tptt) REVERT: G 89 ILE cc_start: 0.7284 (mm) cc_final: 0.6748 (OUTLIER) REVERT: H 9 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8843 (mp) REVERT: H 81 ARG cc_start: 0.7409 (ttp-110) cc_final: 0.6734 (mtp180) REVERT: H 124 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.7530 (ttp80) REVERT: I 51 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6777 (m-30) REVERT: I 53 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8194 (pp) REVERT: K 59 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8477 (pt) REVERT: K 98 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8655 (ttp80) REVERT: K 119 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8466 (ttpp) REVERT: K 123 ASP cc_start: 0.8299 (m-30) cc_final: 0.7981 (m-30) REVERT: L 15 MET cc_start: 0.7522 (tpp) cc_final: 0.7298 (tpp) REVERT: L 44 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8634 (mmt) REVERT: M 105 SER cc_start: 0.7364 (t) cc_final: 0.7016 (p) REVERT: M 121 GLN cc_start: 0.6643 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: M 286 MET cc_start: 0.4260 (mmm) cc_final: 0.3932 (mmm) REVERT: M 389 MET cc_start: 0.2809 (ptp) cc_final: 0.2332 (ptt) REVERT: N 152 LYS cc_start: 0.5805 (ptpt) cc_final: 0.5408 (ptpt) REVERT: N 253 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6249 (tt0) REVERT: N 328 LYS cc_start: 0.7481 (mtpp) cc_final: 0.7217 (mmtm) REVERT: N 333 LYS cc_start: 0.6626 (mmmt) cc_final: 0.6350 (mttt) REVERT: N 343 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6426 (mmmm) REVERT: N 375 VAL cc_start: 0.7465 (t) cc_final: 0.7199 (m) REVERT: O 85 MET cc_start: 0.7477 (ttm) cc_final: 0.7265 (ttt) REVERT: O 186 ASP cc_start: 0.5500 (p0) cc_final: 0.4737 (m-30) REVERT: O 275 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7033 (pt0) REVERT: O 340 LYS cc_start: 0.7476 (mmmt) cc_final: 0.6901 (mtmm) REVERT: O 373 LYS cc_start: 0.6188 (OUTLIER) cc_final: 0.5431 (mmtm) REVERT: O 379 GLN cc_start: 0.6406 (OUTLIER) cc_final: 0.6080 (mp10) REVERT: O 419 ARG cc_start: 0.6849 (mmm160) cc_final: 0.6483 (mtp85) REVERT: O 422 TYR cc_start: 0.7384 (m-80) cc_final: 0.7078 (m-80) REVERT: O 456 GLU cc_start: 0.7206 (pt0) cc_final: 0.6926 (pp20) REVERT: O 459 ARG cc_start: 0.7120 (tpp-160) cc_final: 0.6611 (mtm110) REVERT: O 503 LYS cc_start: 0.7455 (ttmm) cc_final: 0.7174 (tmtp) REVERT: O 531 MET cc_start: 0.6535 (mtm) cc_final: 0.6315 (ttm) REVERT: P 85 MET cc_start: 0.0169 (mpp) cc_final: -0.1147 (ppp) REVERT: P 230 LEU cc_start: 0.5118 (OUTLIER) cc_final: 0.4649 (tt) REVERT: P 292 VAL cc_start: 0.7559 (p) cc_final: 0.6998 (t) REVERT: Q 43 TYR cc_start: 0.7161 (m-80) cc_final: 0.6625 (m-80) REVERT: Q 54 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: Q 67 THR cc_start: 0.8045 (t) cc_final: 0.7728 (p) REVERT: Q 73 TYR cc_start: 0.7501 (m-10) cc_final: 0.7225 (m-10) REVERT: Q 76 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.5415 (pp20) REVERT: Q 110 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6326 (mpp) REVERT: Q 111 MET cc_start: 0.5904 (tpp) cc_final: 0.5697 (tpp) outliers start: 207 outliers final: 112 residues processed: 790 average time/residue: 0.7310 time to fit residues: 709.4164 Evaluate side-chains 771 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 623 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 346 LYS Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1020 MET Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain C residue 11 ARG Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 47 TYR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 24 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 37 ARG Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 247 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 262 THR Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 379 GLN Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 418 SER Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 235 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 76 GLU Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 50 optimal weight: 0.5980 chunk 355 optimal weight: 0.5980 chunk 271 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 492 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 chunk 455 optimal weight: 10.0000 chunk 226 optimal weight: 0.6980 chunk 279 optimal weight: 1.9990 chunk 289 optimal weight: 0.9990 chunk 480 optimal weight: 9.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 219 ASN A 290 ASN A 314 GLN A 732 ASN A 872 GLN A 990 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN B 100 HIS ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN K 45 HIS K 97 GLN M 68 ASN ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 457 ASN O 475 GLN P 181 ASN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.201569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.126066 restraints weight = 53123.076| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.50 r_work: 0.3112 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 45599 Z= 0.118 Angle : 0.557 10.255 62047 Z= 0.285 Chirality : 0.043 0.265 6978 Planarity : 0.004 0.100 7603 Dihedral : 15.886 177.596 7050 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.47 % Allowed : 17.76 % Favored : 78.77 % 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: 0.42 (0.12), residues: 5269 helix: 1.65 (0.12), residues: 2064 sheet: -0.19 (0.19), residues: 674 loop : -0.74 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 100 TYR 0.019 0.001 TYR Q 56 PHE 0.042 0.001 PHE G 157 TRP 0.009 0.001 TRP P 313 HIS 0.007 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (45571) covalent geometry : angle 0.54720 / 0.28 (62008) hydrogen bonds : bond 0.03547 / 2.31 ( 1962) hydrogen bonds : angle 4.29015 / 3.05 ( 5559) metal coordination : bond 0.00597 / 0.30 ( 26) metal coordination : angle 4.19109 / 2.61 ( 39) Misc. bond : bond 0.00024 / 0.01 ( 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 837 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 674 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8722 (pttp) cc_final: 0.8263 (ptpt) REVERT: A 65 LYS cc_start: 0.8307 (tptp) cc_final: 0.8046 (tptp) REVERT: A 76 LEU cc_start: 0.9083 (tp) cc_final: 0.8865 (tm) REVERT: A 107 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7390 (mpp) REVERT: A 111 THR cc_start: 0.8330 (m) cc_final: 0.7934 (p) REVERT: A 124 GLN cc_start: 0.6904 (tt0) cc_final: 0.6600 (tm-30) REVERT: A 216 GLU cc_start: 0.8383 (tt0) cc_final: 0.8091 (tt0) REVERT: A 270 LEU cc_start: 0.2312 (OUTLIER) cc_final: 0.1992 (pp) REVERT: A 307 MET cc_start: 0.8032 (tpp) cc_final: 0.7681 (mmm) REVERT: A 311 ASP cc_start: 0.7960 (t0) cc_final: 0.7663 (t0) REVERT: A 339 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7034 (ttm-80) REVERT: A 398 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8404 (mtmm) REVERT: A 428 MET cc_start: 0.7903 (ppp) cc_final: 0.7538 (pp-130) REVERT: A 755 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7323 (tp30) REVERT: A 760 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7855 (ttp-170) REVERT: A 852 MET cc_start: 0.9175 (mtp) cc_final: 0.8619 (mtp) REVERT: A 947 LEU cc_start: 0.8604 (tt) cc_final: 0.8248 (mm) REVERT: A 954 LYS cc_start: 0.7847 (ptpt) cc_final: 0.7365 (mmtt) REVERT: A 978 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8115 (pt0) REVERT: A 979 LYS cc_start: 0.8300 (mptt) cc_final: 0.7883 (mtmm) REVERT: A 989 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7648 (mm) REVERT: A 1061 MET cc_start: 0.6944 (ptp) cc_final: 0.6638 (ptp) REVERT: A 1115 GLU cc_start: 0.7449 (pt0) cc_final: 0.7015 (tm-30) REVERT: A 1141 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7376 (mtp85) REVERT: A 1161 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7871 (mmtp) REVERT: A 1222 LYS cc_start: 0.8096 (mttp) cc_final: 0.7564 (mptt) REVERT: A 1245 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8356 (mpt180) REVERT: B 25 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: B 39 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8450 (mt) REVERT: B 117 ILE cc_start: 0.7760 (pt) cc_final: 0.7540 (pp) REVERT: B 136 MET cc_start: 0.9176 (tpp) cc_final: 0.8847 (tpt) REVERT: B 139 MET cc_start: 0.9464 (ttm) cc_final: 0.8886 (ttm) REVERT: B 223 PHE cc_start: 0.8706 (m-80) cc_final: 0.8419 (m-80) REVERT: B 328 PHE cc_start: 0.8494 (m-80) cc_final: 0.7860 (m-80) REVERT: B 374 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7929 (pp20) REVERT: B 406 MET cc_start: 0.6541 (mtm) cc_final: 0.6177 (mmm) REVERT: B 409 ASP cc_start: 0.8274 (m-30) cc_final: 0.7978 (m-30) REVERT: B 413 ASN cc_start: 0.8408 (m-40) cc_final: 0.8153 (m-40) REVERT: B 423 ASN cc_start: 0.8102 (p0) cc_final: 0.7181 (m-40) REVERT: B 451 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.7442 (ttp) REVERT: B 506 MET cc_start: 0.9199 (mpp) cc_final: 0.8454 (mmt) REVERT: B 507 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7635 (mm-30) REVERT: B 508 ASP cc_start: 0.8267 (p0) cc_final: 0.7937 (p0) REVERT: B 613 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8061 (mt-10) REVERT: B 719 MET cc_start: 0.9417 (mmm) cc_final: 0.9127 (mmm) REVERT: B 729 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8753 (mm-30) REVERT: B 781 ARG cc_start: 0.7455 (mmt90) cc_final: 0.6820 (mmt180) REVERT: B 784 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.7079 (p0) REVERT: B 859 LYS cc_start: 0.8785 (mptt) cc_final: 0.8402 (mmtm) REVERT: B 938 MET cc_start: 0.8995 (mtm) cc_final: 0.8476 (mtm) REVERT: C 64 ASP cc_start: 0.8749 (m-30) cc_final: 0.8456 (m-30) REVERT: C 141 ARG cc_start: 0.9005 (ttm-80) cc_final: 0.8643 (ttt180) REVERT: C 316 LEU cc_start: 0.8683 (pt) cc_final: 0.8453 (mt) REVERT: D 10 LEU cc_start: 0.8195 (mt) cc_final: 0.7957 (mm) REVERT: D 47 TYR cc_start: 0.6986 (t80) cc_final: 0.6657 (t80) REVERT: D 68 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7713 (tp30) REVERT: D 82 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6790 (mm-30) REVERT: D 100 MET cc_start: 0.4159 (mmm) cc_final: 0.3140 (mtt) REVERT: D 113 ILE cc_start: 0.7007 (mm) cc_final: 0.6608 (mm) REVERT: D 116 LEU cc_start: 0.7181 (mt) cc_final: 0.6766 (pp) REVERT: E 12 LYS cc_start: 0.7478 (OUTLIER) cc_final: 0.7156 (tppp) REVERT: E 49 SER cc_start: 0.7419 (p) cc_final: 0.7030 (m) REVERT: E 202 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.7073 (mtm180) REVERT: F 51 ARG cc_start: 0.7443 (mtm-85) cc_final: 0.5005 (mmp-170) REVERT: F 86 GLU cc_start: 0.8175 (tp30) cc_final: 0.7942 (tp30) REVERT: G 29 GLU cc_start: 0.8423 (tp30) cc_final: 0.8080 (mp0) REVERT: G 41 ASN cc_start: 0.8776 (m-40) cc_final: 0.8497 (m110) REVERT: G 50 ASP cc_start: 0.8755 (p0) cc_final: 0.8498 (p0) REVERT: G 53 LYS cc_start: 0.7893 (tptt) cc_final: 0.7609 (tptt) REVERT: G 89 ILE cc_start: 0.7144 (mm) cc_final: 0.6543 (OUTLIER) REVERT: H 20 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.7894 (tptp) REVERT: H 81 ARG cc_start: 0.7439 (ttp-110) cc_final: 0.6788 (mtp180) REVERT: H 124 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.7562 (ttp80) REVERT: I 13 ILE cc_start: 0.7214 (pt) cc_final: 0.6679 (pp) REVERT: I 51 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6614 (m-30) REVERT: I 53 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8210 (pp) REVERT: K 98 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8594 (ttp80) REVERT: K 119 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8490 (ttpp) REVERT: K 123 ASP cc_start: 0.8322 (m-30) cc_final: 0.7981 (m-30) REVERT: L 15 MET cc_start: 0.7538 (tpp) cc_final: 0.7297 (tpp) REVERT: L 44 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8161 (mmt) REVERT: M 105 SER cc_start: 0.7478 (t) cc_final: 0.7096 (p) REVERT: M 286 MET cc_start: 0.4135 (mmm) cc_final: 0.3797 (mmm) REVERT: M 389 MET cc_start: 0.2672 (ptp) cc_final: 0.2216 (ptt) REVERT: N 152 LYS cc_start: 0.5704 (ptpt) cc_final: 0.5436 (ptpt) REVERT: N 328 LYS cc_start: 0.7468 (mtpp) cc_final: 0.7213 (mmtm) REVERT: N 333 LYS cc_start: 0.6908 (mmmt) cc_final: 0.6619 (mttt) REVERT: N 343 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.6471 (mmmm) REVERT: N 375 VAL cc_start: 0.7439 (t) cc_final: 0.7179 (m) REVERT: N 390 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7190 (tp30) REVERT: N 396 LYS cc_start: 0.6363 (OUTLIER) cc_final: 0.6137 (pptt) REVERT: O 85 MET cc_start: 0.7467 (ttm) cc_final: 0.7266 (ttt) REVERT: O 186 ASP cc_start: 0.5502 (p0) cc_final: 0.4750 (m-30) REVERT: O 273 MET cc_start: 0.8359 (tpt) cc_final: 0.7765 (mmp) REVERT: O 275 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7088 (pt0) REVERT: O 320 LEU cc_start: 0.7369 (mp) cc_final: 0.7107 (mt) REVERT: O 321 GLU cc_start: 0.7453 (mp0) cc_final: 0.7085 (mp0) REVERT: O 340 LYS cc_start: 0.7466 (mmmt) cc_final: 0.6908 (mtmm) REVERT: O 373 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5468 (mmtm) REVERT: O 379 GLN cc_start: 0.6522 (OUTLIER) cc_final: 0.6196 (mp10) REVERT: O 408 GLU cc_start: 0.7848 (tp30) cc_final: 0.7608 (tp30) REVERT: O 419 ARG cc_start: 0.6834 (mmm160) cc_final: 0.6453 (mtp85) REVERT: O 422 TYR cc_start: 0.7270 (m-80) cc_final: 0.6972 (m-80) REVERT: O 456 GLU cc_start: 0.7234 (pt0) cc_final: 0.6905 (pp20) REVERT: O 503 LYS cc_start: 0.7458 (ttmm) cc_final: 0.7187 (tmtp) REVERT: O 531 MET cc_start: 0.6534 (mtm) cc_final: 0.6282 (ttm) REVERT: P 85 MET cc_start: -0.0399 (mpp) cc_final: -0.1070 (ppp) REVERT: P 230 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4649 (tt) REVERT: P 267 MET cc_start: 0.4745 (mmm) cc_final: 0.3720 (mmm) REVERT: P 292 VAL cc_start: 0.7582 (p) cc_final: 0.6982 (t) REVERT: Q 43 TYR cc_start: 0.7163 (m-80) cc_final: 0.6563 (m-80) REVERT: Q 54 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6540 (mp0) REVERT: Q 73 TYR cc_start: 0.7525 (m-10) cc_final: 0.7304 (m-10) REVERT: Q 111 MET cc_start: 0.5940 (tpp) cc_final: 0.5708 (tpp) outliers start: 163 outliers final: 73 residues processed: 771 average time/residue: 0.6318 time to fit residues: 597.6601 Evaluate side-chains 732 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 634 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 247 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain N residue 396 LYS Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 262 THR Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 379 GLN Chi-restraints excluded: chain O residue 418 SER Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 235 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 489 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 412 optimal weight: 7.9990 chunk 519 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 260 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 307 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 154 ASN A 219 ASN A 225 ASN A 314 GLN A 732 ASN A 990 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1202 GLN B 703 ASN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN M 68 ASN ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN P 181 ASN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.197714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117988 restraints weight = 52573.321| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.21 r_work: 0.3043 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 45599 Z= 0.228 Angle : 0.640 11.100 62047 Z= 0.326 Chirality : 0.046 0.262 6978 Planarity : 0.005 0.050 7603 Dihedral : 15.878 177.306 7050 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.26 % Allowed : 17.65 % Favored : 78.09 % 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: 0.32 (0.11), residues: 5269 helix: 1.53 (0.11), residues: 2061 sheet: -0.29 (0.19), residues: 692 loop : -0.74 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 459 TYR 0.024 0.002 TYR P 219 PHE 0.047 0.002 PHE G 157 TRP 0.011 0.001 TRP A 595 HIS 0.014 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (45571) covalent geometry : angle 0.62783 / 0.33 (62008) hydrogen bonds : bond 0.04267 / 2.81 ( 1962) hydrogen bonds : angle 4.44916 / 3.16 ( 5559) metal coordination : bond 0.01217 / 0.64 ( 26) metal coordination : angle 5.01562 / 2.94 ( 39) Misc. bond : bond 0.00033 / 0.02 ( 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 854 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 654 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7505 (mp0) cc_final: 0.7039 (pm20) REVERT: A 39 LYS cc_start: 0.8823 (pttp) cc_final: 0.8243 (ptpt) REVERT: A 65 LYS cc_start: 0.8400 (tptp) cc_final: 0.8134 (tptp) REVERT: A 76 LEU cc_start: 0.9115 (tp) cc_final: 0.8855 (tm) REVERT: A 124 GLN cc_start: 0.6933 (tt0) cc_final: 0.6388 (tm-30) REVERT: A 216 GLU cc_start: 0.8421 (tt0) cc_final: 0.8218 (tt0) REVERT: A 270 LEU cc_start: 0.2442 (OUTLIER) cc_final: 0.2083 (pp) REVERT: A 307 MET cc_start: 0.7890 (tpp) cc_final: 0.7464 (mmm) REVERT: A 311 ASP cc_start: 0.7793 (t0) cc_final: 0.7439 (t0) REVERT: A 339 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7276 (ttm-80) REVERT: A 398 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8385 (mtmm) REVERT: A 428 MET cc_start: 0.7786 (ppp) cc_final: 0.7407 (pp-130) REVERT: A 728 ILE cc_start: 0.7760 (mm) cc_final: 0.7380 (mt) REVERT: A 755 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7264 (tp30) REVERT: A 760 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7534 (ttp-110) REVERT: A 804 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 852 MET cc_start: 0.9192 (mtp) cc_final: 0.8842 (mtp) REVERT: A 954 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7344 (mmtt) REVERT: A 978 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8150 (tt0) REVERT: A 979 LYS cc_start: 0.8362 (mptt) cc_final: 0.7916 (mtmm) REVERT: A 989 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7950 (mm) REVERT: A 1061 MET cc_start: 0.7170 (ptp) cc_final: 0.6782 (ptp) REVERT: A 1112 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: A 1115 GLU cc_start: 0.7413 (pt0) cc_final: 0.6853 (tm-30) REVERT: A 1141 ARG cc_start: 0.7811 (mtt90) cc_final: 0.7300 (mtp85) REVERT: A 1153 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8287 (mm) REVERT: A 1161 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7785 (mmtp) REVERT: A 1222 LYS cc_start: 0.8052 (mttp) cc_final: 0.7458 (mptt) REVERT: A 1245 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.8097 (mpt180) REVERT: B 25 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8286 (tp30) REVERT: B 39 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8613 (mt) REVERT: B 136 MET cc_start: 0.9176 (tpp) cc_final: 0.8785 (tpt) REVERT: B 139 MET cc_start: 0.9457 (ttm) cc_final: 0.8878 (ttm) REVERT: B 328 PHE cc_start: 0.8406 (m-80) cc_final: 0.7935 (m-80) REVERT: B 406 MET cc_start: 0.6589 (mtm) cc_final: 0.6326 (mmm) REVERT: B 409 ASP cc_start: 0.8296 (m-30) cc_final: 0.8003 (m-30) REVERT: B 413 ASN cc_start: 0.8421 (m-40) cc_final: 0.8144 (m-40) REVERT: B 451 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8099 (ttp) REVERT: B 506 MET cc_start: 0.9227 (mpp) cc_final: 0.8460 (mmt) REVERT: B 507 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7653 (mm-30) REVERT: B 508 ASP cc_start: 0.8414 (p0) cc_final: 0.7984 (p0) REVERT: B 513 LYS cc_start: 0.7834 (tttp) cc_final: 0.7372 (tptt) REVERT: B 719 MET cc_start: 0.9473 (mmm) cc_final: 0.9176 (mmm) REVERT: B 729 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8788 (mm-30) REVERT: B 752 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7547 (mm-30) REVERT: B 784 ASN cc_start: 0.7447 (OUTLIER) cc_final: 0.6963 (p0) REVERT: B 851 TYR cc_start: 0.7820 (m-80) cc_final: 0.7611 (m-10) REVERT: B 859 LYS cc_start: 0.8781 (mptt) cc_final: 0.8379 (mmtm) REVERT: B 870 MET cc_start: 0.9344 (ttp) cc_final: 0.9036 (ttp) REVERT: B 938 MET cc_start: 0.9236 (mtm) cc_final: 0.8689 (mtm) REVERT: B 1020 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.9034 (ttt) REVERT: C 5 GLN cc_start: 0.8659 (tt0) cc_final: 0.8260 (tp40) REVERT: C 145 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8492 (tmt-80) REVERT: C 248 GLU cc_start: 0.7702 (pm20) cc_final: 0.7431 (mm-30) REVERT: D 47 TYR cc_start: 0.7178 (t80) cc_final: 0.6934 (t80) REVERT: D 68 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7686 (tp30) REVERT: D 82 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6786 (mm-30) REVERT: D 100 MET cc_start: 0.4232 (mmm) cc_final: 0.3173 (mtt) REVERT: D 113 ILE cc_start: 0.7075 (mm) cc_final: 0.6740 (mm) REVERT: D 116 LEU cc_start: 0.7250 (mt) cc_final: 0.6941 (pp) REVERT: E 12 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.7035 (tppp) REVERT: E 49 SER cc_start: 0.7300 (p) cc_final: 0.6893 (m) REVERT: E 202 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7176 (mtm180) REVERT: F 51 ARG cc_start: 0.7459 (mtm-85) cc_final: 0.4922 (mmp-170) REVERT: F 80 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8072 (mpp) REVERT: F 86 GLU cc_start: 0.8248 (tp30) cc_final: 0.7937 (tp30) REVERT: G 33 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8646 (ttmt) REVERT: G 50 ASP cc_start: 0.8800 (p0) cc_final: 0.8420 (p0) REVERT: G 53 LYS cc_start: 0.7810 (tptt) cc_final: 0.7469 (tptt) REVERT: G 73 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8135 (mtm180) REVERT: G 89 ILE cc_start: 0.7091 (mm) cc_final: 0.6547 (OUTLIER) REVERT: H 9 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8829 (mp) REVERT: H 20 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8540 (tmtt) REVERT: H 81 ARG cc_start: 0.7491 (ttp-110) cc_final: 0.6858 (mtp180) REVERT: H 124 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.7422 (ttp80) REVERT: I 13 ILE cc_start: 0.7188 (pt) cc_final: 0.6643 (pp) REVERT: I 51 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: I 53 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8148 (pt) REVERT: K 59 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8595 (pt) REVERT: K 98 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8820 (ttt180) REVERT: K 115 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8550 (mt-10) REVERT: K 119 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8389 (ttpp) REVERT: K 123 ASP cc_start: 0.8376 (m-30) cc_final: 0.8066 (m-30) REVERT: L 15 MET cc_start: 0.7702 (tpp) cc_final: 0.7428 (tpp) REVERT: L 35 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8043 (ttp80) REVERT: M 37 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7359 (mtm) REVERT: M 105 SER cc_start: 0.7396 (t) cc_final: 0.7117 (p) REVERT: M 132 ILE cc_start: 0.8904 (mt) cc_final: 0.8618 (mt) REVERT: M 144 LYS cc_start: 0.6908 (mttt) cc_final: 0.6417 (tptt) REVERT: M 286 MET cc_start: 0.4153 (mmm) cc_final: 0.3837 (mmm) REVERT: M 389 MET cc_start: 0.3063 (ptp) cc_final: 0.2649 (ptt) REVERT: N 253 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6062 (tm-30) REVERT: N 328 LYS cc_start: 0.7482 (mtpp) cc_final: 0.7221 (mmtm) REVERT: N 333 LYS cc_start: 0.6863 (mmmt) cc_final: 0.6546 (mttt) REVERT: N 343 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6465 (mmmm) REVERT: N 361 VAL cc_start: 0.6922 (p) cc_final: 0.6651 (m) REVERT: O 22 GLU cc_start: 0.7406 (pp20) cc_final: 0.6982 (pt0) REVERT: O 186 ASP cc_start: 0.6252 (p0) cc_final: 0.5483 (m-30) REVERT: O 273 MET cc_start: 0.8363 (tpt) cc_final: 0.7925 (mtt) REVERT: O 320 LEU cc_start: 0.7439 (mp) cc_final: 0.7065 (mt) REVERT: O 321 GLU cc_start: 0.7425 (mp0) cc_final: 0.7042 (mp0) REVERT: O 333 MET cc_start: 0.5508 (mmm) cc_final: 0.4156 (mtp) REVERT: O 373 LYS cc_start: 0.6140 (OUTLIER) cc_final: 0.5447 (mmtm) REVERT: O 379 GLN cc_start: 0.6491 (OUTLIER) cc_final: 0.6132 (mp10) REVERT: O 408 GLU cc_start: 0.7797 (tp30) cc_final: 0.7561 (tp30) REVERT: O 419 ARG cc_start: 0.6856 (mmm160) cc_final: 0.6486 (mtp85) REVERT: O 422 TYR cc_start: 0.7336 (m-80) cc_final: 0.7015 (m-80) REVERT: O 459 ARG cc_start: 0.7139 (tpp-160) cc_final: 0.6634 (mtm110) REVERT: O 503 LYS cc_start: 0.7419 (ttmm) cc_final: 0.7132 (tmtp) REVERT: O 531 MET cc_start: 0.6631 (mtm) cc_final: 0.6361 (ttm) REVERT: P 85 MET cc_start: -0.0475 (mpp) cc_final: -0.1158 (ppp) REVERT: P 228 VAL cc_start: 0.5314 (OUTLIER) cc_final: 0.4955 (t) REVERT: P 230 LEU cc_start: 0.5212 (OUTLIER) cc_final: 0.4762 (tt) REVERT: P 267 MET cc_start: 0.4950 (mmm) cc_final: 0.3858 (mmm) REVERT: Q 43 TYR cc_start: 0.7203 (m-80) cc_final: 0.6603 (m-80) REVERT: Q 54 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: Q 66 GLU cc_start: 0.7677 (tp30) cc_final: 0.7044 (mp0) REVERT: Q 67 THR cc_start: 0.8007 (t) cc_final: 0.7670 (p) REVERT: Q 71 MET cc_start: 0.7769 (mtp) cc_final: 0.7303 (ttm) REVERT: Q 92 MET cc_start: 0.2367 (OUTLIER) cc_final: 0.1027 (ptt) REVERT: Q 110 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6350 (mpp) REVERT: Q 111 MET cc_start: 0.5783 (tpp) cc_final: 0.5566 (tpp) REVERT: V 29 SER cc_start: 0.7116 (m) cc_final: 0.6580 (t) outliers start: 200 outliers final: 113 residues processed: 777 average time/residue: 0.5286 time to fit residues: 505.7200 Evaluate side-chains 770 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 622 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1275 MET Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 494 LYS Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 752 GLU Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1020 MET Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 205 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 24 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 247 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 262 THR Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 379 GLN Chi-restraints excluded: chain O residue 418 SER Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 222 GLU Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 235 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 92 MET Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 43 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 247 optimal weight: 3.9990 chunk 451 optimal weight: 30.0000 chunk 183 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 400 optimal weight: 6.9990 chunk 236 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 510 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 219 ASN A 314 GLN A 732 ASN A 872 GLN A 990 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1202 GLN B 282 GLN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN K 97 GLN M 68 ASN ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.197625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119947 restraints weight = 52936.473| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.39 r_work: 0.3033 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 45599 Z= 0.201 Angle : 0.626 12.116 62047 Z= 0.319 Chirality : 0.045 0.320 6978 Planarity : 0.005 0.050 7603 Dihedral : 15.830 177.394 7050 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.79 % Allowed : 18.42 % Favored : 77.79 % 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: 0.29 (0.11), residues: 5269 helix: 1.51 (0.11), residues: 2064 sheet: -0.34 (0.19), residues: 686 loop : -0.74 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 100 TYR 0.026 0.002 TYR P 219 PHE 0.030 0.002 PHE G 157 TRP 0.010 0.001 TRP A 595 HIS 0.012 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (45571) covalent geometry : angle 0.61397 / 0.32 (62008) hydrogen bonds : bond 0.04064 / 2.67 ( 1962) hydrogen bonds : angle 4.43877 / 3.15 ( 5559) metal coordination : bond 0.01142 / 0.60 ( 26) metal coordination : angle 4.95318 / 2.89 ( 39) Misc. bond : bond 0.00023 / 0.01 ( 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 816 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 638 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8826 (pttp) cc_final: 0.8263 (ptpt) REVERT: A 65 LYS cc_start: 0.8458 (tptp) cc_final: 0.8194 (tptp) REVERT: A 76 LEU cc_start: 0.9135 (tp) cc_final: 0.8854 (tm) REVERT: A 216 GLU cc_start: 0.8394 (tt0) cc_final: 0.8124 (tt0) REVERT: A 234 ASP cc_start: 0.8552 (t0) cc_final: 0.8292 (t0) REVERT: A 270 LEU cc_start: 0.2335 (OUTLIER) cc_final: 0.1977 (pp) REVERT: A 307 MET cc_start: 0.8040 (tpp) cc_final: 0.7460 (mmp) REVERT: A 311 ASP cc_start: 0.7906 (t0) cc_final: 0.7505 (t0) REVERT: A 339 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7302 (ttm-80) REVERT: A 398 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8381 (mtmm) REVERT: A 428 MET cc_start: 0.7849 (ppp) cc_final: 0.7472 (pp-130) REVERT: A 544 ASP cc_start: 0.8352 (t70) cc_final: 0.8070 (t0) REVERT: A 728 ILE cc_start: 0.7941 (mm) cc_final: 0.7573 (mt) REVERT: A 755 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7281 (tp30) REVERT: A 760 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7777 (ttp-110) REVERT: A 852 MET cc_start: 0.9188 (mtp) cc_final: 0.8764 (mtp) REVERT: A 954 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7496 (mmtt) REVERT: A 979 LYS cc_start: 0.8532 (mptt) cc_final: 0.8080 (mtmm) REVERT: A 989 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 1061 MET cc_start: 0.7162 (ptp) cc_final: 0.6755 (ptp) REVERT: A 1112 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: A 1115 GLU cc_start: 0.7532 (pt0) cc_final: 0.7189 (pt0) REVERT: A 1141 ARG cc_start: 0.7969 (mtt90) cc_final: 0.7473 (mtp85) REVERT: A 1161 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7876 (mmtp) REVERT: A 1214 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7278 (tt) REVERT: A 1245 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8321 (mpt180) REVERT: B 25 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8411 (tp30) REVERT: B 39 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8580 (mt) REVERT: B 95 ARG cc_start: 0.7706 (ttt-90) cc_final: 0.7186 (ttt180) REVERT: B 136 MET cc_start: 0.9197 (tpp) cc_final: 0.8872 (tpt) REVERT: B 139 MET cc_start: 0.9470 (ttm) cc_final: 0.8914 (ttm) REVERT: B 328 PHE cc_start: 0.8567 (m-80) cc_final: 0.8233 (m-80) REVERT: B 409 ASP cc_start: 0.8352 (m-30) cc_final: 0.8077 (m-30) REVERT: B 413 ASN cc_start: 0.8602 (m-40) cc_final: 0.8352 (m-40) REVERT: B 451 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: B 506 MET cc_start: 0.9225 (mpp) cc_final: 0.8463 (mmt) REVERT: B 507 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7657 (mm-30) REVERT: B 508 ASP cc_start: 0.8454 (p0) cc_final: 0.8032 (p0) REVERT: B 513 LYS cc_start: 0.7957 (tttp) cc_final: 0.7535 (tptt) REVERT: B 522 ASP cc_start: 0.8418 (t0) cc_final: 0.8172 (t0) REVERT: B 707 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.9020 (t) REVERT: B 719 MET cc_start: 0.9451 (mmm) cc_final: 0.9172 (mmm) REVERT: B 784 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7115 (p0) REVERT: B 859 LYS cc_start: 0.8824 (mptt) cc_final: 0.8441 (mmtm) REVERT: B 938 MET cc_start: 0.9163 (mtm) cc_final: 0.8946 (mtm) REVERT: B 1020 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.9030 (ttt) REVERT: C 5 GLN cc_start: 0.8773 (tt0) cc_final: 0.8299 (tp40) REVERT: D 68 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7671 (tp30) REVERT: D 82 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6676 (mm-30) REVERT: D 100 MET cc_start: 0.4194 (mmm) cc_final: 0.3106 (mtt) REVERT: D 113 ILE cc_start: 0.7107 (mm) cc_final: 0.6763 (mm) REVERT: D 116 LEU cc_start: 0.7239 (mt) cc_final: 0.6835 (pp) REVERT: E 202 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7235 (mtm180) REVERT: F 51 ARG cc_start: 0.7499 (mtm-85) cc_final: 0.5056 (mmp-170) REVERT: F 80 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8117 (mpp) REVERT: F 86 GLU cc_start: 0.8310 (tp30) cc_final: 0.8059 (tp30) REVERT: G 33 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8708 (ttmt) REVERT: G 40 TYR cc_start: 0.8570 (t80) cc_final: 0.8327 (t80) REVERT: G 41 ASN cc_start: 0.8735 (m-40) cc_final: 0.8446 (m110) REVERT: G 50 ASP cc_start: 0.8851 (p0) cc_final: 0.8423 (p0) REVERT: G 53 LYS cc_start: 0.7902 (tptt) cc_final: 0.7617 (tptt) REVERT: G 73 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8234 (mtm180) REVERT: G 89 ILE cc_start: 0.7089 (mm) cc_final: 0.6538 (OUTLIER) REVERT: H 9 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8850 (mp) REVERT: H 20 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8554 (tmtt) REVERT: H 35 PHE cc_start: 0.6212 (m-80) cc_final: 0.5796 (m-80) REVERT: H 81 ARG cc_start: 0.7490 (ttp-110) cc_final: 0.6943 (mtp180) REVERT: H 124 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.7595 (ttp80) REVERT: I 13 ILE cc_start: 0.7481 (pt) cc_final: 0.6962 (pp) REVERT: I 51 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: I 53 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8285 (pt) REVERT: J 1 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8527 (ttt) REVERT: K 30 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7885 (t) REVERT: K 59 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8474 (pt) REVERT: K 98 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8884 (ttt180) REVERT: K 115 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8573 (mt-10) REVERT: K 119 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8555 (ttpp) REVERT: K 123 ASP cc_start: 0.8578 (m-30) cc_final: 0.8283 (m-30) REVERT: L 15 MET cc_start: 0.7785 (tpp) cc_final: 0.7561 (tpp) REVERT: L 35 ARG cc_start: 0.8519 (ttm-80) cc_final: 0.8167 (ttp80) REVERT: L 44 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8702 (mmt) REVERT: M 37 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7467 (mtm) REVERT: M 105 SER cc_start: 0.7547 (t) cc_final: 0.7293 (p) REVERT: M 132 ILE cc_start: 0.8974 (mt) cc_final: 0.8671 (mt) REVERT: M 144 LYS cc_start: 0.6945 (mttt) cc_final: 0.6593 (tptp) REVERT: M 286 MET cc_start: 0.4107 (mmm) cc_final: 0.3758 (mmm) REVERT: M 389 MET cc_start: 0.3024 (ptp) cc_final: 0.2614 (ptt) REVERT: N 328 LYS cc_start: 0.7570 (mtpp) cc_final: 0.7344 (mmtm) REVERT: N 333 LYS cc_start: 0.7015 (mmmt) cc_final: 0.6706 (mttt) REVERT: N 343 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.6680 (mmmm) REVERT: N 361 VAL cc_start: 0.7474 (p) cc_final: 0.7243 (m) REVERT: N 390 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7363 (tp30) REVERT: O 22 GLU cc_start: 0.7424 (pp20) cc_final: 0.6982 (pt0) REVERT: O 139 MET cc_start: 0.5754 (tpp) cc_final: 0.5383 (tpp) REVERT: O 186 ASP cc_start: 0.6239 (p0) cc_final: 0.5503 (m-30) REVERT: O 273 MET cc_start: 0.8337 (tpt) cc_final: 0.7924 (mtt) REVERT: O 275 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7112 (pt0) REVERT: O 320 LEU cc_start: 0.7288 (mp) cc_final: 0.7072 (mt) REVERT: O 321 GLU cc_start: 0.7381 (mp0) cc_final: 0.7091 (mp0) REVERT: O 373 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5501 (mmtm) REVERT: O 379 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.6244 (mp10) REVERT: O 408 GLU cc_start: 0.7946 (tp30) cc_final: 0.7665 (tp30) REVERT: O 419 ARG cc_start: 0.6814 (mmm160) cc_final: 0.6435 (mtp85) REVERT: O 422 TYR cc_start: 0.7349 (m-80) cc_final: 0.7058 (m-80) REVERT: O 459 ARG cc_start: 0.7120 (tpp-160) cc_final: 0.6607 (mtm110) REVERT: O 461 LEU cc_start: 0.5702 (tm) cc_final: 0.5277 (mt) REVERT: O 503 LYS cc_start: 0.7480 (ttmm) cc_final: 0.7190 (tmtp) REVERT: P 85 MET cc_start: -0.0493 (mpp) cc_final: -0.1154 (ppp) REVERT: P 228 VAL cc_start: 0.5397 (OUTLIER) cc_final: 0.4940 (t) REVERT: P 230 LEU cc_start: 0.5095 (OUTLIER) cc_final: 0.4790 (tt) REVERT: P 267 MET cc_start: 0.4285 (mmm) cc_final: 0.3421 (mmm) REVERT: P 292 VAL cc_start: 0.7379 (p) cc_final: 0.6848 (t) REVERT: Q 43 TYR cc_start: 0.7290 (m-80) cc_final: 0.6711 (m-80) REVERT: Q 54 GLU cc_start: 0.7005 (mp0) cc_final: 0.6597 (mp0) REVERT: Q 66 GLU cc_start: 0.7688 (tp30) cc_final: 0.7036 (mp0) REVERT: Q 67 THR cc_start: 0.8023 (t) cc_final: 0.7703 (p) REVERT: Q 71 MET cc_start: 0.7810 (mtp) cc_final: 0.7330 (ttm) REVERT: Q 92 MET cc_start: 0.2394 (OUTLIER) cc_final: 0.1001 (ptt) REVERT: Q 110 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6388 (mpp) REVERT: Q 111 MET cc_start: 0.5792 (tpp) cc_final: 0.5588 (tpp) REVERT: V 29 SER cc_start: 0.7003 (m) cc_final: 0.6509 (t) outliers start: 178 outliers final: 108 residues processed: 748 average time/residue: 0.4975 time to fit residues: 459.1186 Evaluate side-chains 748 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 606 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1125 ASP Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1020 MET Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 20 LYS Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 24 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 77 GLU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 37 MET Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 247 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 262 THR Chi-restraints excluded: chain O residue 271 LEU Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 379 GLN Chi-restraints excluded: chain O residue 418 SER Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 235 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 92 MET Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 329 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 277 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 494 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 495 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 446 optimal weight: 6.9990 chunk 302 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 154 ASN A 219 ASN A 314 GLN A 990 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1202 GLN A1277 ASN ** E 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN M 68 ASN ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.198478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121030 restraints weight = 52577.740| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.41 r_work: 0.3046 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45599 Z= 0.148 Angle : 0.604 12.462 62047 Z= 0.305 Chirality : 0.044 0.553 6978 Planarity : 0.004 0.051 7603 Dihedral : 15.750 177.342 7050 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.32 % Allowed : 19.53 % Favored : 77.15 % 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: 0.38 (0.12), residues: 5269 helix: 1.61 (0.11), residues: 2066 sheet: -0.26 (0.19), residues: 690 loop : -0.72 (0.12), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 459 TYR 0.027 0.001 TYR P 219 PHE 0.026 0.001 PHE G 157 TRP 0.010 0.001 TRP P 313 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (45571) covalent geometry : angle 0.59280 / 0.30 (62008) hydrogen bonds : bond 0.03778 / 2.46 ( 1962) hydrogen bonds : angle 4.38307 / 3.11 ( 5559) metal coordination : bond 0.00830 / 0.43 ( 26) metal coordination : angle 4.70223 / 2.78 ( 39) Misc. bond : bond 0.00028 / 0.01 ( 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 777 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 621 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8785 (pttp) cc_final: 0.8223 (ptpt) REVERT: A 76 LEU cc_start: 0.9119 (tp) cc_final: 0.8860 (tm) REVERT: A 128 TYR cc_start: 0.7822 (t80) cc_final: 0.7527 (t80) REVERT: A 216 GLU cc_start: 0.8395 (tt0) cc_final: 0.8182 (tt0) REVERT: A 234 ASP cc_start: 0.8524 (t0) cc_final: 0.8212 (t0) REVERT: A 270 LEU cc_start: 0.2349 (OUTLIER) cc_final: 0.1982 (pp) REVERT: A 307 MET cc_start: 0.7999 (tpp) cc_final: 0.7440 (mmp) REVERT: A 311 ASP cc_start: 0.7904 (t0) cc_final: 0.7491 (t0) REVERT: A 339 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7266 (ttm-80) REVERT: A 398 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8418 (mtmm) REVERT: A 428 MET cc_start: 0.8015 (ppp) cc_final: 0.7590 (pp-130) REVERT: A 544 ASP cc_start: 0.8353 (t70) cc_final: 0.8076 (t0) REVERT: A 728 ILE cc_start: 0.7930 (mm) cc_final: 0.7558 (mt) REVERT: A 755 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7240 (tp30) REVERT: A 760 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8073 (ttp-170) REVERT: A 852 MET cc_start: 0.9145 (mtp) cc_final: 0.8707 (mtp) REVERT: A 954 LYS cc_start: 0.7966 (ptpt) cc_final: 0.7510 (mmtt) REVERT: A 979 LYS cc_start: 0.8570 (mptt) cc_final: 0.8103 (mtmm) REVERT: A 989 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7990 (mm) REVERT: A 1061 MET cc_start: 0.7148 (ptp) cc_final: 0.6760 (ptp) REVERT: A 1112 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: A 1115 GLU cc_start: 0.7656 (pt0) cc_final: 0.7266 (pt0) REVERT: A 1136 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7407 (tpp80) REVERT: A 1141 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7330 (mtp85) REVERT: A 1161 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7902 (mmtp) REVERT: A 1222 LYS cc_start: 0.7982 (mttp) cc_final: 0.7709 (mtpt) REVERT: A 1245 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8300 (mpt180) REVERT: A 1375 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.7127 (ttm-80) REVERT: B 25 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8436 (tp30) REVERT: B 39 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8585 (mt) REVERT: B 95 ARG cc_start: 0.7818 (ttt-90) cc_final: 0.7285 (ttt180) REVERT: B 136 MET cc_start: 0.9191 (tpp) cc_final: 0.8866 (tpt) REVERT: B 139 MET cc_start: 0.9470 (ttm) cc_final: 0.8919 (ttm) REVERT: B 326 PHE cc_start: 0.7669 (m-80) cc_final: 0.7430 (m-80) REVERT: B 328 PHE cc_start: 0.8543 (m-80) cc_final: 0.8129 (m-80) REVERT: B 409 ASP cc_start: 0.8305 (m-30) cc_final: 0.8011 (m-30) REVERT: B 413 ASN cc_start: 0.8586 (m-40) cc_final: 0.8328 (m-40) REVERT: B 451 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: B 506 MET cc_start: 0.9211 (mpp) cc_final: 0.8420 (mmt) REVERT: B 507 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7653 (mm-30) REVERT: B 508 ASP cc_start: 0.8461 (p0) cc_final: 0.8035 (p0) REVERT: B 513 LYS cc_start: 0.7929 (tttp) cc_final: 0.7508 (tptt) REVERT: B 522 ASP cc_start: 0.8447 (t0) cc_final: 0.8201 (t0) REVERT: B 613 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8060 (mt-10) REVERT: B 719 MET cc_start: 0.9437 (mmm) cc_final: 0.9160 (mmm) REVERT: B 784 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7165 (p0) REVERT: B 859 LYS cc_start: 0.8827 (mptt) cc_final: 0.8435 (mmtm) REVERT: B 938 MET cc_start: 0.9162 (mtm) cc_final: 0.8633 (mtm) REVERT: C 5 GLN cc_start: 0.8742 (tt0) cc_final: 0.8267 (tp40) REVERT: D 68 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7671 (tp30) REVERT: D 82 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6657 (mm-30) REVERT: D 100 MET cc_start: 0.4499 (mmm) cc_final: 0.3476 (mtt) REVERT: D 113 ILE cc_start: 0.7111 (mm) cc_final: 0.6752 (mm) REVERT: D 116 LEU cc_start: 0.7240 (mt) cc_final: 0.6834 (pp) REVERT: E 202 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7257 (mtm180) REVERT: F 51 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.5098 (mmp-170) REVERT: F 80 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8061 (mpp) REVERT: G 33 LYS cc_start: 0.8886 (ttpp) cc_final: 0.8681 (ttmt) REVERT: G 41 ASN cc_start: 0.8778 (m-40) cc_final: 0.8441 (m110) REVERT: G 50 ASP cc_start: 0.8861 (p0) cc_final: 0.8484 (p0) REVERT: G 53 LYS cc_start: 0.7862 (tptt) cc_final: 0.7574 (tptt) REVERT: G 73 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8230 (mtm180) REVERT: G 89 ILE cc_start: 0.7003 (mm) cc_final: 0.6441 (OUTLIER) REVERT: H 9 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8831 (mp) REVERT: H 81 ARG cc_start: 0.7467 (ttp-110) cc_final: 0.6953 (mtp180) REVERT: H 124 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.7585 (ttp80) REVERT: I 13 ILE cc_start: 0.7514 (pt) cc_final: 0.7003 (pp) REVERT: I 51 ASP cc_start: 0.7137 (OUTLIER) cc_final: 0.6763 (m-30) REVERT: J 1 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8443 (ttt) REVERT: K 30 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7828 (t) REVERT: K 59 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8385 (pt) REVERT: K 98 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8875 (ttt180) REVERT: K 115 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8546 (mt-10) REVERT: K 119 LYS cc_start: 0.8955 (ttpp) cc_final: 0.8531 (ttpp) REVERT: K 123 ASP cc_start: 0.8637 (m-30) cc_final: 0.8337 (m-30) REVERT: L 15 MET cc_start: 0.7781 (tpp) cc_final: 0.7526 (tpp) REVERT: L 35 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8158 (ttp80) REVERT: L 44 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8586 (mmt) REVERT: L 51 ARG cc_start: 0.8781 (mtm110) cc_final: 0.8580 (mtm110) REVERT: M 105 SER cc_start: 0.7573 (t) cc_final: 0.7322 (p) REVERT: M 132 ILE cc_start: 0.8968 (mt) cc_final: 0.8664 (mt) REVERT: M 144 LYS cc_start: 0.7040 (mttt) cc_final: 0.6639 (tptp) REVERT: M 270 MET cc_start: 0.1844 (tpt) cc_final: 0.1539 (mmt) REVERT: M 286 MET cc_start: 0.4119 (mmm) cc_final: 0.3770 (mmm) REVERT: M 389 MET cc_start: 0.2954 (ptp) cc_final: 0.2583 (ptt) REVERT: N 328 LYS cc_start: 0.7582 (mtpp) cc_final: 0.7349 (mmtm) REVERT: N 333 LYS cc_start: 0.6914 (mmmt) cc_final: 0.6601 (mttt) REVERT: N 343 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6675 (mmmm) REVERT: N 361 VAL cc_start: 0.7474 (p) cc_final: 0.7260 (m) REVERT: N 390 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7319 (tp30) REVERT: O 22 GLU cc_start: 0.7408 (pp20) cc_final: 0.6971 (pt0) REVERT: O 139 MET cc_start: 0.5664 (tpp) cc_final: 0.5225 (tpp) REVERT: O 186 ASP cc_start: 0.6236 (p0) cc_final: 0.5508 (m-30) REVERT: O 273 MET cc_start: 0.8374 (tpt) cc_final: 0.7974 (mtt) REVERT: O 275 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7091 (pt0) REVERT: O 320 LEU cc_start: 0.7284 (mp) cc_final: 0.7072 (mt) REVERT: O 321 GLU cc_start: 0.7325 (mp0) cc_final: 0.7061 (mp0) REVERT: O 333 MET cc_start: 0.5393 (mmm) cc_final: 0.4140 (mtp) REVERT: O 373 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.5407 (mmtm) REVERT: O 379 GLN cc_start: 0.6498 (OUTLIER) cc_final: 0.6161 (mp10) REVERT: O 385 MET cc_start: 0.7653 (mtt) cc_final: 0.7387 (mtm) REVERT: O 408 GLU cc_start: 0.7911 (tp30) cc_final: 0.7650 (tp30) REVERT: O 419 ARG cc_start: 0.6806 (mmm160) cc_final: 0.6424 (mtp85) REVERT: O 459 ARG cc_start: 0.7054 (tpp-160) cc_final: 0.6563 (mtm110) REVERT: O 461 LEU cc_start: 0.5693 (tm) cc_final: 0.5269 (mt) REVERT: O 503 LYS cc_start: 0.7460 (ttmm) cc_final: 0.7173 (tmtp) REVERT: O 531 MET cc_start: 0.6685 (mtt) cc_final: 0.6485 (ttm) REVERT: P 85 MET cc_start: -0.0523 (mpp) cc_final: -0.1146 (ppp) REVERT: P 228 VAL cc_start: 0.5354 (OUTLIER) cc_final: 0.4987 (t) REVERT: P 230 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4795 (tt) REVERT: P 267 MET cc_start: 0.4412 (mmm) cc_final: 0.2966 (tmm) REVERT: P 292 VAL cc_start: 0.7400 (p) cc_final: 0.6890 (t) REVERT: Q 43 TYR cc_start: 0.7277 (m-80) cc_final: 0.6734 (m-80) REVERT: Q 54 GLU cc_start: 0.6923 (mp0) cc_final: 0.6575 (mp0) REVERT: Q 67 THR cc_start: 0.7963 (t) cc_final: 0.7646 (p) REVERT: Q 71 MET cc_start: 0.7805 (mtp) cc_final: 0.7221 (ttm) REVERT: Q 92 MET cc_start: 0.2377 (OUTLIER) cc_final: 0.1057 (ptm) REVERT: Q 110 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6405 (mpp) outliers start: 156 outliers final: 96 residues processed: 719 average time/residue: 0.4919 time to fit residues: 435.7647 Evaluate side-chains 731 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 607 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 73 ARG Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 24 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 247 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 262 THR Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 379 GLN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 235 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 92 MET Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 136 optimal weight: 1.9990 chunk 225 optimal weight: 0.0980 chunk 101 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 106 optimal weight: 0.0870 chunk 482 optimal weight: 9.9990 chunk 436 optimal weight: 8.9990 chunk 251 optimal weight: 0.0010 chunk 299 optimal weight: 4.9990 chunk 527 optimal weight: 40.0000 chunk 274 optimal weight: 3.9990 overall best weight: 1.0368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 154 ASN A 219 ASN A 314 GLN A 990 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN A1202 GLN B 390 GLN B 438 GLN K 97 GLN M 68 ASN ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 25 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.198741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119310 restraints weight = 52823.071| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.34 r_work: 0.3064 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 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 : 0.003 0.060 45599 Z= 0.140 Angle : 0.602 12.141 62047 Z= 0.304 Chirality : 0.044 0.273 6978 Planarity : 0.004 0.050 7603 Dihedral : 15.625 177.119 7048 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.85 % Allowed : 20.02 % Favored : 77.13 % 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: 0.43 (0.12), residues: 5269 helix: 1.65 (0.12), residues: 2063 sheet: -0.23 (0.19), residues: 699 loop : -0.71 (0.12), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 100 TYR 0.027 0.001 TYR P 219 PHE 0.023 0.001 PHE G 157 TRP 0.010 0.001 TRP P 313 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (45571) covalent geometry : angle 0.59057 / 0.30 (62008) hydrogen bonds : bond 0.03662 / 2.39 ( 1962) hydrogen bonds : angle 4.33666 / 3.08 ( 5559) metal coordination : bond 0.00747 / 0.38 ( 26) metal coordination : angle 4.61661 / 2.80 ( 39) Misc. bond : bond 0.00032 / 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 756 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 622 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8772 (pttp) cc_final: 0.8207 (ptpt) REVERT: A 65 LYS cc_start: 0.8267 (tptp) cc_final: 0.7888 (ttpt) REVERT: A 76 LEU cc_start: 0.9135 (tp) cc_final: 0.8876 (tm) REVERT: A 128 TYR cc_start: 0.7876 (t80) cc_final: 0.7543 (t80) REVERT: A 216 GLU cc_start: 0.8340 (tt0) cc_final: 0.8076 (tt0) REVERT: A 234 ASP cc_start: 0.8530 (t0) cc_final: 0.8241 (t0) REVERT: A 270 LEU cc_start: 0.2379 (OUTLIER) cc_final: 0.1996 (pp) REVERT: A 294 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7877 (tttm) REVERT: A 307 MET cc_start: 0.7952 (tpp) cc_final: 0.7564 (mmt) REVERT: A 311 ASP cc_start: 0.7773 (t0) cc_final: 0.7360 (t0) REVERT: A 339 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7250 (ttm-80) REVERT: A 398 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8409 (mtmm) REVERT: A 428 MET cc_start: 0.8058 (ppp) cc_final: 0.7565 (pp-130) REVERT: A 544 ASP cc_start: 0.8284 (t70) cc_final: 0.7996 (t0) REVERT: A 728 ILE cc_start: 0.7878 (mm) cc_final: 0.7527 (mt) REVERT: A 755 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7286 (tp30) REVERT: A 760 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7984 (ttp-170) REVERT: A 852 MET cc_start: 0.9127 (mtp) cc_final: 0.8664 (mtp) REVERT: A 954 LYS cc_start: 0.7891 (ptpt) cc_final: 0.7658 (mmtt) REVERT: A 979 LYS cc_start: 0.8539 (mptt) cc_final: 0.8085 (mtmm) REVERT: A 989 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7957 (mm) REVERT: A 1061 MET cc_start: 0.6999 (ptp) cc_final: 0.6703 (ptp) REVERT: A 1112 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: A 1115 GLU cc_start: 0.7633 (pt0) cc_final: 0.7244 (pt0) REVERT: A 1136 ARG cc_start: 0.7952 (tpp80) cc_final: 0.7475 (tpp80) REVERT: A 1141 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7307 (mtp85) REVERT: A 1153 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 1161 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7946 (mmtp) REVERT: A 1245 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.8310 (mpt180) REVERT: A 1375 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.7089 (ttm-80) REVERT: B 25 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: B 39 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8510 (mt) REVERT: B 95 ARG cc_start: 0.7970 (ttt-90) cc_final: 0.7460 (ttp80) REVERT: B 136 MET cc_start: 0.9175 (tpp) cc_final: 0.8837 (tpt) REVERT: B 139 MET cc_start: 0.9456 (ttm) cc_final: 0.8905 (ttm) REVERT: B 328 PHE cc_start: 0.8454 (m-80) cc_final: 0.8063 (m-80) REVERT: B 409 ASP cc_start: 0.8289 (m-30) cc_final: 0.8025 (m-30) REVERT: B 413 ASN cc_start: 0.8577 (m-40) cc_final: 0.8319 (m-40) REVERT: B 451 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.7516 (ttp) REVERT: B 506 MET cc_start: 0.9203 (mpp) cc_final: 0.8419 (mmt) REVERT: B 507 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 508 ASP cc_start: 0.8445 (p0) cc_final: 0.8013 (p0) REVERT: B 513 LYS cc_start: 0.7912 (tttp) cc_final: 0.7492 (tptt) REVERT: B 522 ASP cc_start: 0.8343 (t0) cc_final: 0.8110 (t0) REVERT: B 613 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 719 MET cc_start: 0.9432 (mmm) cc_final: 0.9148 (mmm) REVERT: B 784 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7163 (p0) REVERT: B 859 LYS cc_start: 0.8814 (mptt) cc_final: 0.8480 (mmtm) REVERT: B 957 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7952 (ptm-80) REVERT: C 5 GLN cc_start: 0.8716 (tt0) cc_final: 0.8254 (tp40) REVERT: C 131 GLU cc_start: 0.7621 (pm20) cc_final: 0.7262 (pm20) REVERT: C 316 LEU cc_start: 0.8706 (pt) cc_final: 0.8497 (mt) REVERT: D 68 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7685 (tp30) REVERT: D 82 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6662 (mm-30) REVERT: D 100 MET cc_start: 0.4511 (mmm) cc_final: 0.3459 (mtt) REVERT: D 113 ILE cc_start: 0.7117 (mm) cc_final: 0.6756 (mm) REVERT: D 116 LEU cc_start: 0.7221 (mt) cc_final: 0.6804 (pp) REVERT: F 51 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.5109 (mmp-170) REVERT: F 80 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8045 (mpp) REVERT: G 41 ASN cc_start: 0.8775 (m-40) cc_final: 0.8516 (m110) REVERT: G 50 ASP cc_start: 0.8848 (p0) cc_final: 0.8619 (p0) REVERT: G 53 LYS cc_start: 0.7839 (tptt) cc_final: 0.7544 (tptt) REVERT: G 89 ILE cc_start: 0.6992 (mm) cc_final: 0.6432 (OUTLIER) REVERT: H 81 ARG cc_start: 0.7502 (ttp-110) cc_final: 0.7019 (mtp180) REVERT: H 124 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.7597 (ttp80) REVERT: I 13 ILE cc_start: 0.7553 (pt) cc_final: 0.7048 (pp) REVERT: I 51 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: J 1 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8406 (ttt) REVERT: K 98 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8849 (ttt180) REVERT: K 115 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8542 (mt-10) REVERT: K 119 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8554 (ttpp) REVERT: K 123 ASP cc_start: 0.8628 (m-30) cc_final: 0.8335 (m-30) REVERT: L 15 MET cc_start: 0.7849 (tpp) cc_final: 0.7591 (tpp) REVERT: L 35 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8149 (ttp80) REVERT: L 44 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8500 (mmt) REVERT: M 105 SER cc_start: 0.7544 (t) cc_final: 0.7307 (p) REVERT: M 132 ILE cc_start: 0.8974 (mt) cc_final: 0.8675 (mt) REVERT: M 144 LYS cc_start: 0.7036 (mttt) cc_final: 0.6645 (tptp) REVERT: M 270 MET cc_start: 0.1923 (tpt) cc_final: 0.1647 (mmt) REVERT: M 286 MET cc_start: 0.4180 (mmm) cc_final: 0.3812 (mmm) REVERT: M 389 MET cc_start: 0.2990 (ptp) cc_final: 0.2606 (ptt) REVERT: N 328 LYS cc_start: 0.7582 (mtpp) cc_final: 0.7358 (mmtm) REVERT: N 333 LYS cc_start: 0.6824 (mmmt) cc_final: 0.6555 (mttt) REVERT: N 343 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6664 (mmmm) REVERT: N 361 VAL cc_start: 0.7471 (p) cc_final: 0.7263 (m) REVERT: N 375 VAL cc_start: 0.7717 (t) cc_final: 0.7452 (m) REVERT: N 390 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7301 (tp30) REVERT: O 22 GLU cc_start: 0.7400 (pp20) cc_final: 0.6954 (pt0) REVERT: O 139 MET cc_start: 0.5646 (tpp) cc_final: 0.5213 (tpp) REVERT: O 186 ASP cc_start: 0.6241 (p0) cc_final: 0.5534 (m-30) REVERT: O 273 MET cc_start: 0.8356 (tpt) cc_final: 0.7791 (mmp) REVERT: O 275 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: O 320 LEU cc_start: 0.7383 (mp) cc_final: 0.7153 (mt) REVERT: O 321 GLU cc_start: 0.7312 (mp0) cc_final: 0.7042 (mp0) REVERT: O 333 MET cc_start: 0.5405 (mmm) cc_final: 0.4157 (mtp) REVERT: O 373 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5436 (mmtm) REVERT: O 379 GLN cc_start: 0.6479 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: O 385 MET cc_start: 0.7647 (mtt) cc_final: 0.7384 (mtm) REVERT: O 419 ARG cc_start: 0.6807 (mmm160) cc_final: 0.6436 (mtp85) REVERT: O 459 ARG cc_start: 0.6996 (tpp-160) cc_final: 0.6499 (mtm110) REVERT: O 461 LEU cc_start: 0.5689 (tm) cc_final: 0.5277 (mt) REVERT: O 503 LYS cc_start: 0.7444 (ttmm) cc_final: 0.7164 (tmtp) REVERT: O 531 MET cc_start: 0.6709 (mtt) cc_final: 0.6508 (ttm) REVERT: P 85 MET cc_start: -0.0554 (mpp) cc_final: -0.1149 (ppp) REVERT: P 228 VAL cc_start: 0.5371 (OUTLIER) cc_final: 0.5007 (t) REVERT: P 230 LEU cc_start: 0.5146 (OUTLIER) cc_final: 0.4777 (tt) REVERT: P 267 MET cc_start: 0.4324 (mmm) cc_final: 0.2822 (tmm) REVERT: P 292 VAL cc_start: 0.7367 (p) cc_final: 0.6828 (t) REVERT: Q 43 TYR cc_start: 0.7173 (m-80) cc_final: 0.6678 (m-80) REVERT: Q 54 GLU cc_start: 0.6891 (mp0) cc_final: 0.6460 (mp0) REVERT: Q 67 THR cc_start: 0.7912 (t) cc_final: 0.7608 (p) REVERT: Q 71 MET cc_start: 0.7677 (mtp) cc_final: 0.7059 (ttm) REVERT: Q 92 MET cc_start: 0.2317 (OUTLIER) cc_final: 0.1059 (ptm) REVERT: Q 110 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6357 (mpp) REVERT: Q 111 MET cc_start: 0.5579 (tpp) cc_final: 0.5366 (mmt) outliers start: 134 outliers final: 97 residues processed: 708 average time/residue: 0.4523 time to fit residues: 393.9364 Evaluate side-chains 725 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 603 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 582 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 760 ARG Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1046 THR Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1153 ILE Chi-restraints excluded: chain A residue 1208 SER Chi-restraints excluded: chain A residue 1266 THR Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain A residue 1344 SER Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 936 SER Chi-restraints excluded: chain B residue 1046 ARG Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 24 LYS Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 243 SER Chi-restraints excluded: chain M residue 247 MET Chi-restraints excluded: chain M residue 298 MET Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 343 LYS Chi-restraints excluded: chain N residue 344 VAL Chi-restraints excluded: chain O residue 154 THR Chi-restraints excluded: chain O residue 259 MET Chi-restraints excluded: chain O residue 262 THR Chi-restraints excluded: chain O residue 275 GLU Chi-restraints excluded: chain O residue 308 LEU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 373 LYS Chi-restraints excluded: chain O residue 379 GLN Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 198 SER Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 230 LEU Chi-restraints excluded: chain P residue 235 ILE Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 92 MET Chi-restraints excluded: chain Q residue 110 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 533 random chunks: chunk 243 optimal weight: 1.9990 chunk 516 optimal weight: 0.5980 chunk 320 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 449 optimal weight: 4.9990 chunk 288 optimal weight: 0.3980 chunk 446 optimal weight: 3.9990 chunk 118 optimal weight: 0.0770 chunk 265 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 154 ASN A 219 ASN A 314 GLN A 990 ASN ** A1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 GLN K 97 GLN M 68 ASN N 270 GLN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN ** P 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.199005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119629 restraints weight = 52940.462| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.22 r_work: 0.3102 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 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 : 0.003 0.057 45599 Z= 0.127 Angle : 0.601 11.549 62047 Z= 0.302 Chirality : 0.043 0.267 6978 Planarity : 0.004 0.051 7603 Dihedral : 15.573 176.958 7048 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.94 % Allowed : 20.10 % Favored : 76.96 % 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: 0.47 (0.12), residues: 5269 helix: 1.68 (0.12), residues: 2063 sheet: -0.19 (0.19), residues: 698 loop : -0.69 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 100 TYR 0.031 0.001 TYR O 422 PHE 0.024 0.001 PHE H 35 TRP 0.020 0.001 TRP Q 103 HIS 0.008 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (45571) covalent geometry : angle 0.59016 / 0.30 (62008) hydrogen bonds : bond 0.03548 / 2.31 ( 1962) hydrogen bonds : angle 4.31054 / 3.07 ( 5559) metal coordination : bond 0.00655 / 0.33 ( 26) metal coordination : angle 4.49811 / 2.74 ( 39) Misc. bond : bond 0.00040 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19709.76 seconds wall clock time: 334 minutes 28.73 seconds (20068.73 seconds total)