Starting phenix.real_space_refine on Tue Jul 7 05:40:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k36_62006/07_2026/9k36_62006.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k36_62006/07_2026/9k36_62006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k36_62006/07_2026/9k36_62006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k36_62006/07_2026/9k36_62006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k36_62006/07_2026/9k36_62006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k36_62006/07_2026/9k36_62006.map" } resolution = 2.9 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 115 5.49 5 Mg 1 5.21 5 S 285 5.16 5 C 27836 2.51 5 N 7756 2.21 5 O 8597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 44600 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 10814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1378, 10814 Classifications: {'peptide': 1378} Link IDs: {'PTRANS': 64, 'TRANS': 1313} Chain: "B" Number of atoms: 8736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8736 Classifications: {'peptide': 1105} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1053} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2736 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 17, 'TRANS': 325} Chain: "D" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 985 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1715 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "G" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1337 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain breaks: 2 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 822 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3382 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 23, 'TRANS': 398} Chain breaks: 1 Chain: "N" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1128 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain breaks: 2 Chain: "O" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4075 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 22, 'TRANS': 489} Chain breaks: 1 Chain: "P" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2403 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain: "Q" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 754 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 12, 'TRANS': 74} Chain: "V" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 246 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "X" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1049 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Y" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1042 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "Z" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 209 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 7} Link IDs: {'rna3p': 9} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 543 SG CYS A 69 55.472 112.126 87.657 1.00103.58 S ATOM 565 SG CYS A 72 55.994 115.609 89.340 1.00106.71 S ATOM 613 SG CYS A 79 59.173 113.770 87.666 1.00104.11 S ATOM 854 SG CYS A 109 68.802 83.938 124.509 1.00114.77 S ATOM 876 SG CYS A 112 66.392 86.273 126.785 1.00118.64 S ATOM 1245 SG CYS A 156 69.278 85.004 128.615 1.00130.18 S ATOM 1271 SG CYS A 159 66.391 82.785 127.894 1.00130.36 S ATOM 19137 SG CYS B1080 58.257 117.675 105.758 1.00102.14 S ATOM 19156 SG CYS B1083 59.626 113.910 105.733 1.00101.99 S ATOM 19222 SG CYS B1092 57.072 114.998 103.322 1.00 97.16 S ATOM 19250 SG CYS B1095 56.204 114.108 107.401 1.00100.21 S ATOM 28160 SG CYS I 5 117.443 46.271 102.591 1.00130.73 S ATOM 28177 SG CYS I 8 113.628 47.312 101.006 1.00130.05 S ATOM 28307 SG CYS I 25 113.607 48.902 104.429 1.00130.27 S ATOM 28328 SG CYS I 28 114.426 45.350 104.153 1.00128.16 S ATOM 28600 SG CYS J 7 111.115 127.394 45.078 1.00 75.41 S ATOM 28624 SG CYS J 10 112.326 130.735 43.990 1.00 75.83 S ATOM 28888 SG CYS J 44 114.823 128.382 45.437 1.00 81.33 S ATOM 28894 SG CYS J 45 113.613 127.899 41.645 1.00 82.39 S ATOM 29937 SG CYS L 19 78.344 101.263 35.845 1.00103.46 S ATOM 29956 SG CYS L 22 79.198 99.724 31.494 1.00109.30 S ATOM 30073 SG CYS L 36 75.165 101.255 33.493 1.00117.09 S ATOM 30099 SG CYS L 39 77.027 98.149 33.743 1.00117.30 S Time building chain proxies: 8.87, per 1000 atoms: 0.20 Number of scatterers: 44600 At special positions: 0 Unit cell: (167.9, 182.558, 177.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 285 16.00 P 115 15.00 Mg 1 11.99 O 8597 8.00 N 7756 7.00 C 27836 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: 3.81 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 P 401 " pdb="FE1 SF4 P 401 " - pdb=" SG CYS P 290 " pdb="FE4 SF4 P 401 " - pdb=" SG CYS P 307 " pdb="FE3 SF4 P 401 " - pdb=" SG CYS P 287 " pdb="FE2 SF4 P 401 " - pdb=" SG CYS P 296 " Number of angles added : 12 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 69 " pdb="ZN ZN A1401 " - pdb=" SG CYS A 79 " pdb=" ZN A1402 " pdb="ZN ZN A1402 " - pdb=" SG CYS A 112 " 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 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 B1083 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1092 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 28 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 25 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb=" ZN J2000 " pdb="ZN ZN J2000 " - pdb=" SG CYS J 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 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " 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: 200 helices and 59 sheets defined 42.6% alpha, 17.3% beta 33 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 6.52 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.503A 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: 3.789A 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: 4.366A 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: 3.732A 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 388 Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 492 through 497 removed outlier: 3.748A 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: 3.751A pdb=" N LYS A 578 " --> pdb=" O LYS A 575 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 579 " --> pdb=" O ASP A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 3.766A pdb=" N ILE A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.892A 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: 3.864A 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: 3.772A pdb=" N ALA A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 905 Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 920 through 932 Processing helix chain 'A' and resid 941 through 954 removed outlier: 3.541A pdb=" N LYS A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 987 Processing helix chain 'A' and resid 997 through 1003 Processing helix chain 'A' and resid 1007 through 1025 Processing helix chain 'A' and resid 1032 through 1048 Proline residue: A1044 - end of helix Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1094 through 1106 Processing helix chain 'A' and resid 1110 through 1113 No H-bonds generated for 'chain 'A' and resid 1110 through 1113' Processing helix chain 'A' and resid 1133 through 1141 Processing helix chain 'A' and resid 1145 through 1153 Processing helix chain 'A' and resid 1188 through 1196 Processing helix chain 'A' and resid 1231 through 1238 removed outlier: 3.573A 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: 3.857A pdb=" N HIS A1278 " --> pdb=" O THR A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.958A 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: 3.737A pdb=" N GLY A1358 " --> pdb=" O ILE A1355 " (cutoff:3.500A) removed outlier: 3.663A 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: 4.236A pdb=" N TRP B 27 " --> pdb=" O GLU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.833A pdb=" N ALA B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 removed outlier: 3.660A 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: 3.660A 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: 4.147A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 453 removed outlier: 3.912A 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: 3.625A pdb=" N VAL B 512 " --> pdb=" O ASP B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 removed outlier: 3.531A pdb=" N LEU B 526 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 533 removed outlier: 3.629A 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: 3.945A pdb=" N ASP B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 665 removed outlier: 3.551A 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: 4.323A pdb=" N SER B 936 " --> pdb=" O HIS B 932 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 937 " --> pdb=" O GLY B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 3.785A 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 1069 through 1073 removed outlier: 3.594A pdb=" N ASP B1073 " --> pdb=" O MET B1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1069 through 1073' Processing helix chain 'B' and resid 1108 through 1120 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 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: 3.515A 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: 3.776A 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: 3.764A pdb=" N VAL D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 39 removed outlier: 3.635A 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: 4.060A pdb=" N ALA D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 34 Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.795A 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: 3.512A pdb=" N GLY K 52 " --> pdb=" O ASP K 48 " (cutoff:3.500A) removed outlier: 3.865A 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: 3.981A pdb=" N GLU M 203 " --> pdb=" O LYS M 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 223 removed outlier: 3.855A pdb=" N GLU M 219 " --> pdb=" O ASP M 215 " (cutoff:3.500A) removed outlier: 4.073A 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: 3.673A pdb=" N VAL M 267 " --> pdb=" O PRO M 264 " (cutoff:3.500A) removed outlier: 4.546A 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: 3.693A pdb=" N LYS M 316 " --> pdb=" O ARG M 312 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL M 317 " --> pdb=" O GLY M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 333 removed outlier: 3.689A pdb=" N LEU M 332 " --> pdb=" O LYS M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 363 removed outlier: 3.571A 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: 3.997A 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: 4.080A 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: 3.907A 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: 3.755A 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: 4.019A 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: 4.079A pdb=" N VAL O 144 " --> pdb=" O ASP O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 259 removed outlier: 3.505A pdb=" N PHE O 242 " --> pdb=" O ASN O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 278 removed outlier: 4.503A pdb=" N ILE O 276 " --> pdb=" O ARG O 272 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR O 277 " --> pdb=" O MET O 273 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 297 Processing helix chain 'O' and resid 304 through 317 Processing helix chain 'O' and resid 337 through 359 Processing helix chain 'O' and resid 359 through 372 Processing helix chain 'O' and resid 376 through 385 Processing helix chain 'O' and resid 390 through 401 Processing helix chain 'O' and resid 416 through 418 No H-bonds generated for 'chain 'O' and resid 416 through 418' Processing helix chain 'O' and resid 427 through 457 Processing helix chain 'O' and resid 457 through 473 removed outlier: 4.104A pdb=" N ILE O 471 " --> pdb=" O VAL O 467 " (cutoff:3.500A) Processing helix chain 'O' and resid 480 through 484 removed outlier: 3.619A pdb=" N GLN O 483 " --> pdb=" O GLU O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 491 through 530 removed outlier: 3.997A pdb=" N GLU O 495 " --> pdb=" O ILE O 491 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN O 497 " --> pdb=" O ALA O 493 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN O 498 " --> pdb=" O PRO O 494 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP O 517 " --> pdb=" O GLU O 513 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU O 518 " --> pdb=" O ILE O 514 " (cutoff:3.500A) removed outlier: 4.052A 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: 3.640A pdb=" N GLU P 92 " --> pdb=" O SER P 88 " (cutoff:3.500A) removed outlier: 5.643A 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: 3.630A 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: 3.913A 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: 3.599A 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: 7.348A pdb=" N LYS B1127 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE A 18 " --> pdb=" O ARG B1125 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ARG B1125 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE A 20 " --> pdb=" O ILE B1123 " (cutoff:3.500A) removed outlier: 6.611A 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: 6.766A pdb=" N THR A 253 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N LEU A 90 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 10.499A 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: 3.844A pdb=" N SER A 268 " --> pdb=" O GLY A 273 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY A 273 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.580A pdb=" N LYS A 359 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1021 through 1023 removed outlier: 8.045A pdb=" N PHE A 486 " --> pdb=" O ARG A 366 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 368 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N PHE A 488 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.940A 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: 4.135A pdb=" N PHE A 420 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N HIS A 453 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 6.717A 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: 6.928A 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: 7.067A pdb=" N TYR A1223 " --> pdb=" O LEU A1089 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A1089 " --> pdb=" O TYR A1223 " (cutoff:3.500A) removed outlier: 11.075A pdb=" N THR A1086 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N THR A1244 " --> pdb=" O THR A1086 " (cutoff:3.500A) removed outlier: 4.393A 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: 3.922A 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: 3.716A 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: 6.757A pdb=" N ASP B 116 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE B 80 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B 114 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ALA B 111 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG B 135 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 113 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 5.861A 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: 7.100A pdb=" N TYR B 119 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 5.255A 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: 3.654A 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: 6.465A 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: 5.405A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU B 541 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N VAL B 583 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 538 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 585 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 6.427A 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: 6.610A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.781A 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: 6.610A pdb=" N LEU B 880 " --> pdb=" O ILE B 871 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE B 871 " --> pdb=" O LEU B 880 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS B 882 " --> pdb=" O VAL B 869 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL B 869 " --> pdb=" O LYS B 882 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 884 " --> pdb=" O GLU B 867 " (cutoff:3.500A) removed outlier: 5.250A 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: 7.307A 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: 6.756A pdb=" N LEU B 757 " --> pdb=" O ILE B 910 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 927 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B 929 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 4.026A 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: 3.555A 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: 6.823A 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: 4.051A 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: 7.211A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.690A 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: 4.319A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.883A 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: 3.700A 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: 3.670A 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: 6.596A pdb=" N GLU G 6 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA D 6 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU G 4 " --> pdb=" O ALA D 6 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N HIS G 67 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA G 57 " --> pdb=" O HIS G 67 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LYS G 69 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU G 55 " --> pdb=" O LYS G 69 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.340A 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: 6.631A pdb=" N PHE G 49 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N PHE G 77 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N CYS G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 58 through 63 removed outlier: 5.987A pdb=" N THR E 59 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL E 74 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU E 61 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA E 63 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP E 70 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 7.120A 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: 5.951A 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: 3.652A 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: 3.660A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.728A 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: 3.874A pdb=" N ASP G 105 " --> pdb=" O LEU G 101 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU G 101 " --> pdb=" O ASP G 105 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE G 107 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL G 99 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 5.620A 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: 6.905A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 5.492A 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: 6.088A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.994A 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: 8.489A pdb=" N LEU M 124 " --> pdb=" O GLU M 12 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP M 14 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU M 126 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TYR M 16 " --> pdb=" O LEU M 126 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N LEU N 383 " --> pdb=" O LEU N 266 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE N 268 " --> pdb=" O LEU N 383 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N CYS N 385 " --> pdb=" O PHE N 268 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN N 270 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL N 337 " --> pdb=" O VAL N 348 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN N 325 " --> pdb=" O LEU M 17 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU M 17 " --> pdb=" O GLN N 325 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY N 327 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE N 331 " --> pdb=" O GLN M 11 " (cutoff:3.500A) removed outlier: 5.507A 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: 6.926A pdb=" N LEU M 25 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU M 133 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU M 27 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU M 135 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLN M 29 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ALA M 61 " --> pdb=" O HIS M 44 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N HIS M 44 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU M 45 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR M 210 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N HIS M 207 " --> pdb=" O GLY N 371 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N MET N 373 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N HIS M 209 " --> pdb=" O MET N 373 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N VAL N 375 " --> pdb=" O HIS M 209 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TYR M 211 " --> pdb=" O VAL N 375 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N GLY N 377 " --> pdb=" O TYR M 211 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU N 360 " --> pdb=" O LEU N 376 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N HIS N 378 " --> pdb=" O GLN N 358 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLN N 358 " --> pdb=" O HIS N 378 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG M 33 " --> pdb=" O LEU N 357 " (cutoff:3.500A) removed outlier: 11.789A pdb=" N GLU N 359 " --> pdb=" O PRO M 31 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N VAL N 361 " --> pdb=" O GLN M 29 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N GLN M 29 " --> pdb=" O VAL N 361 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N VAL N 363 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 9.291A 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: 6.575A pdb=" N CYS V 28 " --> pdb=" O VAL V 34 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL V 34 " --> pdb=" O CYS V 28 " (cutoff:3.500A) 1907 hydrogen bonds defined for protein. 5400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 15.20 Time building geometry restraints manager: 5.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 18146 1.41 - 1.63: 27054 1.63 - 1.85: 443 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 45655 Sorted by residual: bond pdb=" O3' U Z 9 " pdb=" P U Z 10 " ideal model delta sigma weight residual 1.607 1.438 0.169 1.50e-02 4.44e+03 1.27e+02 bond pdb=" O3' DT Y -12 " pdb=" P DC Y -11 " ideal model delta sigma weight residual 1.607 1.445 0.162 1.50e-02 4.44e+03 1.17e+02 bond pdb=" O3' DT Y -13 " pdb=" P DT Y -12 " ideal model delta sigma weight residual 1.607 1.471 0.136 1.50e-02 4.44e+03 8.17e+01 bond pdb=" O5' U Z 10 " pdb=" C5' U Z 10 " ideal model delta sigma weight residual 1.420 1.292 0.128 1.50e-02 4.44e+03 7.24e+01 bond pdb=" C1' DG X 15 " pdb=" N9 DG X 15 " ideal model delta sigma weight residual 1.468 1.361 0.107 1.40e-02 5.10e+03 5.83e+01 ... (remaining 45650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 62085 5.34 - 10.68: 41 10.68 - 16.02: 6 16.02 - 21.36: 4 21.36 - 26.70: 1 Bond angle restraints: 62137 Sorted by residual: angle pdb=" C3' DT Y -12 " pdb=" O3' DT Y -12 " pdb=" P DC Y -11 " ideal model delta sigma weight residual 120.20 99.47 20.73 1.50e+00 4.44e-01 1.91e+02 angle pdb=" C4' U Z 9 " pdb=" C3' U Z 9 " pdb=" O3' U Z 9 " ideal model delta sigma weight residual 113.00 95.02 17.98 1.50e+00 4.44e-01 1.44e+02 angle pdb=" O3' DT Y -12 " pdb=" P DC Y -11 " pdb=" OP1 DC Y -11 " ideal model delta sigma weight residual 108.00 81.30 26.70 3.00e+00 1.11e-01 7.92e+01 angle pdb=" C3' U Z 10 " pdb=" C2' U Z 10 " pdb=" O2' U Z 10 " ideal model delta sigma weight residual 110.70 98.54 12.16 1.50e+00 4.44e-01 6.57e+01 angle pdb=" O3' U Z 10 " pdb=" C3' U Z 10 " pdb=" C2' U Z 10 " ideal model delta sigma weight residual 113.70 124.75 -11.05 1.50e+00 4.44e-01 5.42e+01 ... (remaining 62132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 27202 35.88 - 71.76: 594 71.76 - 107.65: 27 107.65 - 143.53: 0 143.53 - 179.41: 9 Dihedral angle restraints: 27832 sinusoidal: 12353 harmonic: 15479 Sorted by residual: dihedral pdb=" CA TYR A1187 " pdb=" C TYR A1187 " pdb=" N VAL A1188 " pdb=" CA VAL A1188 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" O1A 3AT B1202 " pdb=" O3A 3AT B1202 " pdb=" PA 3AT B1202 " pdb=" PB 3AT B1202 " ideal model delta sinusoidal sigma weight residual 157.19 -20.12 177.31 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5' 3AT B1202 " pdb=" O3A 3AT B1202 " pdb=" PA 3AT B1202 " pdb=" PB 3AT B1202 " ideal model delta sinusoidal sigma weight residual 270.98 94.17 176.81 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 27829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 6707 0.099 - 0.197: 285 0.197 - 0.296: 5 0.296 - 0.395: 0 0.395 - 0.494: 1 Chirality restraints: 6998 Sorted by residual: chirality pdb=" P U Z 10 " pdb=" OP1 U Z 10 " pdb=" OP2 U Z 10 " pdb=" O5' U Z 10 " both_signs ideal model delta sigma weight residual True 2.41 -1.92 0.49 2.00e-01 2.50e+01 6.09e+00 chirality pdb=" P U Z 9 " pdb=" OP1 U Z 9 " pdb=" OP2 U Z 9 " pdb=" O5' U Z 9 " both_signs ideal model delta sigma weight residual True 2.41 -2.13 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C3' U Z 10 " pdb=" C4' U Z 10 " pdb=" O3' U Z 10 " pdb=" C2' U Z 10 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 6995 not shown) Planarity restraints: 7607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA X 13 " 0.031 2.00e-02 2.50e+03 1.69e-02 7.87e+00 pdb=" N9 DA X 13 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA X 13 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA X 13 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DA X 13 " -0.030 2.00e-02 2.50e+03 pdb=" C6 DA X 13 " 0.011 2.00e-02 2.50e+03 pdb=" N6 DA X 13 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA X 13 " 0.014 2.00e-02 2.50e+03 pdb=" C2 DA X 13 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA X 13 " -0.019 2.00e-02 2.50e+03 pdb=" C4 DA X 13 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 467 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO B 468 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 468 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 468 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA Y -25 " 0.033 2.00e-02 2.50e+03 1.41e-02 5.50e+00 pdb=" N9 DA Y -25 " -0.007 2.00e-02 2.50e+03 pdb=" C8 DA Y -25 " -0.011 2.00e-02 2.50e+03 pdb=" N7 DA Y -25 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DA Y -25 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DA Y -25 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA Y -25 " 0.024 2.00e-02 2.50e+03 pdb=" N1 DA Y -25 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA Y -25 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DA Y -25 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA Y -25 " -0.010 2.00e-02 2.50e+03 ... (remaining 7604 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.07: 13 2.07 - 2.78: 9028 2.78 - 3.49: 61278 3.49 - 4.19: 105994 4.19 - 4.90: 185460 Nonbonded interactions: 361773 Sorted by model distance: nonbonded pdb=" N1 DA X 17 " pdb=" C7 DT Y -17 " model vdw 1.369 3.540 nonbonded pdb=" NE ARG P 284 " pdb=" O PRO Q 47 " model vdw 1.667 3.120 nonbonded pdb=" N6 DA X 17 " pdb=" O4 DT Y -17 " model vdw 1.688 3.120 nonbonded pdb=" OG1 THR A 303 " pdb=" NE2 GLN O 377 " model vdw 1.724 3.120 nonbonded pdb=" CG ARG P 284 " pdb=" O VAL Q 46 " model vdw 1.817 3.440 ... (remaining 361768 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: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 63.530 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 1.057 45685 Z= 0.617 Angle : 0.769 47.047 62182 Z= 0.380 Chirality : 0.042 0.494 6998 Planarity : 0.003 0.060 7607 Dihedral : 13.105 179.411 17828 Min Nonbonded Distance : 1.369 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 0.94 % Allowed : 3.49 % Favored : 95.57 % 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: -1.00 (0.11), residues: 5269 helix: 0.34 (0.11), residues: 2052 sheet: -1.00 (0.18), residues: 708 loop : -1.38 (0.11), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 87 TYR 0.011 0.001 TYR A1116 PHE 0.008 0.001 PHE D 69 TRP 0.006 0.001 TRP P 313 HIS 0.003 0.000 HIS M 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.30 (45655) covalent geometry : angle 0.56776 / 0.37 (62137) hydrogen bonds : bond 0.14690 / 9.77 ( 1961) hydrogen bonds : angle 5.85100 / 4.14 ( 5558) metal coordination : bond 0.37360 / 21.43 ( 28) metal coordination : angle 19.28614 / 11.00 ( 45) Misc. bond : bond 0.69698 / 35.68 ( 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 1388 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 1344 time to evaluate : 1.643 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: A 4 GLU cc_start: 0.7095 (tp30) cc_final: 0.6879 (mp0) REVERT: A 58 HIS cc_start: 0.6253 (m-70) cc_final: 0.5551 (m-70) REVERT: A 249 ASP cc_start: 0.6222 (m-30) cc_final: 0.5943 (m-30) REVERT: A 262 ILE cc_start: 0.7499 (mt) cc_final: 0.7239 (mt) REVERT: A 280 THR cc_start: 0.6651 (m) cc_final: 0.6393 (m) REVERT: A 311 ASP cc_start: 0.7797 (t0) cc_final: 0.7299 (m-30) REVERT: A 312 PHE cc_start: 0.8059 (t80) cc_final: 0.7650 (t80) REVERT: A 343 GLN cc_start: 0.7038 (mp10) cc_final: 0.6662 (mp-120) REVERT: A 360 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.7128 (mtt90) REVERT: A 637 TYR cc_start: 0.7237 (t80) cc_final: 0.6785 (t80) REVERT: A 646 MET cc_start: 0.8591 (mmp) cc_final: 0.8286 (mmm) REVERT: A 722 LYS cc_start: 0.6657 (mtmt) cc_final: 0.6393 (ptmm) REVERT: A 761 ASP cc_start: 0.7262 (m-30) cc_final: 0.6994 (m-30) REVERT: A 770 GLU cc_start: 0.7562 (pp20) cc_final: 0.7361 (tt0) REVERT: A 811 ASP cc_start: 0.7170 (p0) cc_final: 0.6691 (m-30) REVERT: A 814 GLU cc_start: 0.7517 (tt0) cc_final: 0.7283 (mt-10) REVERT: A 827 LEU cc_start: 0.8085 (mt) cc_final: 0.7829 (mm) REVERT: A 836 ASN cc_start: 0.6496 (m-40) cc_final: 0.6293 (m-40) REVERT: A 872 GLN cc_start: 0.7781 (tp40) cc_final: 0.7490 (tp-100) REVERT: A 947 LEU cc_start: 0.7656 (tt) cc_final: 0.7017 (mt) REVERT: A 978 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6608 (mm-30) REVERT: A 998 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7731 (mtp180) REVERT: A 1019 ARG cc_start: 0.7502 (tmm160) cc_final: 0.7264 (ttp-110) REVERT: A 1020 ASP cc_start: 0.7439 (t70) cc_final: 0.7102 (t0) REVERT: A 1023 MET cc_start: 0.7777 (mmt) cc_final: 0.7544 (mmm) REVERT: A 1151 TYR cc_start: 0.8295 (t80) cc_final: 0.7891 (t80) REVERT: A 1179 GLU cc_start: 0.8098 (pt0) cc_final: 0.7253 (tm-30) REVERT: A 1214 ILE cc_start: 0.7655 (pt) cc_final: 0.7438 (pp) REVERT: A 1222 LYS cc_start: 0.7153 (pttt) cc_final: 0.6838 (pttm) REVERT: A 1310 LYS cc_start: 0.7583 (mttt) cc_final: 0.7174 (mtmt) REVERT: A 1355 ILE cc_start: 0.8335 (pt) cc_final: 0.8063 (pp) REVERT: B 27 TRP cc_start: 0.7737 (p-90) cc_final: 0.7263 (p-90) REVERT: B 35 LYS cc_start: 0.7372 (mmmm) cc_final: 0.7140 (mttt) REVERT: B 86 ASP cc_start: 0.7286 (m-30) cc_final: 0.6600 (p0) REVERT: B 139 MET cc_start: 0.8363 (ttm) cc_final: 0.7908 (ttt) REVERT: B 157 LYS cc_start: 0.8379 (mttp) cc_final: 0.8044 (mtmt) REVERT: B 192 GLU cc_start: 0.7467 (pt0) cc_final: 0.6978 (pm20) REVERT: B 237 VAL cc_start: 0.8288 (t) cc_final: 0.8074 (m) REVERT: B 258 GLU cc_start: 0.7810 (mp0) cc_final: 0.7228 (mp0) REVERT: B 277 ILE cc_start: 0.7652 (mm) cc_final: 0.7437 (mm) REVERT: B 285 LYS cc_start: 0.7332 (ttmm) cc_final: 0.7054 (tmtt) REVERT: B 307 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6759 (tm-30) REVERT: B 332 CYS cc_start: 0.8731 (m) cc_final: 0.8172 (m) REVERT: B 380 PHE cc_start: 0.5378 (t80) cc_final: 0.4780 (t80) REVERT: B 499 MET cc_start: 0.9022 (ttp) cc_final: 0.8285 (ttp) REVERT: B 506 MET cc_start: 0.8648 (mpp) cc_final: 0.8407 (mpt) REVERT: B 526 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7628 (pp) REVERT: B 530 GLU cc_start: 0.7326 (mp0) cc_final: 0.7102 (mp0) REVERT: B 557 ASN cc_start: 0.7722 (m-40) cc_final: 0.7300 (m-40) REVERT: B 600 LYS cc_start: 0.7543 (mtpt) cc_final: 0.7184 (mttp) REVERT: B 609 LYS cc_start: 0.8288 (tmmt) cc_final: 0.7424 (tppt) REVERT: B 611 MET cc_start: 0.8751 (mmm) cc_final: 0.8169 (mmp) REVERT: B 612 GLU cc_start: 0.7993 (tp30) cc_final: 0.7674 (tp30) REVERT: B 664 LEU cc_start: 0.7675 (tp) cc_final: 0.7423 (tt) REVERT: B 722 THR cc_start: 0.7761 (m) cc_final: 0.7480 (m) REVERT: B 723 LYS cc_start: 0.6458 (mttt) cc_final: 0.6244 (mtpt) REVERT: B 822 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6824 (mp0) REVERT: B 859 LYS cc_start: 0.7766 (mptt) cc_final: 0.7564 (mmmt) REVERT: B 863 ASP cc_start: 0.8153 (m-30) cc_final: 0.7742 (m-30) REVERT: B 916 MET cc_start: 0.8272 (mmt) cc_final: 0.7898 (mmp) REVERT: B 960 TYR cc_start: 0.7979 (m-80) cc_final: 0.7650 (m-80) REVERT: B 1037 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6446 (tm-30) REVERT: B 1062 MET cc_start: 0.8101 (mmm) cc_final: 0.7802 (mmm) REVERT: B 1069 MET cc_start: 0.7891 (tmm) cc_final: 0.7324 (tpp) REVERT: B 1105 ARG cc_start: 0.7449 (mmm160) cc_final: 0.6897 (mtp85) REVERT: B 1120 MET cc_start: 0.8614 (mtp) cc_final: 0.8382 (mtp) REVERT: C 5 GLN cc_start: 0.7341 (tp40) cc_final: 0.7096 (tm-30) REVERT: C 28 ASP cc_start: 0.8248 (p0) cc_final: 0.7729 (p0) REVERT: C 98 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7888 (p) REVERT: C 141 ARG cc_start: 0.6962 (tpt90) cc_final: 0.6729 (tpt170) REVERT: C 180 ASN cc_start: 0.7909 (m110) cc_final: 0.7607 (t0) REVERT: C 290 ASN cc_start: 0.7354 (t0) cc_final: 0.6958 (t0) REVERT: C 311 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6850 (pt0) REVERT: D 1 MET cc_start: 0.4648 (mmp) cc_final: 0.4319 (mmm) REVERT: D 14 TYR cc_start: 0.6595 (t80) cc_final: 0.5595 (t80) REVERT: D 41 ASN cc_start: 0.6370 (p0) cc_final: 0.6069 (p0) REVERT: D 43 ASN cc_start: 0.7116 (m110) cc_final: 0.6577 (p0) REVERT: D 69 PHE cc_start: 0.7605 (t80) cc_final: 0.7351 (t80) REVERT: D 76 HIS cc_start: 0.6966 (m170) cc_final: 0.6605 (m90) REVERT: D 79 THR cc_start: 0.5348 (t) cc_final: 0.4599 (p) REVERT: D 82 GLU cc_start: 0.6166 (mt-10) cc_final: 0.4945 (mt-10) REVERT: E 14 ARG cc_start: 0.7161 (ttt90) cc_final: 0.6873 (ttm-80) REVERT: E 21 CYS cc_start: 0.7634 (m) cc_final: 0.7005 (m) REVERT: E 22 HIS cc_start: 0.8025 (t-90) cc_final: 0.7772 (t-170) REVERT: E 34 ASP cc_start: 0.6542 (t0) cc_final: 0.5917 (p0) REVERT: E 36 THR cc_start: 0.6609 (t) cc_final: 0.6370 (m) REVERT: E 70 ASP cc_start: 0.6493 (t0) cc_final: 0.5758 (t0) REVERT: E 73 PHE cc_start: 0.6286 (t80) cc_final: 0.4473 (t80) REVERT: E 87 ILE cc_start: 0.8151 (mm) cc_final: 0.7941 (mt) REVERT: E 88 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7956 (mmmt) REVERT: E 139 ILE cc_start: 0.7662 (mt) cc_final: 0.7320 (tt) REVERT: E 167 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7340 (tt0) REVERT: E 187 ARG cc_start: 0.6076 (ttm-80) cc_final: 0.5580 (mmm-85) REVERT: F 51 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.4085 (mmp-170) REVERT: F 98 LYS cc_start: 0.8237 (ttpp) cc_final: 0.7995 (ttmm) REVERT: F 100 ARG cc_start: 0.7027 (mtp85) cc_final: 0.6741 (mmt-90) REVERT: G 32 LYS cc_start: 0.8019 (mtpt) cc_final: 0.7596 (mtmt) REVERT: G 41 ASN cc_start: 0.8655 (m-40) cc_final: 0.8368 (m-40) REVERT: G 53 LYS cc_start: 0.6834 (tptt) cc_final: 0.6434 (tppp) REVERT: G 69 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7885 (tttp) REVERT: G 82 ASP cc_start: 0.5912 (m-30) cc_final: 0.5503 (m-30) REVERT: G 84 ILE cc_start: 0.7339 (mt) cc_final: 0.7056 (mm) REVERT: G 150 PHE cc_start: 0.5275 (t80) cc_final: 0.4066 (t80) REVERT: H 44 ASN cc_start: 0.6355 (t0) cc_final: 0.6088 (t0) REVERT: H 51 ASP cc_start: 0.7260 (m-30) cc_final: 0.7020 (m-30) REVERT: H 65 TYR cc_start: 0.6835 (m-10) cc_final: 0.6544 (m-80) REVERT: H 128 ASP cc_start: 0.7605 (m-30) cc_final: 0.7106 (m-30) REVERT: H 136 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7007 (mt-10) REVERT: H 146 LYS cc_start: 0.7607 (tttp) cc_final: 0.7391 (tttm) REVERT: I 1 MET cc_start: 0.3413 (pmm) cc_final: 0.2760 (pmt) REVERT: I 15 GLU cc_start: 0.5793 (pt0) cc_final: 0.5557 (pt0) REVERT: I 26 ASN cc_start: 0.8091 (m-40) cc_final: 0.7668 (t0) REVERT: I 47 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7549 (tttt) REVERT: J 36 ASP cc_start: 0.7746 (m-30) cc_final: 0.7514 (m-30) REVERT: J 41 LYS cc_start: 0.7383 (mttp) cc_final: 0.7172 (tmmt) REVERT: K 37 ARG cc_start: 0.7007 (mmm-85) cc_final: 0.6735 (mtp85) REVERT: K 48 ASP cc_start: 0.6647 (p0) cc_final: 0.6319 (p0) REVERT: K 66 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7313 (tp30) REVERT: K 108 GLN cc_start: 0.7641 (tp40) cc_final: 0.7100 (mm-40) REVERT: K 112 ASP cc_start: 0.8117 (m-30) cc_final: 0.7681 (m-30) REVERT: L 24 THR cc_start: 0.7824 (p) cc_final: 0.7493 (p) REVERT: M 16 TYR cc_start: 0.7374 (m-10) cc_final: 0.6747 (m-10) REVERT: M 19 LYS cc_start: 0.7929 (mmmm) cc_final: 0.7401 (mmtt) REVERT: M 41 ASP cc_start: 0.7589 (m-30) cc_final: 0.6882 (p0) REVERT: M 73 LYS cc_start: 0.7433 (tttp) cc_final: 0.6914 (tmtt) REVERT: M 82 ASP cc_start: 0.4510 (m-30) cc_final: 0.3651 (p0) REVERT: M 97 MET cc_start: 0.6749 (ttt) cc_final: 0.6399 (tpp) REVERT: M 188 ARG cc_start: 0.6339 (mtt180) cc_final: 0.5506 (ptm-80) REVERT: M 286 MET cc_start: 0.4134 (mmm) cc_final: 0.3573 (mmm) REVERT: M 292 MET cc_start: 0.4070 (ptm) cc_final: 0.3309 (ttt) REVERT: M 389 MET cc_start: 0.4610 (ptp) cc_final: 0.4307 (ptm) REVERT: N 328 LYS cc_start: 0.7013 (mtpp) cc_final: 0.6653 (mtpp) REVERT: N 382 LYS cc_start: 0.6790 (tttt) cc_final: 0.6589 (tttt) REVERT: N 385 CYS cc_start: 0.5739 (m) cc_final: 0.5494 (m) REVERT: N 390 GLU cc_start: 0.6188 (tt0) cc_final: 0.5768 (tm-30) REVERT: O 14 GLN cc_start: 0.7832 (tt0) cc_final: 0.7548 (tm-30) REVERT: O 15 GLU cc_start: 0.8250 (tp30) cc_final: 0.8010 (tp30) REVERT: O 22 GLU cc_start: 0.7779 (pp20) cc_final: 0.7440 (pp20) REVERT: O 75 TYR cc_start: 0.7255 (m-80) cc_final: 0.6846 (m-80) REVERT: O 76 GLU cc_start: 0.8343 (tt0) cc_final: 0.7064 (pm20) REVERT: O 270 MET cc_start: 0.6616 (mtp) cc_final: 0.6285 (mtp) REVERT: O 306 GLN cc_start: 0.6457 (pp30) cc_final: 0.5960 (pt0) REVERT: O 355 GLN cc_start: 0.8352 (tt0) cc_final: 0.7893 (tt0) REVERT: O 381 GLU cc_start: 0.6601 (mt-10) cc_final: 0.6311 (tm-30) REVERT: O 408 GLU cc_start: 0.6881 (tt0) cc_final: 0.6372 (tp30) REVERT: O 419 ARG cc_start: 0.7466 (ptp-170) cc_final: 0.7075 (ptm-80) REVERT: O 507 ASN cc_start: 0.7997 (m-40) cc_final: 0.7617 (m110) REVERT: O 531 MET cc_start: 0.5841 (mtm) cc_final: 0.5542 (mtp) REVERT: P 42 MET cc_start: 0.0823 (tpt) cc_final: 0.0424 (tpt) REVERT: P 134 LYS cc_start: 0.1655 (OUTLIER) cc_final: 0.1242 (ttmt) REVERT: Q 46 VAL cc_start: 0.6995 (t) cc_final: 0.6772 (m) REVERT: Q 54 GLU cc_start: 0.6384 (mp0) cc_final: 0.5944 (mp0) REVERT: Q 73 TYR cc_start: 0.7394 (m-80) cc_final: 0.6667 (m-80) REVERT: Q 77 THR cc_start: 0.5691 (OUTLIER) cc_final: 0.5360 (m) REVERT: Q 92 MET cc_start: 0.2454 (ptt) cc_final: 0.2216 (ptt) REVERT: Q 103 TRP cc_start: 0.7160 (m100) cc_final: 0.6900 (m-90) outliers start: 44 outliers final: 12 residues processed: 1372 average time/residue: 0.7137 time to fit residues: 1206.6783 Evaluate side-chains 812 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 795 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 134 LYS Chi-restraints excluded: chain Q residue 77 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 50.0000 chunk 497 optimal weight: 30.0000 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 0.9990 chunk 223 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 44 GLN A 119 GLN A 163 ASN A 225 ASN A 409 GLN A 423 GLN A 528 ASN A 739 GLN A1026 GLN A1039 GLN A1075 ASN B 159 ASN B 253 GLN B 282 GLN B 552 HIS ** B 806 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN D 35 HIS D 85 GLN E 71 GLN E 168 ASN G 115 GLN H 29 HIS H 131 ASN I 40 ASN K 38 HIS M 11 GLN M 44 HIS M 197 GLN O 60 HIS O 66 GLN O 68 HIS O 158 GLN O 437 HIS O 457 ASN O 475 GLN ** P 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 182 GLN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 274 ASN Q 62 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.206673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127662 restraints weight = 54795.229| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.35 r_work: 0.3194 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 45685 Z= 0.225 Angle : 0.726 27.944 62182 Z= 0.361 Chirality : 0.048 0.339 6998 Planarity : 0.006 0.127 7607 Dihedral : 16.254 179.618 7138 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.98 % Allowed : 12.84 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.11), residues: 5269 helix: 1.04 (0.11), residues: 2051 sheet: -0.74 (0.18), residues: 726 loop : -1.04 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG Q 113 TYR 0.028 0.002 TYR A1296 PHE 0.030 0.002 PHE C 225 TRP 0.030 0.002 TRP M 423 HIS 0.012 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (45655) covalent geometry : angle 0.69619 / 0.36 (62137) hydrogen bonds : bond 0.04532 / 3.04 ( 1961) hydrogen bonds : angle 4.68657 / 3.36 ( 5558) metal coordination : bond 0.02353 / 1.23 ( 28) metal coordination : angle 7.72654 / 4.45 ( 45) Misc. bond : bond 0.01962 / 0.93 ( 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 1013 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 826 time to evaluate : 1.715 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 4 GLU cc_start: 0.7455 (tp30) cc_final: 0.7205 (mp0) REVERT: A 131 ARG cc_start: 0.7787 (ptp-110) cc_final: 0.7343 (ptp90) REVERT: A 233 GLU cc_start: 0.8446 (tt0) cc_final: 0.8208 (tp30) REVERT: A 240 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8559 (mtp) REVERT: A 262 ILE cc_start: 0.8413 (mt) cc_final: 0.8101 (mt) REVERT: A 311 ASP cc_start: 0.8314 (t0) cc_final: 0.7850 (m-30) REVERT: A 312 PHE cc_start: 0.8248 (t80) cc_final: 0.7966 (t80) REVERT: A 349 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: A 436 ASN cc_start: 0.8251 (t0) cc_final: 0.7951 (t0) REVERT: A 620 LYS cc_start: 0.7159 (mtmt) cc_final: 0.6276 (mptt) REVERT: A 711 LYS cc_start: 0.8276 (pttm) cc_final: 0.7898 (pttt) REVERT: A 761 ASP cc_start: 0.8222 (m-30) cc_final: 0.7932 (m-30) REVERT: A 790 ILE cc_start: 0.8626 (mm) cc_final: 0.8383 (mp) REVERT: A 814 GLU cc_start: 0.8358 (tt0) cc_final: 0.8083 (tp30) REVERT: A 947 LEU cc_start: 0.8416 (tt) cc_final: 0.7838 (mt) REVERT: A 954 LYS cc_start: 0.8028 (ptpt) cc_final: 0.7799 (mmpt) REVERT: A 970 LYS cc_start: 0.7776 (mttt) cc_final: 0.7446 (mmtt) REVERT: A 982 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7871 (mtpp) REVERT: A 1020 ASP cc_start: 0.8783 (t70) cc_final: 0.8476 (t0) REVERT: A 1023 MET cc_start: 0.9238 (mmt) cc_final: 0.9019 (mmm) REVERT: A 1024 ARG cc_start: 0.8996 (mtm110) cc_final: 0.8632 (mtm180) REVERT: A 1065 LEU cc_start: 0.8297 (tt) cc_final: 0.8070 (tp) REVERT: A 1091 LYS cc_start: 0.7684 (mttt) cc_final: 0.7345 (mmtt) REVERT: A 1151 TYR cc_start: 0.8311 (t80) cc_final: 0.7897 (t80) REVERT: A 1179 GLU cc_start: 0.8195 (pt0) cc_final: 0.7401 (tm-30) REVERT: A 1214 ILE cc_start: 0.7996 (pt) cc_final: 0.7780 (pp) REVERT: A 1222 LYS cc_start: 0.7573 (pttt) cc_final: 0.7158 (pttm) REVERT: A 1277 ASN cc_start: 0.8824 (m-40) cc_final: 0.8523 (m-40) REVERT: A 1354 ASN cc_start: 0.8680 (m-40) cc_final: 0.8176 (m110) REVERT: A 1379 PHE cc_start: 0.8680 (t80) cc_final: 0.8236 (t80) REVERT: B 35 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8164 (mttt) REVERT: B 139 MET cc_start: 0.9262 (ttm) cc_final: 0.8854 (ttt) REVERT: B 192 GLU cc_start: 0.7839 (pt0) cc_final: 0.7488 (pm20) REVERT: B 258 GLU cc_start: 0.8046 (mp0) cc_final: 0.7665 (mp0) REVERT: B 277 ILE cc_start: 0.7927 (mm) cc_final: 0.7712 (mm) REVERT: B 290 LYS cc_start: 0.7875 (mmtm) cc_final: 0.7504 (mppt) REVERT: B 307 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6615 (tm-30) REVERT: B 332 CYS cc_start: 0.9032 (m) cc_final: 0.8564 (m) REVERT: B 380 PHE cc_start: 0.6708 (t80) cc_final: 0.6324 (t80) REVERT: B 431 MET cc_start: 0.7596 (ptm) cc_final: 0.7353 (ppp) REVERT: B 488 GLU cc_start: 0.8211 (tt0) cc_final: 0.7735 (tp30) REVERT: B 499 MET cc_start: 0.9146 (ttp) cc_final: 0.8765 (ttp) REVERT: B 506 MET cc_start: 0.8851 (mpp) cc_final: 0.8598 (mpt) REVERT: B 544 ASN cc_start: 0.8412 (m-40) cc_final: 0.8090 (m-40) REVERT: B 600 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7874 (mttp) REVERT: B 611 MET cc_start: 0.9008 (mmm) cc_final: 0.8742 (mmp) REVERT: B 612 GLU cc_start: 0.8597 (tp30) cc_final: 0.8241 (tp30) REVERT: B 623 ASP cc_start: 0.8942 (m-30) cc_final: 0.8374 (m-30) REVERT: B 627 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8361 (mp0) REVERT: B 822 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8606 (mp0) REVERT: B 1028 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8554 (mtt-85) REVERT: B 1031 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8374 (tp) REVERT: B 1041 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7594 (mtm180) REVERT: B 1062 MET cc_start: 0.9352 (mmm) cc_final: 0.9050 (mmm) REVERT: B 1069 MET cc_start: 0.9013 (tmm) cc_final: 0.8649 (tpp) REVERT: B 1105 ARG cc_start: 0.8322 (mmm160) cc_final: 0.8101 (mtp85) REVERT: C 28 ASP cc_start: 0.8805 (p0) cc_final: 0.8544 (p0) REVERT: C 209 ASP cc_start: 0.8838 (t0) cc_final: 0.8451 (t0) REVERT: C 251 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7517 (tp30) REVERT: C 279 ARG cc_start: 0.8235 (ttt-90) cc_final: 0.7903 (ttt90) REVERT: D 18 GLN cc_start: 0.7168 (mt0) cc_final: 0.6853 (mt0) REVERT: D 64 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: D 76 HIS cc_start: 0.6954 (m170) cc_final: 0.6720 (m90) REVERT: D 82 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6159 (mm-30) REVERT: D 100 MET cc_start: 0.5996 (mmt) cc_final: 0.5702 (mmt) REVERT: E 21 CYS cc_start: 0.8248 (m) cc_final: 0.7691 (m) REVERT: E 33 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8037 (mm) REVERT: E 34 ASP cc_start: 0.6610 (t0) cc_final: 0.6120 (p0) REVERT: E 58 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5724 (mt) REVERT: E 61 LEU cc_start: 0.6725 (mm) cc_final: 0.6469 (mm) REVERT: E 87 ILE cc_start: 0.8241 (mm) cc_final: 0.7981 (pp) REVERT: E 98 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7634 (m-40) REVERT: E 115 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8082 (mtmm) REVERT: E 139 ILE cc_start: 0.8379 (mt) cc_final: 0.8175 (tt) REVERT: F 51 ARG cc_start: 0.7000 (mtm-85) cc_final: 0.4890 (mmp-170) REVERT: F 100 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7882 (mtt90) REVERT: F 121 ASP cc_start: 0.8845 (p0) cc_final: 0.8628 (p0) REVERT: G 19 GLU cc_start: 0.8164 (pm20) cc_final: 0.7906 (pm20) REVERT: G 32 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8288 (mtmt) REVERT: G 37 LYS cc_start: 0.8457 (mmtm) cc_final: 0.8156 (mmtm) REVERT: G 41 ASN cc_start: 0.8822 (m-40) cc_final: 0.8569 (m-40) REVERT: G 44 LEU cc_start: 0.8003 (tt) cc_final: 0.7298 (tm) REVERT: G 50 ASP cc_start: 0.8484 (p0) cc_final: 0.8249 (p0) REVERT: G 53 LYS cc_start: 0.7695 (tptt) cc_final: 0.7288 (tppp) REVERT: G 60 PHE cc_start: 0.8846 (m-10) cc_final: 0.8415 (m-10) REVERT: G 150 PHE cc_start: 0.5454 (t80) cc_final: 0.4020 (t80) REVERT: H 51 ASP cc_start: 0.7898 (m-30) cc_final: 0.7551 (m-30) REVERT: H 52 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8190 (tt) REVERT: H 146 LYS cc_start: 0.9024 (tttp) cc_final: 0.8760 (tttm) REVERT: K 24 LYS cc_start: 0.7330 (ptpp) cc_final: 0.6646 (ptmm) REVERT: K 37 ARG cc_start: 0.7774 (mmm-85) cc_final: 0.7512 (mmm-85) REVERT: K 48 ASP cc_start: 0.8092 (p0) cc_final: 0.7700 (p0) REVERT: M 16 TYR cc_start: 0.7451 (m-10) cc_final: 0.7038 (m-10) REVERT: M 41 ASP cc_start: 0.7845 (m-30) cc_final: 0.7063 (p0) REVERT: M 97 MET cc_start: 0.7029 (ttt) cc_final: 0.6530 (tpp) REVERT: M 210 TYR cc_start: 0.6788 (t80) cc_final: 0.6103 (t80) REVERT: M 389 MET cc_start: 0.4240 (ptp) cc_final: 0.3773 (ptm) REVERT: N 328 LYS cc_start: 0.7094 (mtpp) cc_final: 0.6870 (mtpp) REVERT: N 390 GLU cc_start: 0.7036 (tt0) cc_final: 0.6295 (tm-30) REVERT: O 14 GLN cc_start: 0.7744 (tt0) cc_final: 0.7395 (tm-30) REVERT: O 15 GLU cc_start: 0.8341 (tp30) cc_final: 0.8133 (tp30) REVERT: O 20 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8306 (pp) REVERT: O 76 GLU cc_start: 0.8334 (tt0) cc_final: 0.7221 (pm20) REVERT: O 355 GLN cc_start: 0.8503 (tt0) cc_final: 0.7993 (tt0) REVERT: O 408 GLU cc_start: 0.7583 (tt0) cc_final: 0.7097 (tp30) REVERT: O 419 ARG cc_start: 0.7554 (ptp-170) cc_final: 0.7163 (ptm-80) REVERT: O 420 THR cc_start: 0.7001 (t) cc_final: 0.6315 (p) REVERT: O 531 MET cc_start: 0.6333 (mtm) cc_final: 0.6079 (mtm) REVERT: P 134 LYS cc_start: 0.1479 (OUTLIER) cc_final: 0.1232 (ttmt) REVERT: P 232 MET cc_start: 0.3115 (tpt) cc_final: 0.2089 (tpt) REVERT: P 235 ILE cc_start: 0.6229 (mm) cc_final: 0.5833 (pp) REVERT: Q 40 ASP cc_start: 0.7384 (m-30) cc_final: 0.7064 (m-30) REVERT: Q 62 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7405 (mp10) REVERT: Q 71 MET cc_start: 0.7481 (mmm) cc_final: 0.7013 (ttt) REVERT: Q 73 TYR cc_start: 0.7289 (m-80) cc_final: 0.6608 (m-80) REVERT: Q 77 THR cc_start: 0.5590 (OUTLIER) cc_final: 0.5318 (m) REVERT: Q 92 MET cc_start: 0.2491 (ptt) cc_final: 0.2274 (ptt) REVERT: Q 103 TRP cc_start: 0.7027 (m100) cc_final: 0.6680 (m-90) outliers start: 187 outliers final: 60 residues processed: 937 average time/residue: 0.7199 time to fit residues: 827.9550 Evaluate side-chains 754 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 680 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 982 LYS Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 790 VAL Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 1028 ARG Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LEU Chi-restraints excluded: chain B residue 1041 ARG Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 147 LYS 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 37 ARG Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 512 SER Chi-restraints excluded: chain P residue 134 LYS Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 425 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 428 optimal weight: 8.9990 chunk 304 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 0.2980 chunk 431 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 326 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 163 ASN A 419 ASN A 469 HIS A 599 GLN A1075 ASN A1277 ASN B 260 HIS B 282 GLN B 438 GLN B 616 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS E 168 ASN K 38 HIS ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN O 168 ASN O 402 ASN P 201 ASN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.205931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126679 restraints weight = 54253.560| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.39 r_work: 0.3181 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 45685 Z= 0.136 Angle : 0.613 28.843 62182 Z= 0.299 Chirality : 0.043 0.270 6998 Planarity : 0.004 0.072 7607 Dihedral : 15.976 179.805 7118 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.73 % Allowed : 15.84 % 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: 0.03 (0.11), residues: 5269 helix: 1.37 (0.11), residues: 2068 sheet: -0.64 (0.19), residues: 697 loop : -0.91 (0.12), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 293 TYR 0.029 0.001 TYR P 219 PHE 0.021 0.001 PHE D 17 TRP 0.017 0.001 TRP B 297 HIS 0.009 0.001 HIS M 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (45655) covalent geometry : angle 0.57622 / 0.30 (62137) hydrogen bonds : bond 0.03822 / 2.55 ( 1961) hydrogen bonds : angle 4.44055 / 3.18 ( 5558) metal coordination : bond 0.00747 / 0.39 ( 28) metal coordination : angle 7.82218 / 4.55 ( 45) Misc. bond : bond 0.00395 / 0.20 ( 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 884 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 709 time to evaluate : 1.682 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 4 GLU cc_start: 0.7473 (tp30) cc_final: 0.7215 (mp0) REVERT: A 131 ARG cc_start: 0.7786 (ptp-110) cc_final: 0.7369 (ptp90) REVERT: A 233 GLU cc_start: 0.8505 (tt0) cc_final: 0.8283 (tp30) REVERT: A 240 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8662 (mtp) REVERT: A 252 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8161 (pp) REVERT: A 255 LEU cc_start: 0.8465 (tp) cc_final: 0.8255 (mt) REVERT: A 262 ILE cc_start: 0.8665 (mt) cc_final: 0.8307 (mp) REVERT: A 294 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7729 (mmmt) REVERT: A 308 GLU cc_start: 0.8080 (tp30) cc_final: 0.7831 (tt0) REVERT: A 311 ASP cc_start: 0.8300 (t0) cc_final: 0.7889 (m-30) REVERT: A 436 ASN cc_start: 0.8238 (t0) cc_final: 0.7890 (t0) REVERT: A 575 LYS cc_start: 0.9078 (ptpt) cc_final: 0.8806 (ptpt) REVERT: A 620 LYS cc_start: 0.6773 (mtmt) cc_final: 0.6287 (mptt) REVERT: A 761 ASP cc_start: 0.8248 (m-30) cc_final: 0.7970 (m-30) REVERT: A 790 ILE cc_start: 0.8742 (mm) cc_final: 0.8436 (mp) REVERT: A 814 GLU cc_start: 0.8282 (tt0) cc_final: 0.7933 (tp30) REVERT: A 947 LEU cc_start: 0.8302 (tt) cc_final: 0.7801 (mt) REVERT: A 954 LYS cc_start: 0.8213 (ptpt) cc_final: 0.7926 (mmpt) REVERT: A 962 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7538 (tt0) REVERT: A 970 LYS cc_start: 0.7716 (mttt) cc_final: 0.7367 (mmtt) REVERT: A 982 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7832 (mtpp) REVERT: A 1020 ASP cc_start: 0.8757 (t70) cc_final: 0.8435 (t0) REVERT: A 1023 MET cc_start: 0.9217 (mmt) cc_final: 0.8953 (mmm) REVERT: A 1024 ARG cc_start: 0.9006 (mtm110) cc_final: 0.8617 (mtm180) REVERT: A 1065 LEU cc_start: 0.8332 (tt) cc_final: 0.8131 (tp) REVERT: A 1091 LYS cc_start: 0.7701 (mttt) cc_final: 0.7351 (mmtt) REVERT: A 1151 TYR cc_start: 0.8323 (t80) cc_final: 0.7937 (t80) REVERT: A 1179 GLU cc_start: 0.8095 (pt0) cc_final: 0.7411 (tm-30) REVERT: A 1191 PHE cc_start: 0.6970 (t80) cc_final: 0.6502 (t80) REVERT: A 1193 LYS cc_start: 0.8224 (mtmt) cc_final: 0.7946 (ttpp) REVERT: A 1222 LYS cc_start: 0.7507 (pttt) cc_final: 0.7142 (pttm) REVERT: A 1253 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7439 (tt0) REVERT: A 1275 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8636 (mmt) REVERT: A 1277 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8509 (m-40) REVERT: A 1354 ASN cc_start: 0.8580 (m-40) cc_final: 0.8077 (m110) REVERT: B 35 LYS cc_start: 0.8521 (mmmm) cc_final: 0.8159 (mttt) REVERT: B 139 MET cc_start: 0.9239 (ttm) cc_final: 0.8680 (ttp) REVERT: B 192 GLU cc_start: 0.7825 (pt0) cc_final: 0.7468 (pm20) REVERT: B 258 GLU cc_start: 0.8077 (mp0) cc_final: 0.7470 (mp0) REVERT: B 277 ILE cc_start: 0.7946 (mm) cc_final: 0.7734 (mm) REVERT: B 290 LYS cc_start: 0.7869 (mmtm) cc_final: 0.7452 (mppt) REVERT: B 332 CYS cc_start: 0.8852 (m) cc_final: 0.8396 (m) REVERT: B 380 PHE cc_start: 0.6623 (t80) cc_final: 0.6206 (t80) REVERT: B 499 MET cc_start: 0.9045 (ttp) cc_final: 0.8770 (ttp) REVERT: B 506 MET cc_start: 0.8837 (mpp) cc_final: 0.8459 (mpt) REVERT: B 530 GLU cc_start: 0.7671 (mp0) cc_final: 0.7368 (mp0) REVERT: B 544 ASN cc_start: 0.8371 (m-40) cc_final: 0.8027 (m-40) REVERT: B 575 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8449 (p) REVERT: B 600 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7781 (mttp) REVERT: B 611 MET cc_start: 0.9075 (mmm) cc_final: 0.8695 (mmp) REVERT: B 612 GLU cc_start: 0.8558 (tp30) cc_final: 0.8177 (tp30) REVERT: B 623 ASP cc_start: 0.9015 (m-30) cc_final: 0.8511 (m-30) REVERT: B 627 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8339 (mp0) REVERT: B 726 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8598 (mt-10) REVERT: B 778 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8139 (m) REVERT: B 822 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8544 (mp0) REVERT: B 960 TYR cc_start: 0.9089 (m-80) cc_final: 0.8643 (m-80) REVERT: B 1050 MET cc_start: 0.9259 (mtp) cc_final: 0.8980 (mtp) REVERT: B 1062 MET cc_start: 0.9328 (mmm) cc_final: 0.9056 (mmm) REVERT: B 1069 MET cc_start: 0.8995 (tmm) cc_final: 0.8754 (tmm) REVERT: B 1105 ARG cc_start: 0.8269 (mmm160) cc_final: 0.8017 (mtp85) REVERT: C 28 ASP cc_start: 0.8689 (p0) cc_final: 0.8420 (p0) REVERT: C 141 ARG cc_start: 0.8749 (tpt170) cc_final: 0.8494 (tpt170) REVERT: C 209 ASP cc_start: 0.8986 (t0) cc_final: 0.8642 (t0) REVERT: C 251 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7501 (tp30) REVERT: D 18 GLN cc_start: 0.7212 (mt0) cc_final: 0.6847 (mt0) REVERT: D 76 HIS cc_start: 0.6907 (m170) cc_final: 0.6695 (m90) REVERT: D 82 GLU cc_start: 0.6536 (mt-10) cc_final: 0.5860 (mm-30) REVERT: D 100 MET cc_start: 0.5250 (mmt) cc_final: 0.5018 (mmt) REVERT: E 21 CYS cc_start: 0.8150 (m) cc_final: 0.7593 (m) REVERT: E 33 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7948 (mm) REVERT: E 34 ASP cc_start: 0.6894 (t0) cc_final: 0.6172 (p0) REVERT: E 61 LEU cc_start: 0.6551 (mm) cc_final: 0.6326 (mm) REVERT: E 98 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7643 (m-40) REVERT: E 121 MET cc_start: 0.6943 (mmm) cc_final: 0.6734 (mmm) REVERT: F 51 ARG cc_start: 0.6972 (mtm-85) cc_final: 0.4777 (mmp-170) REVERT: F 100 ARG cc_start: 0.8422 (mtp85) cc_final: 0.7830 (mmt-90) REVERT: F 121 ASP cc_start: 0.8878 (p0) cc_final: 0.8605 (p0) REVERT: G 32 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8204 (mtmt) REVERT: G 37 LYS cc_start: 0.8516 (mmtm) cc_final: 0.8033 (mmtm) REVERT: G 41 ASN cc_start: 0.8764 (m-40) cc_final: 0.8495 (m-40) REVERT: G 53 LYS cc_start: 0.7735 (tptt) cc_final: 0.7368 (tppp) REVERT: G 77 PHE cc_start: 0.7545 (t80) cc_final: 0.7064 (t80) REVERT: G 82 ASP cc_start: 0.6375 (m-30) cc_final: 0.5887 (m-30) REVERT: G 150 PHE cc_start: 0.5522 (t80) cc_final: 0.4282 (t80) REVERT: H 11 ASP cc_start: 0.8472 (t70) cc_final: 0.8245 (m-30) REVERT: H 51 ASP cc_start: 0.7967 (m-30) cc_final: 0.7670 (m-30) REVERT: H 52 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8311 (tt) REVERT: H 100 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7646 (mt-10) REVERT: H 146 LYS cc_start: 0.9018 (tttp) cc_final: 0.8779 (tttm) REVERT: I 45 LYS cc_start: 0.7593 (tptt) cc_final: 0.7292 (tmtt) REVERT: J 31 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: K 24 LYS cc_start: 0.7315 (ptpp) cc_final: 0.6641 (ptmm) REVERT: K 48 ASP cc_start: 0.8128 (p0) cc_final: 0.7809 (p0) REVERT: K 60 MET cc_start: 0.9249 (mmm) cc_final: 0.8991 (mmm) REVERT: K 66 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: K 97 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8790 (mt0) REVERT: L 38 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7379 (pp20) REVERT: M 16 TYR cc_start: 0.7542 (m-10) cc_final: 0.7009 (m-10) REVERT: M 41 ASP cc_start: 0.7945 (m-30) cc_final: 0.7142 (p0) REVERT: M 97 MET cc_start: 0.6998 (ttt) cc_final: 0.6497 (tpp) REVERT: M 110 ASN cc_start: 0.7565 (t0) cc_final: 0.7304 (t0) REVERT: M 121 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.5403 (pm20) REVERT: M 286 MET cc_start: 0.4190 (mmm) cc_final: 0.3479 (mmm) REVERT: M 292 MET cc_start: 0.2787 (ptm) cc_final: 0.2250 (ttt) REVERT: M 389 MET cc_start: 0.4457 (ptp) cc_final: 0.4000 (ptm) REVERT: M 421 MET cc_start: 0.5203 (pp-130) cc_final: 0.4483 (mpp) REVERT: N 141 LYS cc_start: 0.5067 (OUTLIER) cc_final: 0.4320 (mtpt) REVERT: N 157 MET cc_start: 0.1827 (tpt) cc_final: 0.0912 (tmm) REVERT: N 328 LYS cc_start: 0.7213 (mtpp) cc_final: 0.6926 (mtpp) REVERT: N 390 GLU cc_start: 0.7046 (tt0) cc_final: 0.6332 (tm-30) REVERT: O 14 GLN cc_start: 0.7639 (tt0) cc_final: 0.7371 (tm-30) REVERT: O 15 GLU cc_start: 0.8342 (tp30) cc_final: 0.8135 (tp30) REVERT: O 76 GLU cc_start: 0.8357 (tt0) cc_final: 0.7183 (pm20) REVERT: O 336 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.6047 (pt) REVERT: O 355 GLN cc_start: 0.8409 (tt0) cc_final: 0.7937 (tt0) REVERT: O 394 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6807 (mtp) REVERT: O 408 GLU cc_start: 0.7212 (tt0) cc_final: 0.6871 (tp30) REVERT: O 419 ARG cc_start: 0.7508 (ptp-170) cc_final: 0.7123 (ptm-80) REVERT: O 420 THR cc_start: 0.7025 (t) cc_final: 0.6506 (p) REVERT: O 507 ASN cc_start: 0.8040 (m-40) cc_final: 0.7608 (m110) REVERT: P 134 LYS cc_start: 0.1657 (OUTLIER) cc_final: 0.1399 (ttmt) REVERT: P 232 MET cc_start: 0.3293 (tpt) cc_final: 0.2985 (tpt) REVERT: Q 54 GLU cc_start: 0.6217 (mp0) cc_final: 0.5970 (mp0) REVERT: Q 62 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7401 (mp10) REVERT: Q 68 MET cc_start: 0.7504 (tpt) cc_final: 0.7286 (tpt) REVERT: Q 71 MET cc_start: 0.7525 (mmm) cc_final: 0.6952 (ttt) REVERT: Q 73 TYR cc_start: 0.7342 (m-80) cc_final: 0.6625 (m-80) REVERT: Q 77 THR cc_start: 0.5572 (OUTLIER) cc_final: 0.5305 (m) REVERT: Q 92 MET cc_start: 0.2465 (ptt) cc_final: 0.2257 (ptt) REVERT: Q 103 TRP cc_start: 0.7293 (m100) cc_final: 0.6981 (m-90) REVERT: Q 110 MET cc_start: 0.6653 (ptp) cc_final: 0.6263 (ptp) outliers start: 175 outliers final: 55 residues processed: 817 average time/residue: 0.7141 time to fit residues: 723.7448 Evaluate side-chains 736 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 660 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 726 GLU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 982 LYS Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1275 MET Chi-restraints excluded: chain A residue 1277 ASN Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 336 ILE Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 134 LYS Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 393 optimal weight: 10.0000 chunk 321 optimal weight: 0.2980 chunk 461 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 523 optimal weight: 50.0000 chunk 236 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 327 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN A 820 HIS A 836 ASN ** A1277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 ASN B 616 GLN B 703 ASN B 930 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS E 168 ASN J 52 HIS K 38 HIS ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 475 GLN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.202342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123004 restraints weight = 54079.226| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.33 r_work: 0.3083 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 45685 Z= 0.176 Angle : 0.625 27.438 62182 Z= 0.308 Chirality : 0.044 0.257 6998 Planarity : 0.004 0.064 7607 Dihedral : 15.878 179.809 7118 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.96 % Allowed : 16.37 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.11), residues: 5269 helix: 1.41 (0.11), residues: 2070 sheet: -0.56 (0.19), residues: 672 loop : -0.84 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 229 TYR 0.038 0.002 TYR E 90 PHE 0.020 0.002 PHE D 17 TRP 0.016 0.001 TRP B 297 HIS 0.014 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (45655) covalent geometry : angle 0.59141 / 0.31 (62137) hydrogen bonds : bond 0.03838 / 2.58 ( 1961) hydrogen bonds : angle 4.42566 / 3.16 ( 5558) metal coordination : bond 0.00705 / 0.36 ( 28) metal coordination : angle 7.48743 / 4.32 ( 45) Misc. bond : bond 0.00214 / 0.11 ( 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 871 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 685 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7464 (tp30) cc_final: 0.7257 (mp0) REVERT: A 131 ARG cc_start: 0.7843 (ptp-110) cc_final: 0.7466 (ptp90) REVERT: A 240 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8794 (mtp) REVERT: A 252 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8285 (pp) REVERT: A 255 LEU cc_start: 0.8720 (tp) cc_final: 0.8501 (mt) REVERT: A 307 MET cc_start: 0.8523 (tpp) cc_final: 0.8175 (mmm) REVERT: A 308 GLU cc_start: 0.8253 (tp30) cc_final: 0.7929 (tt0) REVERT: A 311 ASP cc_start: 0.8449 (t0) cc_final: 0.8102 (m-30) REVERT: A 312 PHE cc_start: 0.8674 (t80) cc_final: 0.8026 (m-80) REVERT: A 349 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8318 (mp10) REVERT: A 424 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5886 (ttt180) REVERT: A 436 ASN cc_start: 0.8354 (t0) cc_final: 0.8056 (t0) REVERT: A 575 LYS cc_start: 0.9101 (ptpt) cc_final: 0.8855 (ptpt) REVERT: A 620 LYS cc_start: 0.6809 (mtmt) cc_final: 0.6371 (mptt) REVERT: A 721 TYR cc_start: 0.8010 (m-10) cc_final: 0.7630 (m-10) REVERT: A 761 ASP cc_start: 0.8372 (m-30) cc_final: 0.8116 (m-30) REVERT: A 790 ILE cc_start: 0.8849 (mm) cc_final: 0.8534 (mp) REVERT: A 814 GLU cc_start: 0.8437 (tt0) cc_final: 0.8117 (tp30) REVERT: A 947 LEU cc_start: 0.8491 (tt) cc_final: 0.7986 (mt) REVERT: A 954 LYS cc_start: 0.8250 (ptpt) cc_final: 0.7885 (mmpt) REVERT: A 962 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: A 970 LYS cc_start: 0.7822 (mttt) cc_final: 0.7501 (mmtt) REVERT: A 1020 ASP cc_start: 0.8867 (t70) cc_final: 0.8576 (t0) REVERT: A 1023 MET cc_start: 0.9334 (mmt) cc_final: 0.9104 (mmm) REVERT: A 1024 ARG cc_start: 0.9039 (mtm110) cc_final: 0.8670 (mtm180) REVERT: A 1065 LEU cc_start: 0.8526 (tt) cc_final: 0.8324 (tp) REVERT: A 1091 LYS cc_start: 0.7866 (mttt) cc_final: 0.7548 (mmtt) REVERT: A 1138 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7832 (ttp80) REVERT: A 1151 TYR cc_start: 0.8237 (t80) cc_final: 0.7856 (t80) REVERT: A 1179 GLU cc_start: 0.8198 (pt0) cc_final: 0.7496 (tm-30) REVERT: A 1193 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7898 (ttpp) REVERT: A 1195 ASP cc_start: 0.8545 (p0) cc_final: 0.8285 (p0) REVERT: B 35 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8242 (mttt) REVERT: B 60 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7672 (ptpp) REVERT: B 100 HIS cc_start: 0.8300 (t-90) cc_final: 0.8085 (t70) REVERT: B 107 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8713 (ptp) REVERT: B 139 MET cc_start: 0.9307 (ttm) cc_final: 0.8947 (ttp) REVERT: B 192 GLU cc_start: 0.7879 (pt0) cc_final: 0.7300 (pm20) REVERT: B 258 GLU cc_start: 0.7973 (mp0) cc_final: 0.7595 (mp0) REVERT: B 290 LYS cc_start: 0.7943 (mmtm) cc_final: 0.7511 (mmmm) REVERT: B 332 CYS cc_start: 0.8808 (m) cc_final: 0.8445 (m) REVERT: B 374 GLU cc_start: 0.8503 (tt0) cc_final: 0.8192 (tt0) REVERT: B 384 MET cc_start: 0.7136 (ttp) cc_final: 0.6782 (mtm) REVERT: B 408 GLN cc_start: 0.7343 (tt0) cc_final: 0.6969 (tt0) REVERT: B 499 MET cc_start: 0.9078 (ttp) cc_final: 0.8794 (ttp) REVERT: B 506 MET cc_start: 0.8828 (mpp) cc_final: 0.8400 (mpt) REVERT: B 530 GLU cc_start: 0.7678 (mp0) cc_final: 0.7375 (mp0) REVERT: B 544 ASN cc_start: 0.8399 (m-40) cc_final: 0.8056 (m-40) REVERT: B 575 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8502 (p) REVERT: B 600 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7893 (mttp) REVERT: B 611 MET cc_start: 0.9147 (mmm) cc_final: 0.8858 (mmp) REVERT: B 612 GLU cc_start: 0.8608 (tp30) cc_final: 0.7556 (tm-30) REVERT: B 616 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7217 (mp10) REVERT: B 623 ASP cc_start: 0.9139 (m-30) cc_final: 0.8651 (m-30) REVERT: B 627 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8344 (mp0) REVERT: B 653 ASP cc_start: 0.8047 (p0) cc_final: 0.7798 (p0) REVERT: B 805 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8102 (ttm110) REVERT: B 822 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8591 (mp0) REVERT: B 1062 MET cc_start: 0.9335 (mmm) cc_final: 0.9070 (mmm) REVERT: B 1105 ARG cc_start: 0.8367 (mmm160) cc_final: 0.8013 (tpt170) REVERT: C 28 ASP cc_start: 0.8898 (p0) cc_final: 0.8676 (p0) REVERT: C 141 ARG cc_start: 0.8862 (tpt170) cc_final: 0.8602 (tpt170) REVERT: C 145 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8195 (tmt170) REVERT: C 209 ASP cc_start: 0.9004 (t0) cc_final: 0.8791 (t0) REVERT: C 230 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7228 (m) REVERT: C 251 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7610 (tp30) REVERT: D 18 GLN cc_start: 0.7446 (mt0) cc_final: 0.7079 (mt0) REVERT: D 64 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: D 82 GLU cc_start: 0.6397 (mt-10) cc_final: 0.5983 (mm-30) REVERT: D 85 GLN cc_start: 0.7709 (mt0) cc_final: 0.7331 (mp10) REVERT: E 21 CYS cc_start: 0.8318 (m) cc_final: 0.7855 (m) REVERT: E 33 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8099 (mm) REVERT: E 34 ASP cc_start: 0.7182 (t0) cc_final: 0.6387 (p0) REVERT: E 46 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6780 (t0) REVERT: E 87 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7931 (pp) REVERT: E 98 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7654 (m-40) REVERT: E 107 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7512 (tm-30) REVERT: E 187 ARG cc_start: 0.8249 (mtp-110) cc_final: 0.8039 (mtp180) REVERT: F 51 ARG cc_start: 0.7147 (mtm-85) cc_final: 0.4975 (mmp-170) REVERT: F 100 ARG cc_start: 0.8432 (mtp85) cc_final: 0.7857 (mmt-90) REVERT: G 32 LYS cc_start: 0.8621 (mtpt) cc_final: 0.8246 (mtmt) REVERT: G 41 ASN cc_start: 0.8858 (m-40) cc_final: 0.8639 (m-40) REVERT: G 50 ASP cc_start: 0.8552 (p0) cc_final: 0.8341 (p0) REVERT: G 53 LYS cc_start: 0.7784 (tptt) cc_final: 0.7526 (tppp) REVERT: G 60 PHE cc_start: 0.9036 (m-10) cc_final: 0.8606 (m-10) REVERT: G 77 PHE cc_start: 0.7821 (t80) cc_final: 0.7363 (t80) REVERT: G 150 PHE cc_start: 0.5613 (t80) cc_final: 0.4260 (t80) REVERT: H 52 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8387 (tt) REVERT: H 100 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7857 (mt-10) REVERT: H 146 LYS cc_start: 0.9092 (tttp) cc_final: 0.8847 (tttm) REVERT: I 40 ASN cc_start: 0.6456 (m110) cc_final: 0.6243 (m-40) REVERT: I 45 LYS cc_start: 0.7666 (tptt) cc_final: 0.7363 (tmtt) REVERT: J 31 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: K 24 LYS cc_start: 0.7405 (ptpp) cc_final: 0.6769 (ptmm) REVERT: K 48 ASP cc_start: 0.8322 (p0) cc_final: 0.7974 (p0) REVERT: K 60 MET cc_start: 0.9271 (mmm) cc_final: 0.8991 (mmm) REVERT: K 66 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: K 124 GLN cc_start: 0.8359 (tt0) cc_final: 0.8093 (tm-30) REVERT: L 38 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: L 42 ARG cc_start: 0.8490 (mtt-85) cc_final: 0.8243 (mtp-110) REVERT: L 44 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8066 (mmm) REVERT: M 16 TYR cc_start: 0.7559 (m-10) cc_final: 0.7233 (m-80) REVERT: M 41 ASP cc_start: 0.7954 (m-30) cc_final: 0.7112 (p0) REVERT: M 97 MET cc_start: 0.7035 (ttt) cc_final: 0.6467 (ttp) REVERT: M 110 ASN cc_start: 0.7727 (t0) cc_final: 0.7493 (t0) REVERT: M 121 GLN cc_start: 0.6287 (OUTLIER) cc_final: 0.5468 (pm20) REVERT: M 286 MET cc_start: 0.4186 (mmm) cc_final: 0.3403 (mmm) REVERT: M 292 MET cc_start: 0.2767 (ptm) cc_final: 0.2168 (ttt) REVERT: M 389 MET cc_start: 0.4663 (ptp) cc_final: 0.3958 (ptm) REVERT: M 421 MET cc_start: 0.4927 (pp-130) cc_final: 0.4194 (mpp) REVERT: N 141 LYS cc_start: 0.5373 (OUTLIER) cc_final: 0.5095 (mmmm) REVERT: N 157 MET cc_start: 0.1903 (tpt) cc_final: 0.0976 (tmm) REVERT: N 390 GLU cc_start: 0.7546 (tt0) cc_final: 0.6721 (tm-30) REVERT: O 14 GLN cc_start: 0.7664 (tt0) cc_final: 0.7413 (tm-30) REVERT: O 76 GLU cc_start: 0.8395 (tt0) cc_final: 0.7276 (pm20) REVERT: O 355 GLN cc_start: 0.8521 (tt0) cc_final: 0.8036 (tt0) REVERT: O 402 ASN cc_start: 0.7402 (t160) cc_final: 0.7200 (t0) REVERT: O 408 GLU cc_start: 0.7472 (tt0) cc_final: 0.7234 (tm-30) REVERT: O 419 ARG cc_start: 0.7407 (ptp-170) cc_final: 0.6992 (ptm-80) REVERT: O 490 MET cc_start: 0.3690 (mpp) cc_final: 0.3356 (ptp) REVERT: O 507 ASN cc_start: 0.8010 (m-40) cc_final: 0.7549 (m110) REVERT: P 222 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6330 (tm-30) REVERT: P 232 MET cc_start: 0.3049 (tpt) cc_final: 0.2225 (tpt) REVERT: P 235 ILE cc_start: 0.6947 (OUTLIER) cc_final: 0.6334 (pp) REVERT: Q 54 GLU cc_start: 0.6164 (mp0) cc_final: 0.5932 (mp0) REVERT: Q 71 MET cc_start: 0.7606 (mmm) cc_final: 0.7065 (ttt) REVERT: Q 73 TYR cc_start: 0.7392 (m-80) cc_final: 0.6737 (m-80) REVERT: Q 110 MET cc_start: 0.6689 (ptp) cc_final: 0.6313 (ptp) REVERT: Q 111 MET cc_start: 0.5706 (OUTLIER) cc_final: 0.5477 (tpp) outliers start: 186 outliers final: 75 residues processed: 805 average time/residue: 0.7419 time to fit residues: 738.0088 Evaluate side-chains 735 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 635 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 HIS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 424 ARG Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 881 ASP Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 805 ARG Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 835 VAL 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 1030 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 256 CYS Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 141 LYS Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 174 SER Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 235 ILE Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 111 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 259 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 449 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 chunk 495 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN A 836 ASN A1354 ASN B 273 GLN B 524 ASN B 982 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS E 168 ASN H 130 ASN K 38 HIS M 11 GLN M 44 HIS ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.198977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115893 restraints weight = 53690.252| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.53 r_work: 0.2995 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 45685 Z= 0.189 Angle : 0.637 28.441 62182 Z= 0.316 Chirality : 0.045 0.257 6998 Planarity : 0.005 0.066 7607 Dihedral : 15.790 179.599 7113 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.26 % Allowed : 16.95 % Favored : 78.79 % 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: 0.11 (0.11), residues: 5269 helix: 1.38 (0.11), residues: 2077 sheet: -0.74 (0.18), residues: 713 loop : -0.77 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1141 TYR 0.050 0.002 TYR E 90 PHE 0.038 0.002 PHE B 380 TRP 0.012 0.001 TRP P 313 HIS 0.014 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (45655) covalent geometry : angle 0.60533 / 0.31 (62137) hydrogen bonds : bond 0.03937 / 2.65 ( 1961) hydrogen bonds : angle 4.46256 / 3.19 ( 5558) metal coordination : bond 0.00723 / 0.37 ( 28) metal coordination : angle 7.41295 / 4.29 ( 45) Misc. bond : bond 0.00273 / 0.14 ( 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 889 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 689 time to evaluate : 1.395 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: A 131 ARG cc_start: 0.7843 (ptp-110) cc_final: 0.7456 (ptp90) REVERT: A 233 GLU cc_start: 0.8856 (tt0) cc_final: 0.8527 (tp30) REVERT: A 240 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8927 (mtp) REVERT: A 252 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8346 (pp) REVERT: A 270 LEU cc_start: 0.0071 (OUTLIER) cc_final: -0.0506 (mp) REVERT: A 307 MET cc_start: 0.8389 (tpp) cc_final: 0.8063 (mmm) REVERT: A 308 GLU cc_start: 0.8149 (tp30) cc_final: 0.7755 (tt0) REVERT: A 311 ASP cc_start: 0.8396 (t0) cc_final: 0.8098 (m-30) REVERT: A 312 PHE cc_start: 0.8608 (t80) cc_final: 0.8016 (m-80) REVERT: A 406 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8556 (mmtm) REVERT: A 436 ASN cc_start: 0.8377 (t0) cc_final: 0.8063 (t0) REVERT: A 505 MET cc_start: 0.9461 (mtp) cc_final: 0.8911 (mtp) REVERT: A 544 ASP cc_start: 0.8781 (m-30) cc_final: 0.8402 (m-30) REVERT: A 575 LYS cc_start: 0.9164 (ptpt) cc_final: 0.8868 (ptpt) REVERT: A 620 LYS cc_start: 0.6864 (mtmt) cc_final: 0.6271 (mptt) REVERT: A 709 LEU cc_start: 0.8627 (tm) cc_final: 0.8403 (tt) REVERT: A 761 ASP cc_start: 0.8447 (m-30) cc_final: 0.8220 (m-30) REVERT: A 769 ARG cc_start: 0.8267 (mtm110) cc_final: 0.7968 (mtm-85) REVERT: A 790 ILE cc_start: 0.8861 (mm) cc_final: 0.8640 (mm) REVERT: A 814 GLU cc_start: 0.8457 (tt0) cc_final: 0.8002 (tp30) REVERT: A 947 LEU cc_start: 0.8512 (tt) cc_final: 0.7962 (mt) REVERT: A 970 LYS cc_start: 0.7696 (mttt) cc_final: 0.7405 (mmtt) REVERT: A 1020 ASP cc_start: 0.8874 (t70) cc_final: 0.8573 (t0) REVERT: A 1023 MET cc_start: 0.9286 (mmt) cc_final: 0.9024 (mmm) REVERT: A 1024 ARG cc_start: 0.9018 (mtm110) cc_final: 0.8638 (mtm180) REVERT: A 1084 ILE cc_start: 0.9043 (mm) cc_final: 0.8815 (mt) REVERT: A 1091 LYS cc_start: 0.7833 (mttt) cc_final: 0.7488 (mmtt) REVERT: A 1151 TYR cc_start: 0.8371 (t80) cc_final: 0.7903 (t80) REVERT: A 1179 GLU cc_start: 0.8183 (pt0) cc_final: 0.7461 (tm-30) REVERT: A 1195 ASP cc_start: 0.8076 (p0) cc_final: 0.7795 (p0) REVERT: A 1275 MET cc_start: 0.9214 (tpp) cc_final: 0.8978 (mmt) REVERT: B 35 LYS cc_start: 0.8465 (mmmm) cc_final: 0.8170 (mttt) REVERT: B 60 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7302 (mtmt) REVERT: B 82 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.7110 (t) REVERT: B 107 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8759 (ptp) REVERT: B 192 GLU cc_start: 0.7737 (pt0) cc_final: 0.7087 (pm20) REVERT: B 258 GLU cc_start: 0.8105 (mp0) cc_final: 0.7632 (mp0) REVERT: B 277 ILE cc_start: 0.8090 (mm) cc_final: 0.7790 (mm) REVERT: B 290 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7557 (mppt) REVERT: B 332 CYS cc_start: 0.8916 (m) cc_final: 0.8533 (m) REVERT: B 374 GLU cc_start: 0.8480 (tt0) cc_final: 0.8092 (tt0) REVERT: B 408 GLN cc_start: 0.7345 (tt0) cc_final: 0.6944 (tt0) REVERT: B 499 MET cc_start: 0.9134 (ttp) cc_final: 0.8836 (ttp) REVERT: B 506 MET cc_start: 0.8839 (mpp) cc_final: 0.8529 (mpp) REVERT: B 530 GLU cc_start: 0.7873 (mp0) cc_final: 0.7637 (mp0) REVERT: B 544 ASN cc_start: 0.8329 (m-40) cc_final: 0.7977 (m-40) REVERT: B 575 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8540 (p) REVERT: B 600 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7842 (mttp) REVERT: B 611 MET cc_start: 0.9023 (mmm) cc_final: 0.8693 (mmp) REVERT: B 612 GLU cc_start: 0.8550 (tp30) cc_final: 0.7907 (mm-30) REVERT: B 616 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7475 (mp10) REVERT: B 627 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8284 (mp0) REVERT: B 722 THR cc_start: 0.8987 (m) cc_final: 0.8749 (p) REVERT: B 753 ASP cc_start: 0.8317 (m-30) cc_final: 0.8114 (m-30) REVERT: B 780 LYS cc_start: 0.7954 (ptmt) cc_final: 0.7696 (pttt) REVERT: B 1050 MET cc_start: 0.9377 (mtp) cc_final: 0.9128 (mtp) REVERT: B 1062 MET cc_start: 0.9396 (mmm) cc_final: 0.9080 (mmm) REVERT: B 1105 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7967 (tpt170) REVERT: C 28 ASP cc_start: 0.9031 (p0) cc_final: 0.8745 (p0) REVERT: C 141 ARG cc_start: 0.8861 (tpt170) cc_final: 0.8464 (tpt170) REVERT: C 145 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8203 (tmt170) REVERT: C 161 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8048 (mm-30) REVERT: D 18 GLN cc_start: 0.7454 (mt0) cc_final: 0.7106 (mt0) REVERT: D 82 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6002 (mm-30) REVERT: D 85 GLN cc_start: 0.7548 (mt0) cc_final: 0.6941 (mp10) REVERT: E 18 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8699 (mmm) REVERT: E 21 CYS cc_start: 0.8355 (m) cc_final: 0.7806 (m) REVERT: E 33 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7918 (mm) REVERT: E 34 ASP cc_start: 0.7633 (t0) cc_final: 0.6750 (p0) REVERT: E 46 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6761 (t0) REVERT: E 47 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7151 (pttm) REVERT: E 87 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7871 (pp) REVERT: E 98 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7686 (m-40) REVERT: E 107 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7579 (tm-30) REVERT: E 187 ARG cc_start: 0.8293 (mtp-110) cc_final: 0.8083 (mtp180) REVERT: F 51 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.4869 (mmp-170) REVERT: F 82 GLU cc_start: 0.7638 (pp20) cc_final: 0.7410 (pp20) REVERT: F 100 ARG cc_start: 0.8463 (mtp85) cc_final: 0.7830 (mmt-90) REVERT: G 32 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8091 (mtmt) REVERT: G 36 ASN cc_start: 0.7899 (m-40) cc_final: 0.6939 (m-40) REVERT: G 41 ASN cc_start: 0.8845 (m-40) cc_final: 0.8608 (m-40) REVERT: G 50 ASP cc_start: 0.8499 (p0) cc_final: 0.8284 (p0) REVERT: G 53 LYS cc_start: 0.7795 (tptt) cc_final: 0.7410 (tppp) REVERT: H 52 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8332 (tt) REVERT: H 100 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7717 (mt-10) REVERT: H 146 LYS cc_start: 0.9050 (tttp) cc_final: 0.8792 (tttm) REVERT: I 22 ARG cc_start: 0.6215 (ptt180) cc_final: 0.5937 (ptt180) REVERT: I 45 LYS cc_start: 0.7605 (tptt) cc_final: 0.7248 (tmtt) REVERT: J 26 GLN cc_start: 0.8380 (tp40) cc_final: 0.7858 (tt0) REVERT: J 41 LYS cc_start: 0.8823 (tmmt) cc_final: 0.8585 (ttmm) REVERT: K 24 LYS cc_start: 0.7433 (ptpp) cc_final: 0.6833 (ptmm) REVERT: K 48 ASP cc_start: 0.8278 (p0) cc_final: 0.7979 (p0) REVERT: K 50 THR cc_start: 0.9021 (OUTLIER) cc_final: 0.8647 (t) REVERT: K 60 MET cc_start: 0.9357 (mmm) cc_final: 0.9032 (mmm) REVERT: K 66 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: K 115 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8458 (mt-10) REVERT: K 124 GLN cc_start: 0.8523 (tt0) cc_final: 0.8126 (tm-30) REVERT: L 44 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8122 (mmm) REVERT: M 97 MET cc_start: 0.7279 (ttt) cc_final: 0.6524 (ttp) REVERT: M 121 GLN cc_start: 0.6370 (OUTLIER) cc_final: 0.5790 (mp10) REVERT: M 209 HIS cc_start: 0.6403 (OUTLIER) cc_final: 0.6065 (p90) REVERT: M 286 MET cc_start: 0.3694 (mmm) cc_final: 0.3036 (mmm) REVERT: M 292 MET cc_start: 0.2487 (ptm) cc_final: 0.1862 (ttt) REVERT: M 389 MET cc_start: 0.4422 (ptp) cc_final: 0.3864 (ptm) REVERT: M 421 MET cc_start: 0.4939 (pp-130) cc_final: 0.4275 (mpp) REVERT: N 271 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8141 (pp) REVERT: N 341 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8113 (tt) REVERT: N 390 GLU cc_start: 0.7522 (tt0) cc_final: 0.6548 (tm-30) REVERT: O 14 GLN cc_start: 0.7669 (tt0) cc_final: 0.7335 (tm-30) REVERT: O 22 GLU cc_start: 0.7977 (pp20) cc_final: 0.7036 (pt0) REVERT: O 76 GLU cc_start: 0.8333 (tt0) cc_final: 0.7106 (pm20) REVERT: O 355 GLN cc_start: 0.8490 (tt0) cc_final: 0.7992 (tt0) REVERT: O 408 GLU cc_start: 0.7743 (tt0) cc_final: 0.7534 (tm-30) REVERT: O 419 ARG cc_start: 0.7169 (ptp-170) cc_final: 0.6728 (ptm-80) REVERT: O 490 MET cc_start: 0.3653 (mpp) cc_final: 0.3365 (ptp) REVERT: O 507 ASN cc_start: 0.7935 (m-40) cc_final: 0.7502 (m110) REVERT: P 232 MET cc_start: 0.3235 (tpt) cc_final: 0.3025 (tpt) REVERT: Q 54 GLU cc_start: 0.6465 (mp0) cc_final: 0.6246 (mp0) REVERT: Q 61 LYS cc_start: 0.7471 (tttt) cc_final: 0.7134 (tttt) REVERT: Q 71 MET cc_start: 0.7573 (mmm) cc_final: 0.7066 (ttt) REVERT: Q 73 TYR cc_start: 0.7181 (m-80) cc_final: 0.6551 (m-80) REVERT: Q 77 THR cc_start: 0.5548 (OUTLIER) cc_final: 0.5318 (m) REVERT: Q 110 MET cc_start: 0.6704 (ptp) cc_final: 0.6295 (ptp) outliers start: 200 outliers final: 95 residues processed: 819 average time/residue: 0.6590 time to fit residues: 664.6564 Evaluate side-chains 754 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 636 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1037 CYS Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain B residue 20 ILE Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 835 VAL 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 C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 35 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 316 CYS Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 241 ARG Chi-restraints excluded: chain O residue 420 THR Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 455 LYS Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 508 optimal weight: 8.9990 chunk 426 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 471 optimal weight: 10.0000 chunk 277 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 217 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 chunk 408 optimal weight: 40.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN A 836 ASN B 260 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 168 ASN H 87 GLN H 130 ASN K 38 HIS ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.197847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114722 restraints weight = 53667.348| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.41 r_work: 0.2977 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 45685 Z= 0.190 Angle : 0.635 28.644 62182 Z= 0.314 Chirality : 0.044 0.247 6998 Planarity : 0.004 0.059 7607 Dihedral : 15.677 179.874 7113 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.81 % Allowed : 17.80 % Favored : 78.39 % 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: 0.14 (0.11), residues: 5269 helix: 1.42 (0.11), residues: 2074 sheet: -0.74 (0.18), residues: 727 loop : -0.76 (0.12), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1138 TYR 0.036 0.002 TYR E 90 PHE 0.026 0.002 PHE B 380 TRP 0.011 0.001 TRP M 423 HIS 0.013 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (45655) covalent geometry : angle 0.60401 / 0.31 (62137) hydrogen bonds : bond 0.03902 / 2.63 ( 1961) hydrogen bonds : angle 4.46430 / 3.18 ( 5558) metal coordination : bond 0.00763 / 0.40 ( 28) metal coordination : angle 7.26565 / 4.21 ( 45) Misc. bond : bond 0.00228 / 0.12 ( 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 843 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 664 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7338 (pm20) cc_final: 0.6903 (pm20) REVERT: A 65 LYS cc_start: 0.8155 (tptp) cc_final: 0.7948 (ttpp) REVERT: A 89 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7535 (tp30) REVERT: A 107 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8391 (mmm) REVERT: A 233 GLU cc_start: 0.8884 (tt0) cc_final: 0.8574 (tp30) REVERT: A 240 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8958 (mtp) REVERT: A 252 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8336 (pp) REVERT: A 270 LEU cc_start: 0.0192 (OUTLIER) cc_final: -0.0413 (mp) REVERT: A 311 ASP cc_start: 0.8406 (t0) cc_final: 0.8106 (m-30) REVERT: A 312 PHE cc_start: 0.8692 (t80) cc_final: 0.8151 (m-80) REVERT: A 406 LYS cc_start: 0.9233 (ttpt) cc_final: 0.8513 (mmtt) REVERT: A 505 MET cc_start: 0.9403 (mtp) cc_final: 0.8882 (mtp) REVERT: A 575 LYS cc_start: 0.9183 (ptpt) cc_final: 0.8890 (ptpt) REVERT: A 620 LYS cc_start: 0.7194 (mtmt) cc_final: 0.6313 (mptt) REVERT: A 709 LEU cc_start: 0.8686 (tm) cc_final: 0.8465 (tt) REVERT: A 761 ASP cc_start: 0.8478 (m-30) cc_final: 0.8187 (m-30) REVERT: A 814 GLU cc_start: 0.8449 (tt0) cc_final: 0.7980 (tp30) REVERT: A 836 ASN cc_start: 0.9146 (m110) cc_final: 0.8886 (m-40) REVERT: A 947 LEU cc_start: 0.8553 (tt) cc_final: 0.8002 (mt) REVERT: A 970 LYS cc_start: 0.7816 (mttt) cc_final: 0.7503 (mmtt) REVERT: A 1020 ASP cc_start: 0.8847 (t70) cc_final: 0.8555 (t0) REVERT: A 1023 MET cc_start: 0.9383 (mmt) cc_final: 0.9134 (mmm) REVERT: A 1024 ARG cc_start: 0.8998 (mtm110) cc_final: 0.8643 (mtm180) REVERT: A 1091 LYS cc_start: 0.8007 (mttt) cc_final: 0.7708 (mmtt) REVERT: A 1138 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.7989 (ttp80) REVERT: A 1151 TYR cc_start: 0.8328 (t80) cc_final: 0.7883 (t80) REVERT: A 1179 GLU cc_start: 0.8206 (pt0) cc_final: 0.7526 (tm-30) REVERT: A 1191 PHE cc_start: 0.7087 (t80) cc_final: 0.6805 (t80) REVERT: A 1195 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7721 (p0) REVERT: A 1275 MET cc_start: 0.9213 (tpp) cc_final: 0.8867 (mmt) REVERT: B 35 LYS cc_start: 0.8509 (mmmm) cc_final: 0.8197 (mttt) REVERT: B 60 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7434 (mtmt) REVERT: B 107 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8773 (ptp) REVERT: B 192 GLU cc_start: 0.7705 (pt0) cc_final: 0.7075 (pm20) REVERT: B 258 GLU cc_start: 0.8104 (mp0) cc_final: 0.7637 (mp0) REVERT: B 277 ILE cc_start: 0.8244 (mm) cc_final: 0.8041 (mm) REVERT: B 290 LYS cc_start: 0.7977 (mmtm) cc_final: 0.7574 (mppt) REVERT: B 332 CYS cc_start: 0.8936 (m) cc_final: 0.8512 (m) REVERT: B 374 GLU cc_start: 0.8546 (tt0) cc_final: 0.8134 (tt0) REVERT: B 408 GLN cc_start: 0.7294 (tt0) cc_final: 0.6748 (tt0) REVERT: B 499 MET cc_start: 0.9190 (ttp) cc_final: 0.8888 (ttp) REVERT: B 506 MET cc_start: 0.8769 (mpp) cc_final: 0.8510 (mpp) REVERT: B 521 GLU cc_start: 0.8969 (mp0) cc_final: 0.8543 (mp0) REVERT: B 530 GLU cc_start: 0.8151 (mp0) cc_final: 0.7863 (mp0) REVERT: B 575 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8501 (p) REVERT: B 600 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7795 (mttp) REVERT: B 611 MET cc_start: 0.9030 (mmm) cc_final: 0.8727 (mmp) REVERT: B 612 GLU cc_start: 0.8540 (tp30) cc_final: 0.7575 (mm-30) REVERT: B 616 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7152 (mp10) REVERT: B 623 ASP cc_start: 0.9009 (m-30) cc_final: 0.8662 (m-30) REVERT: B 780 LYS cc_start: 0.7983 (ptmt) cc_final: 0.7688 (pttt) REVERT: B 916 MET cc_start: 0.9408 (mmm) cc_final: 0.8992 (mtp) REVERT: B 1028 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8466 (mtt-85) REVERT: B 1062 MET cc_start: 0.9393 (mmm) cc_final: 0.9039 (mmm) REVERT: B 1105 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8078 (tpt170) REVERT: C 28 ASP cc_start: 0.9016 (p0) cc_final: 0.8716 (p0) REVERT: C 141 ARG cc_start: 0.8841 (tpt170) cc_final: 0.8314 (tpt90) REVERT: C 143 GLN cc_start: 0.8701 (tt0) cc_final: 0.8453 (tt0) REVERT: C 145 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8144 (tmt170) REVERT: C 161 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8199 (mm-30) REVERT: D 18 GLN cc_start: 0.7410 (mt0) cc_final: 0.6985 (mt0) REVERT: D 82 GLU cc_start: 0.6553 (mt-10) cc_final: 0.4867 (tm-30) REVERT: D 83 LYS cc_start: 0.7678 (mttt) cc_final: 0.7113 (mttp) REVERT: D 85 GLN cc_start: 0.7640 (mt0) cc_final: 0.7193 (mp10) REVERT: E 21 CYS cc_start: 0.8354 (m) cc_final: 0.7828 (m) REVERT: E 33 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7930 (mm) REVERT: E 34 ASP cc_start: 0.7709 (t0) cc_final: 0.6809 (p0) REVERT: E 46 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6838 (t0) REVERT: E 47 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7278 (pttm) REVERT: E 107 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7686 (tm-30) REVERT: E 172 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8486 (mmt-90) REVERT: F 51 ARG cc_start: 0.7216 (mtm-85) cc_final: 0.4712 (mmp-170) REVERT: F 100 ARG cc_start: 0.8452 (mtp85) cc_final: 0.7787 (mmt-90) REVERT: G 7 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8493 (mmm) REVERT: G 32 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8098 (mtmt) REVERT: G 36 ASN cc_start: 0.8304 (m-40) cc_final: 0.7398 (m-40) REVERT: G 41 ASN cc_start: 0.8821 (m-40) cc_final: 0.8564 (m-40) REVERT: G 50 ASP cc_start: 0.8504 (p0) cc_final: 0.8238 (p0) REVERT: G 53 LYS cc_start: 0.7783 (tptt) cc_final: 0.7416 (tppp) REVERT: G 197 LEU cc_start: 0.5386 (mm) cc_final: 0.5154 (mt) REVERT: H 20 LYS cc_start: 0.8541 (tppt) cc_final: 0.8007 (tptp) REVERT: H 52 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8344 (tt) REVERT: H 55 LYS cc_start: 0.9204 (ttmt) cc_final: 0.8995 (ttmt) REVERT: H 100 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7751 (mt-10) REVERT: H 124 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.7982 (ttp80) REVERT: H 146 LYS cc_start: 0.8983 (tttp) cc_final: 0.8708 (tttm) REVERT: I 22 ARG cc_start: 0.6255 (ptt180) cc_final: 0.5995 (ptt180) REVERT: I 45 LYS cc_start: 0.7644 (tptt) cc_final: 0.7282 (tmtt) REVERT: J 26 GLN cc_start: 0.8419 (tp40) cc_final: 0.7999 (tt0) REVERT: J 31 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: J 41 LYS cc_start: 0.8815 (tmmt) cc_final: 0.8574 (ttmm) REVERT: K 24 LYS cc_start: 0.7456 (ptpp) cc_final: 0.6887 (ptmm) REVERT: K 48 ASP cc_start: 0.8303 (p0) cc_final: 0.8011 (p0) REVERT: K 50 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8592 (t) REVERT: K 60 MET cc_start: 0.9347 (mmm) cc_final: 0.9032 (mmm) REVERT: K 66 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: K 113 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8656 (mttt) REVERT: K 115 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8467 (mt-10) REVERT: K 124 GLN cc_start: 0.8527 (tt0) cc_final: 0.8102 (tm-30) REVERT: L 44 MET cc_start: 0.9273 (OUTLIER) cc_final: 0.8144 (mmm) REVERT: M 97 MET cc_start: 0.7311 (ttt) cc_final: 0.6580 (ttp) REVERT: M 121 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.5878 (mp10) REVERT: M 286 MET cc_start: 0.3707 (mmm) cc_final: 0.3066 (mmm) REVERT: M 292 MET cc_start: 0.2556 (ptm) cc_final: 0.1940 (ttt) REVERT: M 389 MET cc_start: 0.4559 (ptp) cc_final: 0.3959 (ptm) REVERT: M 421 MET cc_start: 0.5206 (pp-130) cc_final: 0.4419 (mpp) REVERT: N 157 MET cc_start: 0.0291 (OUTLIER) cc_final: -0.0539 (tmm) REVERT: N 341 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8203 (tt) REVERT: N 381 HIS cc_start: 0.8419 (m90) cc_final: 0.8050 (m-70) REVERT: N 390 GLU cc_start: 0.7506 (tt0) cc_final: 0.6733 (tm-30) REVERT: O 14 GLN cc_start: 0.7748 (tt0) cc_final: 0.7324 (tm-30) REVERT: O 22 GLU cc_start: 0.8052 (pp20) cc_final: 0.7087 (pt0) REVERT: O 41 HIS cc_start: 0.7851 (t-90) cc_final: 0.7597 (t-90) REVERT: O 76 GLU cc_start: 0.8182 (tt0) cc_final: 0.7143 (pm20) REVERT: O 259 MET cc_start: 0.7533 (mpt) cc_final: 0.7284 (mmt) REVERT: O 355 GLN cc_start: 0.8442 (tt0) cc_final: 0.7901 (tt0) REVERT: O 394 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7077 (mtp) REVERT: O 419 ARG cc_start: 0.6994 (ptp-170) cc_final: 0.6544 (ptm-80) REVERT: O 474 MET cc_start: 0.0161 (pp-130) cc_final: -0.0242 (ppp) REVERT: O 490 MET cc_start: 0.3595 (mpp) cc_final: 0.3359 (ptp) REVERT: O 524 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7983 (tm-30) REVERT: Q 56 TYR cc_start: 0.7687 (t80) cc_final: 0.7319 (t80) REVERT: Q 71 MET cc_start: 0.7723 (mmm) cc_final: 0.7113 (ttt) REVERT: Q 73 TYR cc_start: 0.7306 (m-80) cc_final: 0.6641 (m-80) REVERT: Q 110 MET cc_start: 0.6729 (ptp) cc_final: 0.6376 (ptp) outliers start: 179 outliers final: 94 residues processed: 789 average time/residue: 0.5627 time to fit residues: 550.7154 Evaluate side-chains 747 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 627 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 59 ARG 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 175 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 961 CYS Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1037 CYS Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 689 MET Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 835 VAL 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 1028 ARG Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1127 LYS Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 172 ARG Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 124 ARG Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 44 MET Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain M residue 391 VAL Chi-restraints excluded: chain N residue 157 MET Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 326 VAL Chi-restraints excluded: chain N residue 330 LEU Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 241 ARG Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 429 LEU Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 248 VAL Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 135 optimal weight: 0.0980 chunk 460 optimal weight: 20.0000 chunk 284 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 360 optimal weight: 0.9980 chunk 515 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 347 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN C 290 ASN D 98 GLN E 168 ASN K 38 HIS M 44 HIS M 68 ASN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.200328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119893 restraints weight = 53459.486| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.25 r_work: 0.3052 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 45685 Z= 0.118 Angle : 0.597 28.276 62182 Z= 0.293 Chirality : 0.043 0.255 6998 Planarity : 0.004 0.087 7607 Dihedral : 15.557 179.864 7113 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.75 % Allowed : 19.29 % Favored : 77.96 % 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: 0.32 (0.12), residues: 5269 helix: 1.61 (0.12), residues: 2055 sheet: -0.65 (0.18), residues: 723 loop : -0.68 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG O 466 TYR 0.033 0.001 TYR E 90 PHE 0.032 0.001 PHE B 278 TRP 0.009 0.001 TRP C 40 HIS 0.010 0.001 HIS M 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (45655) covalent geometry : angle 0.56623 / 0.29 (62137) hydrogen bonds : bond 0.03478 / 2.33 ( 1961) hydrogen bonds : angle 4.34828 / 3.10 ( 5558) metal coordination : bond 0.00465 / 0.23 ( 28) metal coordination : angle 7.04435 / 4.10 ( 45) Misc. bond : bond 0.00153 / 0.08 ( 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 784 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 655 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7453 (pm20) cc_final: 0.7147 (pm20) REVERT: A 89 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7529 (tp30) REVERT: A 107 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8400 (mmm) REVERT: A 131 ARG cc_start: 0.7871 (ptp-110) cc_final: 0.7525 (ptp-170) REVERT: A 240 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.9015 (mtp) REVERT: A 270 LEU cc_start: 0.0135 (OUTLIER) cc_final: -0.0478 (mp) REVERT: A 278 ASP cc_start: 0.8421 (m-30) cc_final: 0.8216 (m-30) REVERT: A 311 ASP cc_start: 0.8374 (t0) cc_final: 0.8122 (m-30) REVERT: A 312 PHE cc_start: 0.8670 (t80) cc_final: 0.8145 (m-80) REVERT: A 349 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: A 406 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8552 (mmtt) REVERT: A 505 MET cc_start: 0.9341 (mtp) cc_final: 0.8801 (mtp) REVERT: A 544 ASP cc_start: 0.8602 (m-30) cc_final: 0.8302 (m-30) REVERT: A 575 LYS cc_start: 0.9103 (ptpt) cc_final: 0.8857 (ptpt) REVERT: A 620 LYS cc_start: 0.7197 (mtmt) cc_final: 0.6342 (mptt) REVERT: A 636 SER cc_start: 0.8993 (m) cc_final: 0.8736 (p) REVERT: A 709 LEU cc_start: 0.8686 (tm) cc_final: 0.8445 (tt) REVERT: A 721 TYR cc_start: 0.8170 (m-10) cc_final: 0.7965 (m-10) REVERT: A 754 LYS cc_start: 0.8105 (tppt) cc_final: 0.7566 (tmmt) REVERT: A 814 GLU cc_start: 0.8399 (tt0) cc_final: 0.7970 (tp30) REVERT: A 836 ASN cc_start: 0.9001 (m110) cc_final: 0.8725 (m-40) REVERT: A 947 LEU cc_start: 0.8558 (tt) cc_final: 0.8026 (mt) REVERT: A 970 LYS cc_start: 0.8004 (mttt) cc_final: 0.7710 (mmtt) REVERT: A 1020 ASP cc_start: 0.8813 (t70) cc_final: 0.8546 (t0) REVERT: A 1024 ARG cc_start: 0.9060 (mtm110) cc_final: 0.8727 (mtm180) REVERT: A 1084 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 1091 LYS cc_start: 0.8016 (mttt) cc_final: 0.7764 (mmtt) REVERT: A 1112 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8230 (mp0) REVERT: A 1151 TYR cc_start: 0.8284 (t80) cc_final: 0.7839 (t80) REVERT: A 1179 GLU cc_start: 0.8165 (pt0) cc_final: 0.7442 (tm-30) REVERT: A 1191 PHE cc_start: 0.6860 (t80) cc_final: 0.6585 (t80) REVERT: A 1195 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7878 (p0) REVERT: A 1275 MET cc_start: 0.9250 (tpp) cc_final: 0.8966 (mmt) REVERT: A 1354 ASN cc_start: 0.8853 (m110) cc_final: 0.8494 (m110) REVERT: B 60 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7528 (mtmt) REVERT: B 139 MET cc_start: 0.9307 (ttm) cc_final: 0.9059 (ttm) REVERT: B 192 GLU cc_start: 0.7812 (pt0) cc_final: 0.7206 (pm20) REVERT: B 258 GLU cc_start: 0.8021 (mp0) cc_final: 0.7417 (mp0) REVERT: B 290 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7656 (mppt) REVERT: B 332 CYS cc_start: 0.8892 (m) cc_final: 0.8498 (m) REVERT: B 374 GLU cc_start: 0.8505 (tt0) cc_final: 0.8106 (tt0) REVERT: B 408 GLN cc_start: 0.7351 (tt0) cc_final: 0.6918 (tt0) REVERT: B 499 MET cc_start: 0.9036 (ttp) cc_final: 0.8754 (ttp) REVERT: B 506 MET cc_start: 0.8815 (mpp) cc_final: 0.8600 (mpp) REVERT: B 530 GLU cc_start: 0.8221 (mp0) cc_final: 0.7949 (mp0) REVERT: B 554 LYS cc_start: 0.8703 (ttpt) cc_final: 0.8395 (tmtp) REVERT: B 575 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8497 (p) REVERT: B 600 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7877 (mttp) REVERT: B 611 MET cc_start: 0.9045 (mmm) cc_final: 0.8728 (mmp) REVERT: B 612 GLU cc_start: 0.8589 (tp30) cc_final: 0.7925 (mm-30) REVERT: B 616 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7528 (mp10) REVERT: B 623 ASP cc_start: 0.9008 (m-30) cc_final: 0.8758 (m-30) REVERT: B 641 CYS cc_start: 0.8483 (m) cc_final: 0.7690 (m) REVERT: B 879 PHE cc_start: 0.7434 (m-80) cc_final: 0.7200 (t80) REVERT: B 916 MET cc_start: 0.9381 (mmm) cc_final: 0.8935 (mtp) REVERT: B 1028 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8739 (mtt90) REVERT: B 1062 MET cc_start: 0.9349 (mmm) cc_final: 0.9016 (mmm) REVERT: B 1105 ARG cc_start: 0.8445 (mmm160) cc_final: 0.8068 (tpt170) REVERT: C 28 ASP cc_start: 0.8953 (p0) cc_final: 0.8693 (p0) REVERT: C 141 ARG cc_start: 0.8876 (tpt170) cc_final: 0.8384 (tpt90) REVERT: C 145 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8304 (tmt170) REVERT: C 161 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8304 (mm-30) REVERT: D 18 GLN cc_start: 0.7431 (mt0) cc_final: 0.7084 (mt0) REVERT: D 82 GLU cc_start: 0.6508 (mt-10) cc_final: 0.4758 (tm-30) REVERT: D 83 LYS cc_start: 0.7760 (mttt) cc_final: 0.7159 (mttp) REVERT: E 18 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8838 (mmm) REVERT: E 21 CYS cc_start: 0.8362 (m) cc_final: 0.7850 (m) REVERT: E 33 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7912 (mm) REVERT: E 34 ASP cc_start: 0.7707 (t0) cc_final: 0.6843 (p0) REVERT: E 107 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7644 (tm-30) REVERT: F 51 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.4916 (mmp-170) REVERT: F 100 ARG cc_start: 0.8418 (mtp85) cc_final: 0.7769 (mmt-90) REVERT: G 32 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8066 (mtmt) REVERT: G 36 ASN cc_start: 0.8067 (m-40) cc_final: 0.7155 (m-40) REVERT: G 41 ASN cc_start: 0.8840 (m-40) cc_final: 0.8600 (m-40) REVERT: G 53 LYS cc_start: 0.7798 (tptt) cc_final: 0.7450 (tppp) REVERT: H 20 LYS cc_start: 0.8557 (tppt) cc_final: 0.8018 (tptp) REVERT: H 52 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8322 (tt) REVERT: H 55 LYS cc_start: 0.9224 (ttmt) cc_final: 0.8980 (ttmt) REVERT: H 100 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7725 (mt-10) REVERT: H 146 LYS cc_start: 0.9015 (tttp) cc_final: 0.8722 (tttm) REVERT: I 22 ARG cc_start: 0.6392 (ptt180) cc_final: 0.6119 (ptt180) REVERT: I 45 LYS cc_start: 0.7812 (tptt) cc_final: 0.7455 (tmtt) REVERT: J 26 GLN cc_start: 0.8393 (tp40) cc_final: 0.8030 (tt0) REVERT: J 41 LYS cc_start: 0.8748 (tmmt) cc_final: 0.8545 (ttmm) REVERT: K 24 LYS cc_start: 0.7507 (ptpp) cc_final: 0.6986 (ptmm) REVERT: K 48 ASP cc_start: 0.8295 (p0) cc_final: 0.7993 (p0) REVERT: K 50 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8648 (t) REVERT: K 60 MET cc_start: 0.9253 (mmm) cc_final: 0.8954 (mmm) REVERT: K 66 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8457 (tm-30) REVERT: K 79 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9018 (ttpt) REVERT: K 124 GLN cc_start: 0.8413 (tt0) cc_final: 0.8069 (tm-30) REVERT: M 16 TYR cc_start: 0.7800 (m-10) cc_final: 0.7295 (m-10) REVERT: M 97 MET cc_start: 0.7263 (ttt) cc_final: 0.6538 (ttp) REVERT: M 121 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.5882 (mp10) REVERT: M 286 MET cc_start: 0.3714 (mmm) cc_final: 0.3073 (mmm) REVERT: M 292 MET cc_start: 0.2633 (ptm) cc_final: 0.1999 (ttt) REVERT: M 389 MET cc_start: 0.4647 (ptp) cc_final: 0.4000 (ptm) REVERT: M 421 MET cc_start: 0.4877 (pp-130) cc_final: 0.4254 (mpp) REVERT: N 157 MET cc_start: 0.0277 (OUTLIER) cc_final: -0.0592 (tmm) REVERT: N 271 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8439 (pp) REVERT: N 341 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8246 (tt) REVERT: N 380 LYS cc_start: 0.7707 (tppp) cc_final: 0.7270 (tptp) REVERT: N 390 GLU cc_start: 0.7550 (tt0) cc_final: 0.6814 (tm-30) REVERT: O 14 GLN cc_start: 0.7745 (tt0) cc_final: 0.7411 (tm-30) REVERT: O 41 HIS cc_start: 0.7837 (t-90) cc_final: 0.7589 (t-90) REVERT: O 70 ARG cc_start: 0.6574 (mtt180) cc_final: 0.6356 (mpp-170) REVERT: O 76 GLU cc_start: 0.8232 (tt0) cc_final: 0.7182 (pm20) REVERT: O 259 MET cc_start: 0.7565 (mpt) cc_final: 0.7322 (mmt) REVERT: O 355 GLN cc_start: 0.8444 (tt0) cc_final: 0.7973 (tt0) REVERT: O 402 ASN cc_start: 0.7435 (t160) cc_final: 0.7160 (t0) REVERT: O 419 ARG cc_start: 0.7013 (ptp-170) cc_final: 0.6571 (ptm-80) REVERT: O 490 MET cc_start: 0.3602 (mpp) cc_final: 0.3380 (ptp) REVERT: Q 54 GLU cc_start: 0.6314 (mp0) cc_final: 0.5944 (mp0) REVERT: Q 56 TYR cc_start: 0.7721 (t80) cc_final: 0.7410 (t80) REVERT: Q 58 LEU cc_start: 0.7541 (tt) cc_final: 0.7054 (mp) REVERT: Q 71 MET cc_start: 0.7763 (mmm) cc_final: 0.6735 (ttt) REVERT: Q 73 TYR cc_start: 0.7446 (m-80) cc_final: 0.6798 (m-80) REVERT: Q 110 MET cc_start: 0.6730 (ptp) cc_final: 0.6380 (ptp) outliers start: 129 outliers final: 56 residues processed: 742 average time/residue: 0.4780 time to fit residues: 437.0869 Evaluate side-chains 704 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 628 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1037 CYS Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 835 VAL 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 1028 ARG Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 18 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 52 LEU 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 79 LYS Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 157 MET Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain O residue 522 LEU Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 133 optimal weight: 0.5980 chunk 425 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 361 optimal weight: 2.9990 chunk 368 optimal weight: 0.7980 chunk 453 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 403 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN B 260 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 168 ASN H 130 ASN K 38 HIS M 44 HIS M 68 ASN M 209 HIS ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.199669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.120189 restraints weight = 53595.614| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.24 r_work: 0.3048 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 45685 Z= 0.136 Angle : 0.608 27.081 62182 Z= 0.300 Chirality : 0.043 0.399 6998 Planarity : 0.004 0.076 7607 Dihedral : 15.489 179.928 7112 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.41 % Allowed : 19.91 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.12), residues: 5269 helix: 1.64 (0.12), residues: 2055 sheet: -0.64 (0.18), residues: 724 loop : -0.65 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 99 TYR 0.021 0.001 TYR E 90 PHE 0.024 0.001 PHE B 278 TRP 0.008 0.001 TRP C 40 HIS 0.011 0.001 HIS M 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (45655) covalent geometry : angle 0.57913 / 0.30 (62137) hydrogen bonds : bond 0.03519 / 2.36 ( 1961) hydrogen bonds : angle 4.34036 / 3.09 ( 5558) metal coordination : bond 0.00547 / 0.28 ( 28) metal coordination : angle 6.91885 / 4.00 ( 45) Misc. bond : bond 0.00175 / 0.09 ( 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 759 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 646 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7462 (pm20) cc_final: 0.7171 (pm20) REVERT: A 89 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7544 (tp30) REVERT: A 107 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8475 (mmm) REVERT: A 131 ARG cc_start: 0.7900 (ptp-110) cc_final: 0.7550 (ptp90) REVERT: A 240 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.9003 (mtp) REVERT: A 270 LEU cc_start: 0.0202 (OUTLIER) cc_final: -0.0431 (mp) REVERT: A 311 ASP cc_start: 0.8432 (t0) cc_final: 0.8202 (m-30) REVERT: A 312 PHE cc_start: 0.8713 (t80) cc_final: 0.8221 (m-80) REVERT: A 406 LYS cc_start: 0.9224 (ttpt) cc_final: 0.8673 (mmtt) REVERT: A 505 MET cc_start: 0.9285 (mtp) cc_final: 0.8724 (mtp) REVERT: A 544 ASP cc_start: 0.8603 (m-30) cc_final: 0.8299 (m-30) REVERT: A 575 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8862 (ptpt) REVERT: A 620 LYS cc_start: 0.7205 (mtmt) cc_final: 0.6424 (mptt) REVERT: A 709 LEU cc_start: 0.8795 (tm) cc_final: 0.8534 (tt) REVERT: A 721 TYR cc_start: 0.8214 (m-10) cc_final: 0.8007 (m-10) REVERT: A 754 LYS cc_start: 0.8202 (tppt) cc_final: 0.7717 (tmmt) REVERT: A 814 GLU cc_start: 0.8449 (tt0) cc_final: 0.8074 (tp30) REVERT: A 836 ASN cc_start: 0.8989 (m110) cc_final: 0.8702 (m-40) REVERT: A 947 LEU cc_start: 0.8626 (tt) cc_final: 0.8130 (mt) REVERT: A 970 LYS cc_start: 0.8108 (mttt) cc_final: 0.7810 (mmtt) REVERT: A 1020 ASP cc_start: 0.8829 (t70) cc_final: 0.8570 (t0) REVERT: A 1024 ARG cc_start: 0.9053 (mtm110) cc_final: 0.8732 (mtm180) REVERT: A 1065 LEU cc_start: 0.9094 (tp) cc_final: 0.8870 (mt) REVERT: A 1084 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8929 (mm) REVERT: A 1091 LYS cc_start: 0.8048 (mttt) cc_final: 0.7773 (ttmm) REVERT: A 1112 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8206 (mp0) REVERT: A 1119 GLU cc_start: 0.7297 (pt0) cc_final: 0.6763 (pt0) REVERT: A 1138 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7901 (ttp80) REVERT: A 1151 TYR cc_start: 0.8276 (t80) cc_final: 0.7867 (t80) REVERT: A 1179 GLU cc_start: 0.8172 (pt0) cc_final: 0.7479 (tm-30) REVERT: A 1185 MET cc_start: 0.7328 (pmm) cc_final: 0.6917 (pp-130) REVERT: A 1191 PHE cc_start: 0.6839 (t80) cc_final: 0.6520 (t80) REVERT: A 1195 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7775 (p0) REVERT: A 1206 GLU cc_start: 0.8364 (mp0) cc_final: 0.8000 (mp0) REVERT: A 1275 MET cc_start: 0.9207 (tpp) cc_final: 0.8852 (mmt) REVERT: A 1310 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8692 (mtmm) REVERT: A 1354 ASN cc_start: 0.8980 (m110) cc_final: 0.8663 (m110) REVERT: B 139 MET cc_start: 0.9299 (ttm) cc_final: 0.9040 (ttm) REVERT: B 183 GLN cc_start: 0.8249 (mt0) cc_final: 0.7153 (mt0) REVERT: B 192 GLU cc_start: 0.7855 (pt0) cc_final: 0.7283 (pm20) REVERT: B 258 GLU cc_start: 0.8041 (mp0) cc_final: 0.7518 (mp0) REVERT: B 290 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7610 (mmmm) REVERT: B 332 CYS cc_start: 0.8853 (m) cc_final: 0.8469 (m) REVERT: B 363 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8278 (mt-10) REVERT: B 374 GLU cc_start: 0.8519 (tt0) cc_final: 0.8143 (tt0) REVERT: B 408 GLN cc_start: 0.7274 (tt0) cc_final: 0.6883 (tt0) REVERT: B 433 ARG cc_start: 0.7464 (mtt90) cc_final: 0.6984 (mtt-85) REVERT: B 499 MET cc_start: 0.9019 (ttp) cc_final: 0.8742 (ttp) REVERT: B 505 ASP cc_start: 0.8014 (m-30) cc_final: 0.7626 (m-30) REVERT: B 530 GLU cc_start: 0.8305 (mp0) cc_final: 0.8052 (mp0) REVERT: B 554 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8434 (tmtp) REVERT: B 575 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8531 (p) REVERT: B 600 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7899 (mttp) REVERT: B 611 MET cc_start: 0.9084 (mmm) cc_final: 0.8755 (mmp) REVERT: B 612 GLU cc_start: 0.8664 (tp30) cc_final: 0.7735 (mm-30) REVERT: B 616 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7386 (mp10) REVERT: B 623 ASP cc_start: 0.9067 (m-30) cc_final: 0.8831 (m-30) REVERT: B 879 PHE cc_start: 0.7590 (m-80) cc_final: 0.7364 (t80) REVERT: B 916 MET cc_start: 0.9313 (mmm) cc_final: 0.8903 (mtp) REVERT: B 1062 MET cc_start: 0.9332 (mmm) cc_final: 0.9008 (mmm) REVERT: B 1105 ARG cc_start: 0.8417 (mmm160) cc_final: 0.8106 (tpt170) REVERT: C 28 ASP cc_start: 0.8936 (p0) cc_final: 0.8698 (p0) REVERT: C 161 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8374 (mm-30) REVERT: D 18 GLN cc_start: 0.7374 (mt0) cc_final: 0.7006 (mt0) REVERT: D 82 GLU cc_start: 0.6332 (mt-10) cc_final: 0.4806 (tm-30) REVERT: D 83 LYS cc_start: 0.7883 (mttt) cc_final: 0.7279 (mttp) REVERT: D 100 MET cc_start: 0.5184 (mmt) cc_final: 0.3097 (mtt) REVERT: E 21 CYS cc_start: 0.8394 (m) cc_final: 0.7937 (m) REVERT: E 33 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7746 (mm) REVERT: E 34 ASP cc_start: 0.7677 (t0) cc_final: 0.6828 (p0) REVERT: E 107 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7726 (tm-30) REVERT: F 51 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.4950 (mmp-170) REVERT: F 100 ARG cc_start: 0.8410 (mtp85) cc_final: 0.7836 (mmt-90) REVERT: G 32 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8151 (mtmt) REVERT: G 36 ASN cc_start: 0.8121 (m-40) cc_final: 0.7290 (m-40) REVERT: G 41 ASN cc_start: 0.8858 (m-40) cc_final: 0.8608 (m-40) REVERT: G 53 LYS cc_start: 0.7862 (tptt) cc_final: 0.7551 (tppp) REVERT: G 197 LEU cc_start: 0.6012 (mt) cc_final: 0.5621 (mt) REVERT: H 20 LYS cc_start: 0.8568 (tppt) cc_final: 0.8041 (tptp) REVERT: H 52 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8318 (tt) REVERT: H 55 LYS cc_start: 0.9204 (ttmt) cc_final: 0.8966 (ttmt) REVERT: H 100 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7710 (mt-10) REVERT: H 146 LYS cc_start: 0.9041 (tttp) cc_final: 0.8759 (tttm) REVERT: I 22 ARG cc_start: 0.6521 (ptt180) cc_final: 0.6268 (ptt180) REVERT: I 45 LYS cc_start: 0.7971 (tptt) cc_final: 0.7658 (tmtt) REVERT: J 26 GLN cc_start: 0.8548 (tp40) cc_final: 0.8168 (tt0) REVERT: K 24 LYS cc_start: 0.7571 (ptpp) cc_final: 0.7093 (ptmm) REVERT: K 48 ASP cc_start: 0.8250 (p0) cc_final: 0.7946 (p0) REVERT: K 50 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8709 (t) REVERT: K 60 MET cc_start: 0.9210 (mmm) cc_final: 0.8939 (mmm) REVERT: K 66 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: K 79 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.9067 (ttpt) REVERT: K 124 GLN cc_start: 0.8431 (tt0) cc_final: 0.8155 (tm-30) REVERT: M 16 TYR cc_start: 0.7846 (m-10) cc_final: 0.7336 (m-10) REVERT: M 97 MET cc_start: 0.7263 (ttt) cc_final: 0.6553 (ttp) REVERT: M 102 PHE cc_start: 0.7825 (m-80) cc_final: 0.7388 (m-80) REVERT: M 121 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6096 (mp10) REVERT: M 209 HIS cc_start: 0.6639 (p-80) cc_final: 0.6297 (p90) REVERT: M 286 MET cc_start: 0.3700 (mmm) cc_final: 0.3043 (mmm) REVERT: M 292 MET cc_start: 0.2604 (ptm) cc_final: 0.1966 (ttt) REVERT: M 389 MET cc_start: 0.4663 (ptp) cc_final: 0.3944 (ptm) REVERT: M 421 MET cc_start: 0.4878 (pp-130) cc_final: 0.4235 (mpp) REVERT: N 157 MET cc_start: 0.0269 (OUTLIER) cc_final: -0.0618 (tmm) REVERT: N 271 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8460 (pp) REVERT: N 341 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8244 (tt) REVERT: N 380 LYS cc_start: 0.7689 (tppp) cc_final: 0.7286 (tptp) REVERT: N 390 GLU cc_start: 0.7544 (tt0) cc_final: 0.6869 (tm-30) REVERT: O 14 GLN cc_start: 0.7773 (tt0) cc_final: 0.7448 (tm-30) REVERT: O 41 HIS cc_start: 0.7816 (t-90) cc_final: 0.7586 (t-90) REVERT: O 76 GLU cc_start: 0.8261 (tt0) cc_final: 0.7248 (pm20) REVERT: O 259 MET cc_start: 0.7528 (mpt) cc_final: 0.7262 (mmt) REVERT: O 314 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5093 (mt) REVERT: O 355 GLN cc_start: 0.8514 (tt0) cc_final: 0.8055 (tt0) REVERT: O 402 ASN cc_start: 0.7476 (t160) cc_final: 0.7203 (t0) REVERT: O 419 ARG cc_start: 0.7033 (ptp-170) cc_final: 0.6596 (ptm-80) REVERT: O 474 MET cc_start: 0.0304 (pp-130) cc_final: -0.0079 (ppp) REVERT: P 267 MET cc_start: 0.4175 (tpt) cc_final: 0.3645 (tpt) REVERT: Q 54 GLU cc_start: 0.6334 (mp0) cc_final: 0.5985 (mp0) REVERT: Q 56 TYR cc_start: 0.7755 (t80) cc_final: 0.7468 (t80) REVERT: Q 58 LEU cc_start: 0.7576 (tt) cc_final: 0.7084 (mp) REVERT: Q 71 MET cc_start: 0.7469 (mmm) cc_final: 0.7210 (ttt) REVERT: Q 73 TYR cc_start: 0.7516 (m-80) cc_final: 0.6821 (m-80) REVERT: Q 110 MET cc_start: 0.6715 (ptp) cc_final: 0.6333 (ptp) outliers start: 113 outliers final: 62 residues processed: 722 average time/residue: 0.4791 time to fit residues: 427.2158 Evaluate side-chains 699 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 620 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 116 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1037 CYS Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 835 VAL 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 1030 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 139 ILE Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 52 LEU 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 79 LYS Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 157 MET Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 332 ARG Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 314 LEU Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 472 optimal weight: 7.9990 chunk 242 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 314 optimal weight: 1.9990 chunk 498 optimal weight: 6.9990 chunk 465 optimal weight: 10.0000 chunk 494 optimal weight: 3.9990 chunk 431 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 260 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN K 38 HIS M 44 HIS P 207 ASN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.196962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113353 restraints weight = 53417.485| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.35 r_work: 0.2979 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 45685 Z= 0.181 Angle : 0.643 26.631 62182 Z= 0.319 Chirality : 0.045 0.269 6998 Planarity : 0.005 0.082 7607 Dihedral : 15.458 179.408 7112 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.38 % Allowed : 20.42 % Favored : 77.20 % 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: 0.24 (0.12), residues: 5269 helix: 1.50 (0.12), residues: 2073 sheet: -0.64 (0.18), residues: 726 loop : -0.71 (0.12), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 99 TYR 0.022 0.002 TYR B 357 PHE 0.025 0.002 PHE B 380 TRP 0.009 0.001 TRP A 595 HIS 0.013 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (45655) covalent geometry : angle 0.61474 / 0.32 (62137) hydrogen bonds : bond 0.03842 / 2.58 ( 1961) hydrogen bonds : angle 4.42034 / 3.14 ( 5558) metal coordination : bond 0.00742 / 0.40 ( 28) metal coordination : angle 7.05147 / 4.02 ( 45) Misc. bond : bond 0.00231 / 0.12 ( 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 771 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 659 time to evaluate : 0.976 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 4 GLU cc_start: 0.7577 (pm20) cc_final: 0.7327 (pm20) REVERT: A 89 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7487 (tp30) REVERT: A 107 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8439 (mmm) REVERT: A 131 ARG cc_start: 0.7882 (ptp-110) cc_final: 0.7502 (ptp90) REVERT: A 140 ARG cc_start: 0.7885 (ttm110) cc_final: 0.7640 (ttm110) REVERT: A 163 ASN cc_start: 0.8039 (m-40) cc_final: 0.7784 (m110) REVERT: A 270 LEU cc_start: 0.0854 (OUTLIER) cc_final: 0.0126 (mp) REVERT: A 311 ASP cc_start: 0.8289 (t0) cc_final: 0.7975 (m-30) REVERT: A 312 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: A 406 LYS cc_start: 0.9232 (ttpt) cc_final: 0.8562 (mmtt) REVERT: A 505 MET cc_start: 0.9338 (mtp) cc_final: 0.8848 (mtp) REVERT: A 544 ASP cc_start: 0.8740 (m-30) cc_final: 0.8375 (m-30) REVERT: A 575 LYS cc_start: 0.9159 (ptpt) cc_final: 0.8897 (ptpt) REVERT: A 620 LYS cc_start: 0.7231 (mtmt) cc_final: 0.6334 (mptt) REVERT: A 754 LYS cc_start: 0.8159 (tppt) cc_final: 0.7627 (tmmt) REVERT: A 947 LEU cc_start: 0.8600 (tt) cc_final: 0.8093 (mt) REVERT: A 1020 ASP cc_start: 0.8768 (t70) cc_final: 0.8475 (t0) REVERT: A 1024 ARG cc_start: 0.8959 (mtm110) cc_final: 0.8590 (mtm180) REVERT: A 1065 LEU cc_start: 0.9097 (tp) cc_final: 0.8854 (mt) REVERT: A 1084 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8873 (mm) REVERT: A 1091 LYS cc_start: 0.8044 (mttt) cc_final: 0.7718 (mmtt) REVERT: A 1112 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8240 (mp0) REVERT: A 1138 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7887 (ttp80) REVERT: A 1151 TYR cc_start: 0.8321 (t80) cc_final: 0.7915 (t80) REVERT: A 1179 GLU cc_start: 0.8210 (pt0) cc_final: 0.7410 (tm-30) REVERT: A 1191 PHE cc_start: 0.6807 (t80) cc_final: 0.6485 (t80) REVERT: A 1193 LYS cc_start: 0.8279 (mtmt) cc_final: 0.8008 (mtpp) REVERT: A 1195 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7630 (p0) REVERT: A 1206 GLU cc_start: 0.8329 (mp0) cc_final: 0.7948 (mp0) REVERT: A 1211 VAL cc_start: 0.8663 (m) cc_final: 0.8444 (t) REVERT: A 1275 MET cc_start: 0.9177 (tpp) cc_final: 0.8835 (mmt) REVERT: A 1310 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8594 (mtmm) REVERT: B 60 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7440 (mtmt) REVERT: B 192 GLU cc_start: 0.7730 (pt0) cc_final: 0.7068 (pm20) REVERT: B 258 GLU cc_start: 0.8002 (mp0) cc_final: 0.7496 (mp0) REVERT: B 285 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7866 (tmtt) REVERT: B 290 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7657 (mppt) REVERT: B 332 CYS cc_start: 0.8972 (m) cc_final: 0.8518 (m) REVERT: B 363 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 374 GLU cc_start: 0.8624 (tt0) cc_final: 0.8206 (tt0) REVERT: B 408 GLN cc_start: 0.7189 (tt0) cc_final: 0.6812 (tt0) REVERT: B 431 MET cc_start: 0.7347 (ptp) cc_final: 0.7071 (ppp) REVERT: B 499 MET cc_start: 0.9182 (ttp) cc_final: 0.8887 (ttp) REVERT: B 505 ASP cc_start: 0.8057 (m-30) cc_final: 0.7597 (m-30) REVERT: B 530 GLU cc_start: 0.8361 (mp0) cc_final: 0.8025 (mp0) REVERT: B 554 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8381 (tmtp) REVERT: B 575 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 600 LYS cc_start: 0.8193 (mtpt) cc_final: 0.7801 (mttp) REVERT: B 611 MET cc_start: 0.9007 (mmm) cc_final: 0.8724 (mmp) REVERT: B 612 GLU cc_start: 0.8508 (tp30) cc_final: 0.7505 (mm-30) REVERT: B 616 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7228 (mp10) REVERT: B 623 ASP cc_start: 0.8986 (m-30) cc_final: 0.8685 (m-30) REVERT: B 641 CYS cc_start: 0.8676 (m) cc_final: 0.7865 (m) REVERT: B 879 PHE cc_start: 0.7613 (m-80) cc_final: 0.7275 (t80) REVERT: B 916 MET cc_start: 0.9391 (mmm) cc_final: 0.8972 (mtp) REVERT: B 1062 MET cc_start: 0.9358 (mmm) cc_final: 0.9049 (mmm) REVERT: B 1105 ARG cc_start: 0.8489 (mmm160) cc_final: 0.8100 (tpt170) REVERT: C 28 ASP cc_start: 0.8994 (p0) cc_final: 0.8684 (p0) REVERT: C 143 GLN cc_start: 0.8536 (tt0) cc_final: 0.7661 (mm-40) REVERT: C 209 ASP cc_start: 0.8961 (t0) cc_final: 0.8757 (t0) REVERT: C 279 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.7866 (ttt90) REVERT: D 18 GLN cc_start: 0.7363 (mt0) cc_final: 0.6849 (mt0) REVERT: D 29 GLU cc_start: 0.5868 (mt-10) cc_final: 0.5445 (tm-30) REVERT: D 82 GLU cc_start: 0.6500 (mt-10) cc_final: 0.4904 (tm-30) REVERT: D 83 LYS cc_start: 0.7824 (mttt) cc_final: 0.7259 (mttp) REVERT: D 100 MET cc_start: 0.5147 (mmt) cc_final: 0.3073 (mtt) REVERT: E 21 CYS cc_start: 0.8349 (m) cc_final: 0.7787 (m) REVERT: E 33 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7713 (mm) REVERT: E 34 ASP cc_start: 0.7708 (t0) cc_final: 0.6995 (p0) REVERT: E 107 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7736 (tm-30) REVERT: F 51 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.4796 (mmp-170) REVERT: F 84 GLU cc_start: 0.8476 (pm20) cc_final: 0.8088 (pm20) REVERT: F 100 ARG cc_start: 0.8407 (mtp85) cc_final: 0.7770 (mmt-90) REVERT: G 7 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8437 (mmm) REVERT: G 32 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8071 (mtmt) REVERT: G 36 ASN cc_start: 0.8378 (m-40) cc_final: 0.7548 (m-40) REVERT: G 41 ASN cc_start: 0.8822 (m-40) cc_final: 0.8567 (m-40) REVERT: G 53 LYS cc_start: 0.7757 (tptt) cc_final: 0.7467 (tppp) REVERT: G 197 LEU cc_start: 0.6092 (mt) cc_final: 0.5433 (mt) REVERT: H 20 LYS cc_start: 0.8550 (tppt) cc_final: 0.8009 (tptp) REVERT: H 52 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8302 (tt) REVERT: H 55 LYS cc_start: 0.9266 (ttmt) cc_final: 0.9011 (ttmt) REVERT: H 100 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7714 (mt-10) REVERT: H 146 LYS cc_start: 0.8963 (tttp) cc_final: 0.8684 (tttm) REVERT: I 22 ARG cc_start: 0.6306 (ptt180) cc_final: 0.6066 (ptt180) REVERT: J 26 GLN cc_start: 0.8424 (tp40) cc_final: 0.8119 (tt0) REVERT: K 24 LYS cc_start: 0.7507 (ptpp) cc_final: 0.6979 (ptmm) REVERT: K 48 ASP cc_start: 0.8215 (p0) cc_final: 0.7934 (p0) REVERT: K 50 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8635 (t) REVERT: K 60 MET cc_start: 0.9328 (mmm) cc_final: 0.9038 (mmm) REVERT: K 66 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: K 79 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9096 (ttpt) REVERT: K 124 GLN cc_start: 0.8530 (tt0) cc_final: 0.8123 (tm-30) REVERT: M 60 MET cc_start: 0.6448 (mtm) cc_final: 0.6245 (mtp) REVERT: M 68 ASN cc_start: 0.6377 (m110) cc_final: 0.6116 (m110) REVERT: M 97 MET cc_start: 0.7356 (ttt) cc_final: 0.6702 (mmm) REVERT: M 102 PHE cc_start: 0.7693 (m-80) cc_final: 0.7406 (m-80) REVERT: M 121 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.6286 (mp10) REVERT: M 286 MET cc_start: 0.3579 (mmm) cc_final: 0.2873 (mmm) REVERT: M 292 MET cc_start: 0.2529 (ptm) cc_final: 0.1886 (ttt) REVERT: M 389 MET cc_start: 0.4548 (ptp) cc_final: 0.3848 (ptm) REVERT: M 421 MET cc_start: 0.5165 (pp-130) cc_final: 0.4384 (mpp) REVERT: N 157 MET cc_start: 0.0278 (OUTLIER) cc_final: -0.0533 (tmm) REVERT: N 341 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8088 (tt) REVERT: N 380 LYS cc_start: 0.7728 (tppp) cc_final: 0.7289 (tptp) REVERT: N 390 GLU cc_start: 0.7480 (tt0) cc_final: 0.6748 (tm-30) REVERT: O 14 GLN cc_start: 0.7680 (tt0) cc_final: 0.7401 (tm-30) REVERT: O 41 HIS cc_start: 0.7862 (t-90) cc_final: 0.7609 (t-90) REVERT: O 70 ARG cc_start: 0.6813 (mpp-170) cc_final: 0.6532 (mpp-170) REVERT: O 76 GLU cc_start: 0.8163 (tt0) cc_final: 0.7082 (pm20) REVERT: O 259 MET cc_start: 0.7575 (mpt) cc_final: 0.7326 (mmt) REVERT: O 314 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5130 (mt) REVERT: O 355 GLN cc_start: 0.8445 (tt0) cc_final: 0.7999 (tt0) REVERT: O 402 ASN cc_start: 0.7417 (t160) cc_final: 0.7155 (t0) REVERT: O 419 ARG cc_start: 0.7013 (ptp-170) cc_final: 0.6535 (ptm-80) REVERT: O 474 MET cc_start: 0.0494 (pp-130) cc_final: 0.0128 (ppp) REVERT: O 507 ASN cc_start: 0.8007 (m-40) cc_final: 0.7660 (m110) REVERT: Q 54 GLU cc_start: 0.6576 (mp0) cc_final: 0.6303 (mp0) REVERT: Q 56 TYR cc_start: 0.7688 (t80) cc_final: 0.7346 (t80) REVERT: Q 71 MET cc_start: 0.7728 (mmm) cc_final: 0.6991 (ttt) REVERT: Q 110 MET cc_start: 0.6717 (ptp) cc_final: 0.6373 (ptp) outliers start: 112 outliers final: 61 residues processed: 733 average time/residue: 0.4726 time to fit residues: 429.1714 Evaluate side-chains 708 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 628 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1037 CYS Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain A residue 1280 MET Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 835 VAL 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 1030 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 157 MET Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 314 LEU Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 529 optimal weight: 40.0000 chunk 30 optimal weight: 4.9990 chunk 451 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 377 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A1239 HIS B 260 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN H 130 ASN K 38 HIS M 44 HIS M 209 HIS ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.197468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113957 restraints weight = 53613.881| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.41 r_work: 0.2999 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 45685 Z= 0.148 Angle : 0.634 26.920 62182 Z= 0.313 Chirality : 0.043 0.256 6998 Planarity : 0.004 0.091 7607 Dihedral : 15.418 178.302 7112 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.96 % Allowed : 21.16 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.12), residues: 5269 helix: 1.55 (0.12), residues: 2073 sheet: -0.60 (0.18), residues: 716 loop : -0.70 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 99 TYR 0.023 0.001 TYR M 210 PHE 0.037 0.001 PHE B 278 TRP 0.045 0.001 TRP G 200 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (45655) covalent geometry : angle 0.60583 / 0.31 (62137) hydrogen bonds : bond 0.03657 / 2.45 ( 1961) hydrogen bonds : angle 4.38627 / 3.12 ( 5558) metal coordination : bond 0.00640 / 0.34 ( 28) metal coordination : angle 7.01325 / 4.02 ( 45) Misc. bond : bond 0.00200 / 0.10 ( 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 728 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 636 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7404 (pm20) cc_final: 0.7169 (pm20) REVERT: A 89 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7443 (tp30) REVERT: A 107 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8394 (mmm) REVERT: A 221 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 270 LEU cc_start: 0.0848 (OUTLIER) cc_final: 0.0121 (mp) REVERT: A 307 MET cc_start: 0.8331 (tpp) cc_final: 0.8095 (mmm) REVERT: A 312 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: A 349 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: A 406 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8536 (mmtt) REVERT: A 505 MET cc_start: 0.9343 (mtp) cc_final: 0.8844 (mtp) REVERT: A 523 MET cc_start: 0.9446 (mtp) cc_final: 0.9217 (mtp) REVERT: A 544 ASP cc_start: 0.8618 (m-30) cc_final: 0.8325 (m-30) REVERT: A 575 LYS cc_start: 0.9149 (ptpt) cc_final: 0.8881 (ptpt) REVERT: A 620 LYS cc_start: 0.7202 (mtmt) cc_final: 0.6297 (mptt) REVERT: A 709 LEU cc_start: 0.8714 (tm) cc_final: 0.8499 (tt) REVERT: A 754 LYS cc_start: 0.8110 (tppt) cc_final: 0.7563 (tmmt) REVERT: A 947 LEU cc_start: 0.8563 (tt) cc_final: 0.8060 (mt) REVERT: A 1020 ASP cc_start: 0.8735 (t70) cc_final: 0.8503 (t0) REVERT: A 1024 ARG cc_start: 0.8949 (mtm110) cc_final: 0.8601 (mtm180) REVERT: A 1065 LEU cc_start: 0.9071 (tp) cc_final: 0.8828 (mt) REVERT: A 1091 LYS cc_start: 0.8032 (mttt) cc_final: 0.7717 (mmtt) REVERT: A 1112 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8181 (mp0) REVERT: A 1138 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7841 (ttp80) REVERT: A 1151 TYR cc_start: 0.8327 (t80) cc_final: 0.7926 (t80) REVERT: A 1179 GLU cc_start: 0.8199 (pt0) cc_final: 0.7393 (tm-30) REVERT: A 1185 MET cc_start: 0.7193 (pmm) cc_final: 0.6743 (pp-130) REVERT: A 1191 PHE cc_start: 0.6842 (t80) cc_final: 0.6501 (t80) REVERT: A 1195 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7677 (p0) REVERT: A 1211 VAL cc_start: 0.8627 (m) cc_final: 0.8412 (t) REVERT: A 1275 MET cc_start: 0.9127 (tpp) cc_final: 0.8761 (mmt) REVERT: A 1310 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8543 (mtmm) REVERT: B 60 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7447 (mtmt) REVERT: B 139 MET cc_start: 0.9339 (ttm) cc_final: 0.9052 (ttm) REVERT: B 192 GLU cc_start: 0.7733 (pt0) cc_final: 0.7084 (pm20) REVERT: B 258 GLU cc_start: 0.7988 (mp0) cc_final: 0.7467 (mp0) REVERT: B 285 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7837 (tmtt) REVERT: B 290 LYS cc_start: 0.7992 (mmtm) cc_final: 0.7523 (mmmm) REVERT: B 332 CYS cc_start: 0.8939 (m) cc_final: 0.8448 (m) REVERT: B 374 GLU cc_start: 0.8602 (tt0) cc_final: 0.8180 (tt0) REVERT: B 431 MET cc_start: 0.7313 (ptp) cc_final: 0.7037 (ppp) REVERT: B 499 MET cc_start: 0.9114 (ttp) cc_final: 0.8820 (ttp) REVERT: B 530 GLU cc_start: 0.8398 (mp0) cc_final: 0.8129 (mp0) REVERT: B 554 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8391 (tmtp) REVERT: B 575 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8489 (p) REVERT: B 600 LYS cc_start: 0.8101 (mtpt) cc_final: 0.7772 (mttp) REVERT: B 611 MET cc_start: 0.8990 (mmm) cc_final: 0.8646 (mmp) REVERT: B 612 GLU cc_start: 0.8487 (tp30) cc_final: 0.7489 (mm-30) REVERT: B 616 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7219 (mp10) REVERT: B 623 ASP cc_start: 0.8953 (m-30) cc_final: 0.8665 (m-30) REVERT: B 641 CYS cc_start: 0.8556 (m) cc_final: 0.7745 (m) REVERT: B 879 PHE cc_start: 0.7561 (m-80) cc_final: 0.7287 (t80) REVERT: B 916 MET cc_start: 0.9402 (mmm) cc_final: 0.8965 (mtp) REVERT: B 1062 MET cc_start: 0.9373 (mmm) cc_final: 0.9069 (mmm) REVERT: B 1105 ARG cc_start: 0.8408 (mmm160) cc_final: 0.7996 (tpt170) REVERT: C 28 ASP cc_start: 0.8984 (p0) cc_final: 0.8681 (p0) REVERT: C 141 ARG cc_start: 0.8817 (tpt170) cc_final: 0.8446 (tpt170) REVERT: C 143 GLN cc_start: 0.8422 (tt0) cc_final: 0.7881 (mm-40) REVERT: C 161 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8477 (mm-30) REVERT: C 279 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7806 (ttt90) REVERT: D 18 GLN cc_start: 0.7333 (mt0) cc_final: 0.7064 (mt0) REVERT: D 29 GLU cc_start: 0.5881 (mt-10) cc_final: 0.5450 (tm-30) REVERT: D 82 GLU cc_start: 0.6507 (mt-10) cc_final: 0.4987 (tm-30) REVERT: D 83 LYS cc_start: 0.7819 (mttt) cc_final: 0.7269 (mttp) REVERT: D 85 GLN cc_start: 0.7520 (mt0) cc_final: 0.7071 (mp10) REVERT: D 100 MET cc_start: 0.5120 (mmt) cc_final: 0.3055 (mtt) REVERT: E 21 CYS cc_start: 0.8329 (m) cc_final: 0.7759 (m) REVERT: E 33 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7652 (mm) REVERT: E 34 ASP cc_start: 0.7732 (t0) cc_final: 0.7021 (p0) REVERT: E 107 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7722 (tm-30) REVERT: F 51 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.4760 (mmp-170) REVERT: F 100 ARG cc_start: 0.8371 (mtp85) cc_final: 0.7745 (mmt-90) REVERT: G 32 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8004 (mtmt) REVERT: G 36 ASN cc_start: 0.8218 (m-40) cc_final: 0.7409 (m-40) REVERT: G 41 ASN cc_start: 0.8811 (m-40) cc_final: 0.8554 (m-40) REVERT: G 53 LYS cc_start: 0.7938 (tptt) cc_final: 0.7473 (tppp) REVERT: G 197 LEU cc_start: 0.5882 (mt) cc_final: 0.5620 (mt) REVERT: H 13 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8617 (mmtm) REVERT: H 20 LYS cc_start: 0.8537 (tppt) cc_final: 0.7993 (tptp) REVERT: H 52 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8277 (tt) REVERT: H 55 LYS cc_start: 0.9264 (ttmt) cc_final: 0.8994 (ttmt) REVERT: H 100 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7640 (mt-10) REVERT: H 146 LYS cc_start: 0.8939 (tttp) cc_final: 0.8673 (tttm) REVERT: I 22 ARG cc_start: 0.6337 (ptt180) cc_final: 0.6103 (ptt180) REVERT: J 26 GLN cc_start: 0.8407 (tp40) cc_final: 0.8075 (tt0) REVERT: K 24 LYS cc_start: 0.7515 (ptpp) cc_final: 0.6962 (ptmm) REVERT: K 48 ASP cc_start: 0.8184 (p0) cc_final: 0.7902 (p0) REVERT: K 50 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8549 (t) REVERT: K 60 MET cc_start: 0.9317 (mmm) cc_final: 0.9024 (mmm) REVERT: K 66 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8365 (tm-30) REVERT: K 79 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.9072 (ttpt) REVERT: K 124 GLN cc_start: 0.8484 (tt0) cc_final: 0.8087 (tm-30) REVERT: M 60 MET cc_start: 0.6561 (mtm) cc_final: 0.6291 (mtp) REVERT: M 68 ASN cc_start: 0.6284 (m110) cc_final: 0.6019 (m110) REVERT: M 97 MET cc_start: 0.7347 (ttt) cc_final: 0.6598 (ttp) REVERT: M 102 PHE cc_start: 0.7659 (m-80) cc_final: 0.7349 (m-80) REVERT: M 121 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6235 (mp10) REVERT: M 209 HIS cc_start: 0.6698 (p-80) cc_final: 0.6371 (p90) REVERT: M 286 MET cc_start: 0.3563 (mmm) cc_final: 0.2853 (mmm) REVERT: M 292 MET cc_start: 0.2466 (ptm) cc_final: 0.1834 (ttt) REVERT: M 389 MET cc_start: 0.4460 (ptp) cc_final: 0.3793 (ptm) REVERT: M 421 MET cc_start: 0.5173 (pp-130) cc_final: 0.4402 (mpp) REVERT: N 157 MET cc_start: 0.0279 (OUTLIER) cc_final: -0.0530 (tmm) REVERT: N 341 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8068 (tt) REVERT: N 380 LYS cc_start: 0.7732 (tppp) cc_final: 0.7273 (tptp) REVERT: N 390 GLU cc_start: 0.7406 (tt0) cc_final: 0.6697 (tm-30) REVERT: O 14 GLN cc_start: 0.7651 (tt0) cc_final: 0.7372 (tm-30) REVERT: O 41 HIS cc_start: 0.7854 (t-90) cc_final: 0.7588 (t-90) REVERT: O 70 ARG cc_start: 0.6607 (mpp-170) cc_final: 0.6163 (mpp-170) REVERT: O 76 GLU cc_start: 0.8146 (tt0) cc_final: 0.7043 (pm20) REVERT: O 314 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5150 (mt) REVERT: O 355 GLN cc_start: 0.8418 (tt0) cc_final: 0.7994 (tt0) REVERT: O 402 ASN cc_start: 0.7395 (t160) cc_final: 0.7136 (t0) REVERT: O 419 ARG cc_start: 0.7011 (ptp-170) cc_final: 0.6532 (ptm-80) REVERT: O 474 MET cc_start: 0.0504 (pp-130) cc_final: 0.0141 (ppp) REVERT: Q 54 GLU cc_start: 0.6579 (mp0) cc_final: 0.6316 (mp0) REVERT: Q 56 TYR cc_start: 0.7672 (t80) cc_final: 0.7404 (t80) REVERT: Q 71 MET cc_start: 0.7619 (mmm) cc_final: 0.6869 (ttt) REVERT: Q 92 MET cc_start: 0.2376 (pmt) cc_final: 0.0172 (ptm) REVERT: Q 110 MET cc_start: 0.6861 (ptp) cc_final: 0.6489 (ptp) outliers start: 92 outliers final: 60 residues processed: 694 average time/residue: 0.4541 time to fit residues: 390.0974 Evaluate side-chains 708 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 629 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 312 PHE Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1004 ASP Chi-restraints excluded: chain A residue 1027 MET Chi-restraints excluded: chain A residue 1037 CYS Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1195 ASP Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 835 VAL 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 1030 VAL Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 157 MET Chi-restraints excluded: chain N residue 281 THR Chi-restraints excluded: chain N residue 332 ARG Chi-restraints excluded: chain N residue 341 LEU Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 314 LEU Chi-restraints excluded: chain O residue 400 SER Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 94 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 125 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 413 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 462 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 353 optimal weight: 0.0770 chunk 532 optimal weight: 50.0000 chunk 68 optimal weight: 0.9990 chunk 395 optimal weight: 9.9990 chunk 272 optimal weight: 0.0470 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 154 ASN B 260 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN K 38 HIS M 44 HIS ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 297 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.198989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116469 restraints weight = 53841.102| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.39 r_work: 0.3046 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45685 Z= 0.118 Angle : 0.609 26.300 62182 Z= 0.300 Chirality : 0.042 0.231 6998 Planarity : 0.004 0.084 7607 Dihedral : 15.328 176.282 7112 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.70 % Allowed : 21.52 % Favored : 76.77 % 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: 1.69 (0.12), residues: 2059 sheet: -0.63 (0.18), residues: 734 loop : -0.61 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 99 TYR 0.019 0.001 TYR F 115 PHE 0.034 0.001 PHE B 278 TRP 0.058 0.001 TRP G 200 HIS 0.008 0.001 HIS M 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (45655) covalent geometry : angle 0.58155 / 0.30 (62137) hydrogen bonds : bond 0.03382 / 2.26 ( 1961) hydrogen bonds : angle 4.30556 / 3.06 ( 5558) metal coordination : bond 0.00456 / 0.23 ( 28) metal coordination : angle 6.78265 / 3.89 ( 45) Misc. bond : bond 0.00178 / 0.09 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18493.68 seconds wall clock time: 313 minutes 52.34 seconds (18832.34 seconds total)