Starting phenix.real_space_refine on Mon Aug 10 07:51:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k36_62006/08_2026/9k36_62006.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k36_62006/08_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_62006/08_2026/9k36_62006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k36_62006/08_2026/9k36_62006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k36_62006/08_2026/9k36_62006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k36_62006/08_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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.82, 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: 4.05 Conformation dependent library (CDL) restraints added in 1.8 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: 5.71 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: 13.20 Time building geometry restraints manager: 5.36 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 1.20e-02 6.94e+03 1.99e+02 bond pdb=" O3' DT Y -12 " pdb=" P DC Y -11 " ideal model delta sigma weight residual 1.607 1.445 0.162 1.20e-02 6.94e+03 1.82e+02 bond pdb=" O3' DT Y -13 " pdb=" P DT Y -12 " ideal model delta sigma weight residual 1.607 1.471 0.136 1.20e-02 6.94e+03 1.28e+02 bond pdb=" C5' U Z 10 " pdb=" C4' U Z 10 " ideal model delta sigma weight residual 1.508 1.434 0.074 7.00e-03 2.04e+04 1.11e+02 bond pdb=" O5' U Z 10 " pdb=" C5' U Z 10 " ideal model delta sigma weight residual 1.424 1.292 0.132 1.60e-02 3.91e+03 6.77e+01 ... (remaining 45650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.34: 62085 5.34 - 10.68: 40 10.68 - 16.02: 7 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 119.70 99.47 20.23 1.20e+00 6.94e-01 2.84e+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 2.00e+00 2.50e-01 8.08e+01 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=" 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 1.60e+00 3.91e-01 4.77e+01 angle pdb=" P U Z 10 " pdb=" O5' U Z 10 " pdb=" C5' U Z 10 " ideal model delta sigma weight residual 120.90 110.96 9.94 1.60e+00 3.91e-01 3.86e+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: 6698 0.099 - 0.197: 293 0.197 - 0.296: 6 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.720 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 58.620 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.000 ------------------------------------------------------------------------------- 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= 0.624 Angle : 0.772 47.047 62182 Z= 0.382 Chirality : 0.043 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 0.00398 / 0.31 (45655) covalent geometry : angle 0.57184 / 0.38 (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 : 1.766 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: 0.7095 (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: 0.6663 (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: 0.6977 (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: 0.5502 (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: 0.3650 (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: 0.7547 (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: 0.6312 (tm-30) REVERT: O 408 GLU cc_start: 0.6881 (tt0) cc_final: 0.6373 (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: 0.7616 (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: 0.7580 time to fit residues: 1285.4172 Evaluate side-chains 811 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 794 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 469 HIS 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 616 GLN ** 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: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.206148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128366 restraints weight = 54727.039| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.35 r_work: 0.3155 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 45685 Z= 0.237 Angle : 0.742 27.519 62182 Z= 0.372 Chirality : 0.049 0.353 6998 Planarity : 0.006 0.113 7607 Dihedral : 16.223 179.289 7138 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.00 % Allowed : 12.75 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.11), residues: 5269 helix: 1.02 (0.11), residues: 2052 sheet: -0.70 (0.18), residues: 718 loop : -1.03 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG Q 113 TYR 0.028 0.002 TYR A1296 PHE 0.030 0.002 PHE C 225 TRP 0.020 0.002 TRP M 423 HIS 0.013 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (45655) covalent geometry : angle 0.71342 / 0.37 (62137) hydrogen bonds : bond 0.04586 / 3.08 ( 1961) hydrogen bonds : angle 4.69013 / 3.36 ( 5558) metal coordination : bond 0.02366 / 1.25 ( 28) metal coordination : angle 7.63227 / 4.41 ( 45) Misc. bond : bond 0.03946 / 2.01 ( 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 1018 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 830 time to evaluate : 1.998 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: 0.7499 (tp30) cc_final: 0.7282 (mp0) REVERT: A 131 ARG cc_start: 0.7807 (ptp-110) cc_final: 0.7362 (ptp90) REVERT: A 240 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8594 (mtp) REVERT: A 262 ILE cc_start: 0.8464 (mt) cc_final: 0.8173 (mt) REVERT: A 311 ASP cc_start: 0.8401 (t0) cc_final: 0.7961 (m-30) REVERT: A 312 PHE cc_start: 0.8310 (t80) cc_final: 0.7999 (t80) REVERT: A 349 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8266 (mp10) REVERT: A 436 ASN cc_start: 0.8292 (t0) cc_final: 0.8029 (t0) REVERT: A 505 MET cc_start: 0.9101 (mtp) cc_final: 0.8840 (mtp) REVERT: A 620 LYS cc_start: 0.7192 (mtmt) cc_final: 0.6323 (mptt) REVERT: A 711 LYS cc_start: 0.8293 (pttm) cc_final: 0.8019 (pttt) REVERT: A 761 ASP cc_start: 0.8320 (m-30) cc_final: 0.8029 (m-30) REVERT: A 790 ILE cc_start: 0.8750 (mm) cc_final: 0.8481 (mp) REVERT: A 814 GLU cc_start: 0.8433 (tt0) cc_final: 0.8192 (tp30) REVERT: A 947 LEU cc_start: 0.8481 (tt) cc_final: 0.7929 (mt) REVERT: A 954 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7813 (mmpt) REVERT: A 970 LYS cc_start: 0.7975 (mttt) cc_final: 0.7644 (mmtt) REVERT: A 982 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7975 (mtpp) REVERT: A 1020 ASP cc_start: 0.8861 (t70) cc_final: 0.8577 (t0) REVERT: A 1024 ARG cc_start: 0.9055 (mtm110) cc_final: 0.8715 (mtm180) REVERT: A 1065 LEU cc_start: 0.8431 (tt) cc_final: 0.8152 (tp) REVERT: A 1091 LYS cc_start: 0.7697 (mttt) cc_final: 0.7390 (mmtt) REVERT: A 1119 GLU cc_start: 0.7779 (pt0) cc_final: 0.7528 (pt0) REVERT: A 1151 TYR cc_start: 0.8264 (t80) cc_final: 0.7850 (t80) REVERT: A 1179 GLU cc_start: 0.8186 (pt0) cc_final: 0.7437 (tm-30) REVERT: A 1189 LEU cc_start: 0.7990 (tp) cc_final: 0.7782 (tp) REVERT: A 1214 ILE cc_start: 0.8045 (pt) cc_final: 0.7831 (pp) REVERT: A 1222 LYS cc_start: 0.7620 (pttt) cc_final: 0.7208 (pttm) REVERT: A 1277 ASN cc_start: 0.8868 (m-40) cc_final: 0.8594 (m-40) REVERT: A 1354 ASN cc_start: 0.8752 (m-40) cc_final: 0.8269 (m110) REVERT: A 1379 PHE cc_start: 0.8714 (t80) cc_final: 0.8290 (t80) REVERT: B 35 LYS cc_start: 0.8642 (mmmm) cc_final: 0.8290 (mttt) REVERT: B 139 MET cc_start: 0.9289 (ttm) cc_final: 0.8943 (ttp) REVERT: B 192 GLU cc_start: 0.7894 (pt0) cc_final: 0.7547 (pm20) REVERT: B 258 GLU cc_start: 0.8059 (mp0) cc_final: 0.7568 (mp0) REVERT: B 277 ILE cc_start: 0.7992 (mm) cc_final: 0.7786 (mm) REVERT: B 307 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6687 (tm-30) REVERT: B 332 CYS cc_start: 0.9015 (m) cc_final: 0.8573 (m) REVERT: B 380 PHE cc_start: 0.6864 (t80) cc_final: 0.6434 (t80) REVERT: B 431 MET cc_start: 0.7624 (ptm) cc_final: 0.7390 (ppp) REVERT: B 499 MET cc_start: 0.9121 (ttp) cc_final: 0.8771 (ttp) REVERT: B 506 MET cc_start: 0.8887 (mpp) cc_final: 0.8626 (mpt) REVERT: B 544 ASN cc_start: 0.8504 (m-40) cc_final: 0.8196 (m-40) REVERT: B 600 LYS cc_start: 0.8252 (mtpt) cc_final: 0.7941 (mttp) REVERT: B 611 MET cc_start: 0.9080 (mmm) cc_final: 0.8822 (mmp) REVERT: B 612 GLU cc_start: 0.8699 (tp30) cc_final: 0.8353 (tp30) REVERT: B 627 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8434 (mp0) REVERT: B 822 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8744 (mp0) REVERT: B 1028 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8607 (mtt-85) REVERT: B 1031 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8341 (tp) REVERT: B 1050 MET cc_start: 0.9396 (mtp) cc_final: 0.9116 (mtp) REVERT: B 1062 MET cc_start: 0.9362 (mmm) cc_final: 0.9052 (mmm) REVERT: B 1069 MET cc_start: 0.9043 (tmm) cc_final: 0.8824 (tmm) REVERT: B 1105 ARG cc_start: 0.8398 (mmm160) cc_final: 0.8190 (mtp85) REVERT: C 28 ASP cc_start: 0.8819 (p0) cc_final: 0.8561 (p0) REVERT: C 209 ASP cc_start: 0.8873 (t0) cc_final: 0.8509 (t0) REVERT: C 251 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7584 (tp30) REVERT: C 279 ARG cc_start: 0.8314 (ttt-90) cc_final: 0.7993 (ttt90) REVERT: D 18 GLN cc_start: 0.7234 (mt0) cc_final: 0.6905 (mt0) REVERT: D 64 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: D 76 HIS cc_start: 0.6979 (m170) cc_final: 0.6719 (m90) REVERT: D 82 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6047 (mm-30) REVERT: D 100 MET cc_start: 0.5580 (mmt) cc_final: 0.5243 (mmt) REVERT: E 21 CYS cc_start: 0.8345 (m) cc_final: 0.7837 (m) REVERT: E 33 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8096 (mm) REVERT: E 34 ASP cc_start: 0.6599 (t0) cc_final: 0.6130 (p0) REVERT: E 47 LYS cc_start: 0.6821 (ttpp) cc_final: 0.6604 (ptpp) REVERT: E 58 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5622 (mt) REVERT: E 61 LEU cc_start: 0.6761 (mm) cc_final: 0.6534 (mm) REVERT: E 98 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7606 (m-40) REVERT: E 107 GLN cc_start: 0.7219 (tt0) cc_final: 0.7016 (tm-30) REVERT: E 115 LYS cc_start: 0.8535 (mtmm) cc_final: 0.7974 (mtmt) REVERT: E 121 MET cc_start: 0.6900 (mmm) cc_final: 0.6617 (mmm) REVERT: F 51 ARG cc_start: 0.6981 (mtm-85) cc_final: 0.4936 (mmp-170) REVERT: F 100 ARG cc_start: 0.8500 (mtp85) cc_final: 0.7913 (mmt-90) REVERT: G 19 GLU cc_start: 0.8172 (pm20) cc_final: 0.7899 (pm20) REVERT: G 32 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8387 (mtmt) REVERT: G 37 LYS cc_start: 0.8544 (mmtm) cc_final: 0.8270 (mmtm) REVERT: G 41 ASN cc_start: 0.8838 (m-40) cc_final: 0.8578 (m-40) REVERT: G 44 LEU cc_start: 0.8171 (tt) cc_final: 0.7478 (tm) REVERT: G 50 ASP cc_start: 0.8589 (p0) cc_final: 0.8333 (p0) REVERT: G 53 LYS cc_start: 0.7774 (tptt) cc_final: 0.7388 (tppp) REVERT: G 60 PHE cc_start: 0.8924 (m-10) cc_final: 0.8465 (m-10) REVERT: G 150 PHE cc_start: 0.5505 (t80) cc_final: 0.4061 (t80) REVERT: H 51 ASP cc_start: 0.7984 (m-30) cc_final: 0.7662 (m-30) REVERT: H 52 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8203 (tt) REVERT: H 146 LYS cc_start: 0.9098 (tttp) cc_final: 0.8837 (tttm) REVERT: K 24 LYS cc_start: 0.7383 (ptpp) cc_final: 0.6711 (ptmm) REVERT: K 48 ASP cc_start: 0.8175 (p0) cc_final: 0.7814 (p0) REVERT: M 16 TYR cc_start: 0.7424 (m-10) cc_final: 0.7019 (m-80) REVERT: M 41 ASP cc_start: 0.7890 (m-30) cc_final: 0.7131 (p0) REVERT: M 97 MET cc_start: 0.7027 (ttt) cc_final: 0.6552 (tpp) REVERT: M 210 TYR cc_start: 0.6819 (t80) cc_final: 0.6010 (t80) REVERT: M 286 MET cc_start: 0.4376 (mmm) cc_final: 0.3615 (mmm) REVERT: M 292 MET cc_start: 0.2930 (ptm) cc_final: 0.2393 (ttt) REVERT: M 389 MET cc_start: 0.4353 (ptp) cc_final: 0.3852 (ptm) REVERT: N 328 LYS cc_start: 0.7188 (mtpp) cc_final: 0.6972 (mtpp) REVERT: N 361 VAL cc_start: 0.5723 (m) cc_final: 0.5501 (p) REVERT: N 390 GLU cc_start: 0.7097 (tt0) cc_final: 0.6366 (tm-30) REVERT: O 14 GLN cc_start: 0.7773 (tt0) cc_final: 0.7439 (tm-30) REVERT: O 15 GLU cc_start: 0.8335 (tp30) cc_final: 0.8123 (tp30) REVERT: O 20 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8313 (pp) REVERT: O 76 GLU cc_start: 0.8441 (tt0) cc_final: 0.7347 (pm20) REVERT: O 355 GLN cc_start: 0.8524 (tt0) cc_final: 0.8006 (tt0) REVERT: O 408 GLU cc_start: 0.7576 (tt0) cc_final: 0.7100 (tp30) REVERT: O 419 ARG cc_start: 0.7540 (ptp-170) cc_final: 0.7156 (ptm-80) REVERT: O 420 THR cc_start: 0.7108 (t) cc_final: 0.5748 (t) REVERT: O 531 MET cc_start: 0.6566 (mtm) cc_final: 0.6222 (mtm) REVERT: P 134 LYS cc_start: 0.1509 (OUTLIER) cc_final: 0.1229 (ttmt) REVERT: P 232 MET cc_start: 0.3334 (tpt) cc_final: 0.2521 (tpt) REVERT: P 235 ILE cc_start: 0.6249 (mm) cc_final: 0.5881 (pp) REVERT: P 308 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6854 (mp) REVERT: Q 54 GLU cc_start: 0.6077 (mp0) cc_final: 0.5824 (mp0) REVERT: Q 55 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7244 (mm-30) REVERT: Q 58 LEU cc_start: 0.7664 (tt) cc_final: 0.7307 (mp) REVERT: Q 71 MET cc_start: 0.7511 (mmm) cc_final: 0.7065 (ttt) REVERT: Q 73 TYR cc_start: 0.7344 (m-80) cc_final: 0.6733 (m-80) REVERT: Q 77 THR cc_start: 0.5619 (OUTLIER) cc_final: 0.5342 (m) REVERT: Q 92 MET cc_start: 0.2495 (ptt) cc_final: 0.2279 (ptt) REVERT: Q 103 TRP cc_start: 0.7310 (m100) cc_final: 0.6933 (m-90) REVERT: Q 110 MET cc_start: 0.7081 (mtt) cc_final: 0.6870 (ptp) outliers start: 188 outliers final: 63 residues processed: 943 average time/residue: 0.7604 time to fit residues: 880.8867 Evaluate side-chains 748 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 671 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 1256 LYS 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 297 TRP 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 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 30 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 93 VAL 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 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 P residue 308 ILE 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: 0.9990 chunk 76 optimal weight: 0.9990 chunk 428 optimal weight: 9.9990 chunk 304 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 286 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 431 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 326 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 58 HIS A 163 ASN A 599 GLN A 836 ASN A1075 ASN A1277 ASN B 260 HIS B 282 GLN B 438 GLN B 524 ASN B 616 GLN B 703 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS E 168 ASN H 130 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.204786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125235 restraints weight = 54038.383| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.32 r_work: 0.3141 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 45685 Z= 0.151 Angle : 0.623 29.114 62182 Z= 0.304 Chirality : 0.044 0.294 6998 Planarity : 0.004 0.072 7607 Dihedral : 15.972 179.631 7120 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.07 % Allowed : 15.61 % Favored : 80.33 % 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: -0.01 (0.11), residues: 5269 helix: 1.30 (0.11), residues: 2073 sheet: -0.65 (0.19), residues: 698 loop : -0.92 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 466 TYR 0.025 0.001 TYR P 219 PHE 0.021 0.001 PHE D 17 TRP 0.011 0.001 TRP P 313 HIS 0.010 0.001 HIS M 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (45655) covalent geometry : angle 0.58568 / 0.30 (62137) hydrogen bonds : bond 0.03925 / 2.62 ( 1961) hydrogen bonds : angle 4.48394 / 3.20 ( 5558) metal coordination : bond 0.00724 / 0.39 ( 28) metal coordination : angle 7.87587 / 4.59 ( 45) Misc. bond : bond 0.00442 / 0.23 ( 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 894 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 703 time to evaluate : 1.766 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: 0.7516 (tp30) cc_final: 0.7302 (mp0) REVERT: A 131 ARG cc_start: 0.7815 (ptp-110) cc_final: 0.7407 (ptp90) REVERT: A 240 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8679 (mtp) REVERT: A 252 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8237 (pp) REVERT: A 262 ILE cc_start: 0.8704 (mt) cc_final: 0.8382 (mp) REVERT: A 294 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7831 (mmmt) REVERT: A 308 GLU cc_start: 0.8182 (tp30) cc_final: 0.7925 (tt0) REVERT: A 311 ASP cc_start: 0.8386 (t0) cc_final: 0.8003 (m-30) REVERT: A 312 PHE cc_start: 0.8320 (t80) cc_final: 0.7926 (m-80) REVERT: A 349 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8294 (mp10) REVERT: A 436 ASN cc_start: 0.8302 (t0) cc_final: 0.8009 (t0) REVERT: A 505 MET cc_start: 0.9141 (mtp) cc_final: 0.8876 (mtp) REVERT: A 575 LYS cc_start: 0.9069 (ptpt) cc_final: 0.8843 (ptpt) REVERT: A 620 LYS cc_start: 0.6772 (mtmt) cc_final: 0.6371 (mptt) REVERT: A 711 LYS cc_start: 0.8402 (pttm) cc_final: 0.8091 (pttt) REVERT: A 761 ASP cc_start: 0.8349 (m-30) cc_final: 0.8071 (m-30) REVERT: A 770 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: A 790 ILE cc_start: 0.8854 (mm) cc_final: 0.8576 (mp) REVERT: A 814 GLU cc_start: 0.8374 (tt0) cc_final: 0.8078 (tp30) REVERT: A 947 LEU cc_start: 0.8392 (tt) cc_final: 0.7927 (mt) REVERT: A 954 LYS cc_start: 0.8198 (ptpt) cc_final: 0.7975 (mmpt) REVERT: A 970 LYS cc_start: 0.7929 (mttt) cc_final: 0.7629 (mmtt) REVERT: A 1020 ASP cc_start: 0.8820 (t70) cc_final: 0.8524 (t0) REVERT: A 1024 ARG cc_start: 0.9020 (mtm110) cc_final: 0.8649 (mtm180) REVERT: A 1065 LEU cc_start: 0.8443 (tt) cc_final: 0.8224 (tp) REVERT: A 1091 LYS cc_start: 0.7806 (mttt) cc_final: 0.7511 (mmtt) REVERT: A 1151 TYR cc_start: 0.8307 (t80) cc_final: 0.7912 (t80) REVERT: A 1179 GLU cc_start: 0.8147 (pt0) cc_final: 0.7465 (tm-30) REVERT: A 1191 PHE cc_start: 0.7059 (t80) cc_final: 0.6338 (t80) REVERT: A 1193 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7945 (ttpp) REVERT: A 1222 LYS cc_start: 0.7577 (pttt) cc_final: 0.7212 (pttm) REVERT: A 1253 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7542 (tt0) REVERT: A 1354 ASN cc_start: 0.8610 (m-40) cc_final: 0.8405 (m110) REVERT: B 35 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8316 (mttt) REVERT: B 139 MET cc_start: 0.9273 (ttm) cc_final: 0.8864 (ttt) REVERT: B 192 GLU cc_start: 0.7857 (pt0) cc_final: 0.7497 (pm20) REVERT: B 258 GLU cc_start: 0.7904 (mp0) cc_final: 0.7522 (mp0) REVERT: B 290 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7540 (mppt) REVERT: B 310 ARG cc_start: 0.7394 (ttp-170) cc_final: 0.7136 (ttp-170) REVERT: B 332 CYS cc_start: 0.8855 (m) cc_final: 0.8459 (m) REVERT: B 380 PHE cc_start: 0.6793 (t80) cc_final: 0.6316 (t80) REVERT: B 499 MET cc_start: 0.9046 (ttp) cc_final: 0.8797 (ttp) REVERT: B 506 MET cc_start: 0.8846 (mpp) cc_final: 0.8475 (mpt) REVERT: B 544 ASN cc_start: 0.8407 (m-40) cc_final: 0.8080 (m-40) REVERT: B 575 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8515 (p) REVERT: B 600 LYS cc_start: 0.8176 (mtpt) cc_final: 0.7835 (mttp) REVERT: B 611 MET cc_start: 0.9122 (mmm) cc_final: 0.8764 (mmp) REVERT: B 612 GLU cc_start: 0.8671 (tp30) cc_final: 0.8158 (tp30) REVERT: B 616 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7421 (mm-40) REVERT: B 623 ASP cc_start: 0.9089 (m-30) cc_final: 0.8620 (m-30) REVERT: B 627 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8431 (mp0) REVERT: B 778 THR cc_start: 0.8540 (OUTLIER) cc_final: 0.8269 (m) REVERT: B 822 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8649 (mp0) REVERT: B 938 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8929 (mtp) REVERT: B 1062 MET cc_start: 0.9327 (mmm) cc_final: 0.9058 (mmm) REVERT: C 141 ARG cc_start: 0.8793 (tpt170) cc_final: 0.8573 (tpt170) REVERT: C 209 ASP cc_start: 0.8954 (t0) cc_final: 0.8631 (t0) REVERT: C 251 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7571 (tp30) REVERT: C 279 ARG cc_start: 0.8238 (ttt-90) cc_final: 0.7945 (ttt90) REVERT: D 18 GLN cc_start: 0.7374 (mt0) cc_final: 0.6997 (mt0) REVERT: D 82 GLU cc_start: 0.6411 (mt-10) cc_final: 0.5721 (mm-30) REVERT: D 100 MET cc_start: 0.5578 (mmt) cc_final: 0.5151 (mmt) REVERT: E 21 CYS cc_start: 0.8306 (m) cc_final: 0.7832 (m) REVERT: E 33 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8151 (mm) REVERT: E 34 ASP cc_start: 0.6860 (t0) cc_final: 0.6108 (p0) REVERT: E 46 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6971 (t0) REVERT: E 98 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7640 (m-40) REVERT: E 107 GLN cc_start: 0.7220 (tt0) cc_final: 0.6947 (tm-30) REVERT: E 121 MET cc_start: 0.6995 (mmm) cc_final: 0.6727 (mmm) REVERT: F 51 ARG cc_start: 0.7088 (mtm-85) cc_final: 0.4923 (mmp-170) REVERT: F 100 ARG cc_start: 0.8422 (mtp85) cc_final: 0.7858 (mmt-90) REVERT: G 32 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8329 (mtmt) REVERT: G 41 ASN cc_start: 0.8804 (m-40) cc_final: 0.8552 (m-40) REVERT: G 53 LYS cc_start: 0.7830 (tptt) cc_final: 0.7524 (tppp) REVERT: G 77 PHE cc_start: 0.7619 (t80) cc_final: 0.7162 (t80) REVERT: G 82 ASP cc_start: 0.6404 (m-30) cc_final: 0.5932 (m-30) REVERT: G 150 PHE cc_start: 0.5563 (t80) cc_final: 0.4284 (t80) REVERT: H 51 ASP cc_start: 0.7999 (m-30) cc_final: 0.7652 (m-30) REVERT: H 52 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8371 (tt) REVERT: H 100 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7808 (mt-10) REVERT: H 146 LYS cc_start: 0.9089 (tttp) cc_final: 0.8857 (tttm) REVERT: I 45 LYS cc_start: 0.7632 (tptt) cc_final: 0.7332 (tmtt) REVERT: J 31 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7929 (mp0) REVERT: K 24 LYS cc_start: 0.7404 (ptpp) cc_final: 0.6753 (ptmm) REVERT: K 48 ASP cc_start: 0.8236 (p0) cc_final: 0.7941 (p0) REVERT: K 50 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8704 (t) REVERT: K 60 MET cc_start: 0.9289 (mmm) cc_final: 0.9066 (mmm) REVERT: K 66 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8294 (tm-30) REVERT: K 124 GLN cc_start: 0.8350 (tt0) cc_final: 0.8036 (tm-30) REVERT: L 38 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7412 (pp20) REVERT: M 41 ASP cc_start: 0.7963 (m-30) cc_final: 0.7178 (p0) REVERT: M 97 MET cc_start: 0.7019 (ttt) cc_final: 0.6455 (ttp) REVERT: M 110 ASN cc_start: 0.7612 (t0) cc_final: 0.7327 (t0) REVERT: M 121 GLN cc_start: 0.6233 (OUTLIER) cc_final: 0.5398 (pm20) REVERT: M 286 MET cc_start: 0.4225 (mmm) cc_final: 0.3512 (mmm) REVERT: M 292 MET cc_start: 0.2851 (ptm) cc_final: 0.2319 (ttt) REVERT: M 389 MET cc_start: 0.4530 (ptp) cc_final: 0.4024 (ptm) REVERT: M 421 MET cc_start: 0.4605 (pp-130) cc_final: 0.3968 (mpp) REVERT: N 141 LYS cc_start: 0.5195 (OUTLIER) cc_final: 0.4980 (mmmm) REVERT: N 157 MET cc_start: 0.1833 (tpt) cc_final: 0.0908 (tmm) REVERT: N 328 LYS cc_start: 0.7235 (mtpp) cc_final: 0.7006 (mtpp) REVERT: N 390 GLU cc_start: 0.7208 (tt0) cc_final: 0.6486 (tm-30) REVERT: O 14 GLN cc_start: 0.7669 (tt0) cc_final: 0.7433 (tm-30) REVERT: O 15 GLU cc_start: 0.8338 (tp30) cc_final: 0.8120 (tp30) REVERT: O 20 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8338 (pp) REVERT: O 76 GLU cc_start: 0.8445 (tt0) cc_final: 0.7307 (pm20) REVERT: O 336 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6140 (pt) REVERT: O 355 GLN cc_start: 0.8505 (tt0) cc_final: 0.8047 (tt0) REVERT: O 394 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6942 (mtp) REVERT: O 408 GLU cc_start: 0.7219 (tt0) cc_final: 0.6922 (tp30) REVERT: O 419 ARG cc_start: 0.7504 (ptp-170) cc_final: 0.7148 (ptm-80) REVERT: O 420 THR cc_start: 0.7056 (t) cc_final: 0.6566 (p) REVERT: O 455 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8317 (mptm) REVERT: O 507 ASN cc_start: 0.8043 (m-40) cc_final: 0.7600 (m110) REVERT: O 531 MET cc_start: 0.6446 (mtm) cc_final: 0.6230 (mtm) REVERT: P 134 LYS cc_start: 0.1499 (OUTLIER) cc_final: 0.1237 (ttmt) REVERT: Q 68 MET cc_start: 0.7564 (tpt) cc_final: 0.7342 (tpt) REVERT: Q 71 MET cc_start: 0.7562 (mmm) cc_final: 0.7021 (ttt) REVERT: Q 73 TYR cc_start: 0.7411 (m-80) cc_final: 0.6699 (m-80) REVERT: Q 77 THR cc_start: 0.5611 (OUTLIER) cc_final: 0.5341 (m) REVERT: Q 92 MET cc_start: 0.2489 (ptt) cc_final: 0.2274 (ptt) outliers start: 191 outliers final: 65 residues processed: 821 average time/residue: 0.7414 time to fit residues: 754.6852 Evaluate side-chains 734 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 646 time to evaluate : 1.731 ------------------------------------------------------------------------------- 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 116 MET Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 GLN 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 726 GLU Chi-restraints excluded: chain A residue 767 CYS Chi-restraints excluded: chain A residue 770 GLU 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 1004 ASP Chi-restraints excluded: chain A residue 1027 MET 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 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 319 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 633 LEU 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 B residue 938 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 C residue 265 GLN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 ASP 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 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 30 VAL 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 L residue 38 GLU Chi-restraints excluded: chain M residue 49 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 20 ILE 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 455 LYS Chi-restraints excluded: chain O residue 477 THR Chi-restraints excluded: chain P residue 134 LYS Chi-restraints excluded: chain P residue 174 SER 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: 6.9990 chunk 321 optimal weight: 0.8980 chunk 461 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 523 optimal weight: 50.0000 chunk 236 optimal weight: 3.9990 chunk 352 optimal weight: 10.0000 chunk 327 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 ASN A 820 HIS A 836 ASN A1277 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.202228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121246 restraints weight = 54024.927| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.41 r_work: 0.3071 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 45685 Z= 0.164 Angle : 0.626 27.717 62182 Z= 0.308 Chirality : 0.044 0.294 6998 Planarity : 0.005 0.064 7607 Dihedral : 15.807 179.866 7118 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.02 % Allowed : 16.24 % Favored : 79.73 % 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: 0.09 (0.11), residues: 5269 helix: 1.39 (0.11), residues: 2073 sheet: -0.64 (0.19), residues: 673 loop : -0.84 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 293 TYR 0.043 0.002 TYR E 90 PHE 0.020 0.002 PHE D 17 TRP 0.016 0.001 TRP B 297 HIS 0.013 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (45655) covalent geometry : angle 0.59363 / 0.31 (62137) hydrogen bonds : bond 0.03785 / 2.54 ( 1961) hydrogen bonds : angle 4.42631 / 3.16 ( 5558) metal coordination : bond 0.00688 / 0.35 ( 28) metal coordination : angle 7.41957 / 4.30 ( 45) Misc. bond : bond 0.00393 / 0.20 ( 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 883 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 694 time to evaluate : 1.714 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: 0.7500 (tp30) cc_final: 0.7275 (mp0) REVERT: A 131 ARG cc_start: 0.7852 (ptp-110) cc_final: 0.7467 (ptp90) REVERT: A 216 GLU cc_start: 0.7843 (tt0) cc_final: 0.7586 (tt0) REVERT: A 240 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8804 (mtp) REVERT: A 252 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8303 (pp) REVERT: A 307 MET cc_start: 0.8525 (tpp) cc_final: 0.8183 (mmm) REVERT: A 308 GLU cc_start: 0.8251 (tp30) cc_final: 0.7931 (tt0) REVERT: A 311 ASP cc_start: 0.8466 (t0) cc_final: 0.8132 (m-30) REVERT: A 312 PHE cc_start: 0.8218 (t80) cc_final: 0.7912 (m-80) REVERT: A 349 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: A 424 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5857 (ttt180) REVERT: A 436 ASN cc_start: 0.8369 (t0) cc_final: 0.8069 (t0) REVERT: A 505 MET cc_start: 0.9206 (mtp) cc_final: 0.8844 (mtp) REVERT: A 575 LYS cc_start: 0.9105 (ptpt) cc_final: 0.8863 (ptpt) REVERT: A 620 LYS cc_start: 0.6811 (mtmt) cc_final: 0.6351 (mptt) REVERT: A 761 ASP cc_start: 0.8418 (m-30) cc_final: 0.8174 (m-30) REVERT: A 814 GLU cc_start: 0.8438 (tt0) cc_final: 0.8119 (tp30) REVERT: A 947 LEU cc_start: 0.8518 (tt) cc_final: 0.8041 (mt) REVERT: A 954 LYS cc_start: 0.8220 (ptpt) cc_final: 0.7858 (mmpt) REVERT: A 970 LYS cc_start: 0.7815 (mttt) cc_final: 0.7494 (mmtt) REVERT: A 1020 ASP cc_start: 0.8820 (t70) cc_final: 0.8512 (t0) REVERT: A 1024 ARG cc_start: 0.9034 (mtm110) cc_final: 0.8661 (mtm180) REVERT: A 1091 LYS cc_start: 0.7843 (mttt) cc_final: 0.7534 (mmtt) REVERT: A 1151 TYR cc_start: 0.8263 (t80) cc_final: 0.7877 (t80) REVERT: A 1179 GLU cc_start: 0.8224 (pt0) cc_final: 0.7505 (tm-30) REVERT: A 1193 LYS cc_start: 0.8388 (mtmt) cc_final: 0.8036 (ttpp) REVERT: A 1195 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7772 (p0) REVERT: B 35 LYS cc_start: 0.8646 (mmmm) cc_final: 0.8244 (mttt) REVERT: B 82 VAL cc_start: 0.7064 (OUTLIER) cc_final: 0.6708 (t) REVERT: B 100 HIS cc_start: 0.8340 (t-90) cc_final: 0.8113 (t70) REVERT: B 107 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8711 (ptp) REVERT: B 139 MET cc_start: 0.9320 (ttm) cc_final: 0.8944 (ttm) REVERT: B 192 GLU cc_start: 0.7885 (pt0) cc_final: 0.7306 (pm20) REVERT: B 258 GLU cc_start: 0.8010 (mp0) cc_final: 0.7599 (mp0) REVERT: B 277 ILE cc_start: 0.7961 (mm) cc_final: 0.7643 (mm) REVERT: B 290 LYS cc_start: 0.8037 (mmtm) cc_final: 0.7403 (mppt) REVERT: B 332 CYS cc_start: 0.8804 (m) cc_final: 0.8445 (m) REVERT: B 374 GLU cc_start: 0.8434 (tt0) cc_final: 0.8123 (tt0) REVERT: B 384 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6912 (mtm) REVERT: B 408 GLN cc_start: 0.7387 (tt0) cc_final: 0.7016 (tt0) REVERT: B 499 MET cc_start: 0.9058 (ttp) cc_final: 0.8781 (ttp) REVERT: B 506 MET cc_start: 0.8828 (mpp) cc_final: 0.8419 (mpt) REVERT: B 530 GLU cc_start: 0.7952 (mp0) cc_final: 0.7653 (mp0) REVERT: B 544 ASN cc_start: 0.8420 (m-40) cc_final: 0.8075 (m-40) REVERT: B 575 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8506 (p) REVERT: B 600 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7895 (mttp) REVERT: B 611 MET cc_start: 0.9165 (mmm) cc_final: 0.8852 (mmp) REVERT: B 612 GLU cc_start: 0.8639 (tp30) cc_final: 0.7607 (tm-30) REVERT: B 616 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7258 (mp10) REVERT: B 623 ASP cc_start: 0.9150 (m-30) cc_final: 0.8637 (m-30) REVERT: B 627 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8334 (mp0) REVERT: B 653 ASP cc_start: 0.8233 (p0) cc_final: 0.7933 (p0) REVERT: B 805 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8580 (mtm-85) REVERT: B 1050 MET cc_start: 0.9394 (mtp) cc_final: 0.9150 (mtp) REVERT: B 1062 MET cc_start: 0.9327 (mmm) cc_final: 0.9013 (mmm) REVERT: C 28 ASP cc_start: 0.9093 (p0) cc_final: 0.8841 (p0) REVERT: C 141 ARG cc_start: 0.8877 (tpt170) cc_final: 0.8620 (tpt170) REVERT: C 145 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8224 (tmt170) REVERT: C 251 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7603 (tp30) REVERT: D 18 GLN cc_start: 0.7481 (mt0) cc_final: 0.7024 (mt0) REVERT: D 64 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: D 82 GLU cc_start: 0.6425 (mt-10) cc_final: 0.6023 (mm-30) REVERT: E 21 CYS cc_start: 0.8315 (m) cc_final: 0.7854 (m) REVERT: E 33 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8081 (mm) REVERT: E 34 ASP cc_start: 0.7155 (t0) cc_final: 0.6235 (p0) REVERT: E 46 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.6912 (t0) REVERT: E 98 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7650 (m-40) REVERT: E 107 GLN cc_start: 0.7435 (tt0) cc_final: 0.7059 (tm-30) REVERT: E 121 MET cc_start: 0.6634 (mmm) cc_final: 0.6378 (mmm) REVERT: E 187 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.8087 (mtp180) REVERT: F 51 ARG cc_start: 0.7179 (mtm-85) cc_final: 0.4994 (mmp-170) REVERT: F 86 GLU cc_start: 0.7743 (mp0) cc_final: 0.7524 (pm20) REVERT: F 100 ARG cc_start: 0.8471 (mtp85) cc_final: 0.7885 (mmt-90) REVERT: G 32 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8203 (mtmt) REVERT: G 41 ASN cc_start: 0.8858 (m-40) cc_final: 0.8631 (m-40) REVERT: G 50 ASP cc_start: 0.8546 (p0) cc_final: 0.8292 (p0) REVERT: G 53 LYS cc_start: 0.7854 (tptt) cc_final: 0.7578 (tppp) REVERT: G 60 PHE cc_start: 0.9072 (m-10) cc_final: 0.8672 (m-10) REVERT: G 77 PHE cc_start: 0.7852 (t80) cc_final: 0.7422 (t80) REVERT: G 150 PHE cc_start: 0.5628 (t80) cc_final: 0.4343 (t80) REVERT: H 52 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8367 (tt) REVERT: H 100 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7974 (mt-10) REVERT: H 146 LYS cc_start: 0.9100 (tttp) cc_final: 0.8847 (tttm) REVERT: I 22 ARG cc_start: 0.6403 (ptt180) cc_final: 0.6097 (ptt180) REVERT: I 45 LYS cc_start: 0.7691 (tptt) cc_final: 0.7377 (tmtt) REVERT: J 31 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: K 24 LYS cc_start: 0.7471 (ptpp) cc_final: 0.6865 (ptmm) REVERT: K 48 ASP cc_start: 0.8330 (p0) cc_final: 0.8016 (p0) REVERT: K 50 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8744 (t) REVERT: K 60 MET cc_start: 0.9237 (mmm) cc_final: 0.8939 (mmm) REVERT: K 66 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: K 124 GLN cc_start: 0.8403 (tt0) cc_final: 0.7976 (tm-30) REVERT: L 44 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8110 (mmm) REVERT: M 41 ASP cc_start: 0.7967 (m-30) cc_final: 0.7118 (p0) REVERT: M 97 MET cc_start: 0.7048 (ttt) cc_final: 0.6466 (ttp) REVERT: M 110 ASN cc_start: 0.7742 (t0) cc_final: 0.7534 (t0) REVERT: M 121 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.5814 (mp10) REVERT: M 286 MET cc_start: 0.4153 (mmm) cc_final: 0.3372 (mmm) REVERT: M 292 MET cc_start: 0.2691 (ptm) cc_final: 0.2112 (ttt) REVERT: M 389 MET cc_start: 0.4587 (ptp) cc_final: 0.3939 (ptm) REVERT: M 421 MET cc_start: 0.5000 (pp-130) cc_final: 0.4267 (mpp) REVERT: N 141 LYS cc_start: 0.5401 (OUTLIER) cc_final: 0.5125 (mmmm) REVERT: N 157 MET cc_start: 0.1923 (tpt) cc_final: 0.0993 (tmm) REVERT: N 390 GLU cc_start: 0.7589 (tt0) cc_final: 0.6726 (tm-30) REVERT: O 14 GLN cc_start: 0.7742 (tt0) cc_final: 0.7406 (tm-30) REVERT: O 76 GLU cc_start: 0.8398 (tt0) cc_final: 0.7263 (pm20) REVERT: O 336 ILE cc_start: 0.6540 (OUTLIER) cc_final: 0.6338 (pt) REVERT: O 355 GLN cc_start: 0.8522 (tt0) cc_final: 0.8034 (tt0) REVERT: O 402 ASN cc_start: 0.7492 (t160) cc_final: 0.7278 (t0) REVERT: O 408 GLU cc_start: 0.7342 (tt0) cc_final: 0.7071 (tm-30) REVERT: O 419 ARG cc_start: 0.7387 (ptp-170) cc_final: 0.6983 (ptm-80) REVERT: O 531 MET cc_start: 0.6537 (mtm) cc_final: 0.6249 (mtm) REVERT: P 219 TYR cc_start: 0.6302 (t80) cc_final: 0.5695 (t80) REVERT: P 235 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6265 (pp) REVERT: Q 54 GLU cc_start: 0.6368 (mp0) cc_final: 0.5979 (mp0) REVERT: Q 58 LEU cc_start: 0.7720 (tt) cc_final: 0.7209 (mp) REVERT: Q 61 LYS cc_start: 0.7683 (tttt) cc_final: 0.7287 (tttt) REVERT: Q 71 MET cc_start: 0.7633 (mmm) cc_final: 0.7110 (ttt) REVERT: Q 73 TYR cc_start: 0.7267 (m-80) cc_final: 0.6576 (m-80) REVERT: Q 77 THR cc_start: 0.5608 (OUTLIER) cc_final: 0.5340 (m) REVERT: Q 110 MET cc_start: 0.6689 (ptp) cc_final: 0.6361 (ptp) outliers start: 189 outliers final: 79 residues processed: 817 average time/residue: 0.7211 time to fit residues: 727.5843 Evaluate side-chains 737 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 633 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 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 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 1195 ASP 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 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 384 MET 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 689 MET Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 794 MET 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 64 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 46 ASP 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 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 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 30 VAL 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 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 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 72 VAL Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 336 ILE 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 77 THR Chi-restraints excluded: chain Q residue 94 VAL 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: 2.9990 chunk 495 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 GLN A 225 ASN A 836 ASN A1239 HIS A1277 ASN A1354 ASN B 43 HIS B 273 GLN B 784 ASN B 982 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 HIS E 168 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.196545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.114780 restraints weight = 53515.222| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.43 r_work: 0.2957 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 45685 Z= 0.253 Angle : 0.706 29.743 62182 Z= 0.353 Chirality : 0.048 0.292 6998 Planarity : 0.005 0.065 7607 Dihedral : 15.769 179.924 7114 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.39 % Allowed : 16.63 % Favored : 78.99 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.11), residues: 5269 helix: 1.23 (0.11), residues: 2065 sheet: -0.74 (0.19), residues: 703 loop : -0.86 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1141 TYR 0.055 0.002 TYR E 90 PHE 0.042 0.002 PHE B 380 TRP 0.014 0.002 TRP P 313 HIS 0.016 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.25 (45655) covalent geometry : angle 0.67272 / 0.35 (62137) hydrogen bonds : bond 0.04398 / 2.96 ( 1961) hydrogen bonds : angle 4.64588 / 3.32 ( 5558) metal coordination : bond 0.00976 / 0.52 ( 28) metal coordination : angle 8.04544 / 4.57 ( 45) Misc. bond : bond 0.00158 / 0.08 ( 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 896 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 690 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7631 (tp30) REVERT: A 107 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8392 (mmm) REVERT: A 216 GLU cc_start: 0.7741 (tt0) cc_final: 0.7173 (tt0) REVERT: A 240 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.9016 (mtp) REVERT: A 252 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8400 (pp) REVERT: A 262 ILE cc_start: 0.8708 (mp) cc_final: 0.8375 (mt) REVERT: A 311 ASP cc_start: 0.8447 (t0) cc_final: 0.8180 (m-30) REVERT: A 312 PHE cc_start: 0.8346 (t80) cc_final: 0.8013 (m-80) REVERT: A 349 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8563 (mp10) REVERT: A 406 LYS cc_start: 0.9255 (ttpt) cc_final: 0.8673 (mmtm) REVERT: A 505 MET cc_start: 0.9319 (mtp) cc_final: 0.8901 (mtp) REVERT: A 575 LYS cc_start: 0.9146 (ptpt) cc_final: 0.8889 (ptpt) REVERT: A 620 LYS cc_start: 0.6941 (mtmt) cc_final: 0.6326 (mptt) REVERT: A 709 LEU cc_start: 0.8873 (tm) cc_final: 0.8614 (tt) REVERT: A 729 GLU cc_start: 0.7951 (tp30) cc_final: 0.7524 (pt0) REVERT: A 761 ASP cc_start: 0.8598 (m-30) cc_final: 0.8296 (m-30) REVERT: A 769 ARG cc_start: 0.8458 (mtm110) cc_final: 0.8090 (mtm-85) REVERT: A 814 GLU cc_start: 0.8506 (tt0) cc_final: 0.8070 (tp30) REVERT: A 947 LEU cc_start: 0.8643 (tt) cc_final: 0.8109 (mt) REVERT: A 954 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7851 (mmtm) REVERT: A 970 LYS cc_start: 0.7898 (mttt) cc_final: 0.7625 (mmtt) REVERT: A 1020 ASP cc_start: 0.8839 (t70) cc_final: 0.8553 (t0) REVERT: A 1024 ARG cc_start: 0.9002 (mtm110) cc_final: 0.8644 (mtm180) REVERT: A 1084 ILE cc_start: 0.9219 (mm) cc_final: 0.8969 (mt) REVERT: A 1091 LYS cc_start: 0.7871 (mttt) cc_final: 0.7531 (mmtt) REVERT: A 1138 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7883 (ttp-110) REVERT: A 1151 TYR cc_start: 0.8341 (t80) cc_final: 0.7901 (t80) REVERT: A 1179 GLU cc_start: 0.8167 (pt0) cc_final: 0.7491 (tm-30) REVERT: A 1206 GLU cc_start: 0.8352 (mp0) cc_final: 0.8002 (mp0) REVERT: A 1313 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7340 (mm-30) REVERT: B 107 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8782 (ptp) REVERT: B 139 MET cc_start: 0.9383 (ttm) cc_final: 0.9035 (ttp) REVERT: B 192 GLU cc_start: 0.7774 (pt0) cc_final: 0.7158 (pm20) REVERT: B 233 ASP cc_start: 0.8637 (p0) cc_final: 0.8330 (p0) REVERT: B 258 GLU cc_start: 0.8071 (mp0) cc_final: 0.7625 (mp0) REVERT: B 285 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7713 (tmtt) REVERT: B 290 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7665 (mppt) REVERT: B 325 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6475 (mm-30) REVERT: B 332 CYS cc_start: 0.8943 (m) cc_final: 0.8525 (m) REVERT: B 374 GLU cc_start: 0.8601 (tt0) cc_final: 0.8238 (tt0) REVERT: B 384 MET cc_start: 0.7572 (ttp) cc_final: 0.7326 (mtm) REVERT: B 408 GLN cc_start: 0.7349 (tt0) cc_final: 0.7042 (tt0) REVERT: B 451 MET cc_start: 0.9231 (ttt) cc_final: 0.8811 (ttt) REVERT: B 499 MET cc_start: 0.9189 (ttp) cc_final: 0.8893 (ttp) REVERT: B 506 MET cc_start: 0.8812 (mpp) cc_final: 0.8534 (mpp) REVERT: B 521 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: B 530 GLU cc_start: 0.8112 (mp0) cc_final: 0.7833 (mp0) REVERT: B 575 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 600 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7863 (mttp) REVERT: B 611 MET cc_start: 0.9087 (mmm) cc_final: 0.8754 (mmp) REVERT: B 612 GLU cc_start: 0.8585 (tp30) cc_final: 0.7647 (mm-30) REVERT: B 616 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7177 (mp10) REVERT: B 623 ASP cc_start: 0.9070 (m-30) cc_final: 0.8698 (m-30) REVERT: B 641 CYS cc_start: 0.8730 (m) cc_final: 0.8042 (m) REVERT: B 708 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9195 (tp) REVERT: B 780 LYS cc_start: 0.8068 (ptmt) cc_final: 0.7837 (pttt) REVERT: B 879 PHE cc_start: 0.7839 (m-80) cc_final: 0.7624 (m-80) REVERT: B 916 MET cc_start: 0.9337 (mmm) cc_final: 0.9057 (mtp) REVERT: B 1062 MET cc_start: 0.9415 (mmm) cc_final: 0.9189 (mmm) REVERT: C 28 ASP cc_start: 0.9129 (p0) cc_final: 0.8808 (p0) REVERT: C 141 ARG cc_start: 0.8836 (tpt170) cc_final: 0.8374 (tpt90) REVERT: C 143 GLN cc_start: 0.8637 (tt0) cc_final: 0.8431 (tt0) REVERT: C 145 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8090 (tmt170) REVERT: C 161 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8124 (mm-30) REVERT: C 275 VAL cc_start: 0.8903 (m) cc_final: 0.8660 (t) REVERT: D 18 GLN cc_start: 0.7502 (mt0) cc_final: 0.7086 (mt0) REVERT: D 64 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: D 82 GLU cc_start: 0.6441 (mt-10) cc_final: 0.4865 (tm-30) REVERT: D 83 LYS cc_start: 0.7815 (mttt) cc_final: 0.7231 (mttp) REVERT: E 18 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8866 (mpp) REVERT: E 21 CYS cc_start: 0.8440 (m) cc_final: 0.7955 (m) REVERT: E 33 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8014 (mm) REVERT: E 34 ASP cc_start: 0.7457 (t0) cc_final: 0.6455 (p0) REVERT: E 46 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6909 (t0) REVERT: E 87 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7900 (pp) REVERT: E 98 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7863 (m-40) REVERT: E 107 GLN cc_start: 0.7925 (tt0) cc_final: 0.7502 (tm-30) REVERT: E 172 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.8474 (mmt-90) REVERT: E 187 ARG cc_start: 0.8482 (mtp-110) cc_final: 0.8274 (mtp180) REVERT: F 51 ARG cc_start: 0.7287 (mtm-85) cc_final: 0.4974 (mmp-170) REVERT: F 86 GLU cc_start: 0.7826 (mp0) cc_final: 0.7512 (pm20) REVERT: F 100 ARG cc_start: 0.8463 (mtp85) cc_final: 0.7862 (mmt-90) REVERT: G 32 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8286 (mtmt) REVERT: G 36 ASN cc_start: 0.8042 (m-40) cc_final: 0.7290 (m-40) REVERT: G 41 ASN cc_start: 0.8819 (m-40) cc_final: 0.8568 (m-40) REVERT: G 50 ASP cc_start: 0.8558 (p0) cc_final: 0.8301 (p0) REVERT: G 53 LYS cc_start: 0.7832 (tptt) cc_final: 0.7498 (tppp) REVERT: G 197 LEU cc_start: 0.5358 (mt) cc_final: 0.5134 (mm) REVERT: H 52 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8359 (tt) REVERT: H 100 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7740 (mt-10) REVERT: H 146 LYS cc_start: 0.9021 (tttp) cc_final: 0.8744 (tttm) REVERT: I 22 ARG cc_start: 0.6419 (ptt180) cc_final: 0.6147 (ptt180) REVERT: I 45 LYS cc_start: 0.7842 (tptt) cc_final: 0.7483 (tmtt) REVERT: J 26 GLN cc_start: 0.8550 (tp40) cc_final: 0.8137 (tt0) REVERT: J 31 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: K 24 LYS cc_start: 0.7496 (ptpp) cc_final: 0.6946 (ptmm) REVERT: K 50 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8669 (t) REVERT: K 60 MET cc_start: 0.9350 (mmm) cc_final: 0.9125 (mmm) REVERT: K 66 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: L 44 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.8299 (mmm) REVERT: M 97 MET cc_start: 0.7385 (ttt) cc_final: 0.6560 (ttp) REVERT: M 121 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6004 (mp10) REVERT: M 286 MET cc_start: 0.3967 (mmm) cc_final: 0.3208 (mmm) REVERT: M 292 MET cc_start: 0.2610 (ptm) cc_final: 0.1987 (ttt) REVERT: M 389 MET cc_start: 0.4496 (ptp) cc_final: 0.3928 (ptm) REVERT: M 421 MET cc_start: 0.5266 (pp-130) cc_final: 0.4430 (mpp) REVERT: N 328 LYS cc_start: 0.7113 (mtpp) cc_final: 0.6814 (mtpp) REVERT: N 341 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8106 (tt) REVERT: N 361 VAL cc_start: 0.6150 (m) cc_final: 0.5820 (p) REVERT: N 390 GLU cc_start: 0.7600 (tt0) cc_final: 0.6830 (tm-30) REVERT: O 14 GLN cc_start: 0.7782 (tt0) cc_final: 0.7436 (tm-30) REVERT: O 76 GLU cc_start: 0.8237 (tt0) cc_final: 0.7152 (pm20) REVERT: O 259 MET cc_start: 0.7531 (mpt) cc_final: 0.7247 (mmt) REVERT: O 355 GLN cc_start: 0.8576 (tt0) cc_final: 0.8015 (tt0) REVERT: O 402 ASN cc_start: 0.7560 (t160) cc_final: 0.7292 (t0) REVERT: O 404 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8058 (mtm) REVERT: O 419 ARG cc_start: 0.7104 (ptp-170) cc_final: 0.6674 (ptm-80) REVERT: O 474 MET cc_start: 0.0906 (pp-130) cc_final: 0.0449 (ppp) REVERT: O 490 MET cc_start: 0.3795 (mpp) cc_final: 0.3272 (ptt) REVERT: O 507 ASN cc_start: 0.8057 (m-40) cc_final: 0.7703 (m110) REVERT: O 524 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7936 (tm-30) REVERT: P 232 MET cc_start: 0.3978 (tpt) cc_final: 0.3711 (tpt) REVERT: P 308 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.6925 (mp) REVERT: Q 54 GLU cc_start: 0.6636 (mp0) cc_final: 0.6382 (mp0) REVERT: Q 71 MET cc_start: 0.7719 (mmm) cc_final: 0.7154 (ttt) REVERT: Q 73 TYR cc_start: 0.7401 (m-80) cc_final: 0.6831 (m-80) REVERT: Q 110 MET cc_start: 0.6932 (ptp) cc_final: 0.6670 (ptp) outliers start: 206 outliers final: 92 residues processed: 826 average time/residue: 0.7549 time to fit residues: 770.2797 Evaluate side-chains 753 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 636 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 116 MET Chi-restraints excluded: chain A residue 175 ILE 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 349 GLN Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 544 ASP 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 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 1304 THR 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 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 521 GLU 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 708 LEU 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 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 230 THR Chi-restraints excluded: chain C residue 253 LEU 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 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 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 58 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 82 VAL 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 100 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 172 ARG 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 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 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 66 GLU Chi-restraints excluded: chain K residue 93 VAL 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 194 GLU 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 281 THR Chi-restraints excluded: chain N residue 316 CYS 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 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 404 MET Chi-restraints excluded: chain O residue 420 THR Chi-restraints excluded: chain O residue 435 LEU Chi-restraints excluded: chain O residue 453 GLU 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 248 VAL Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain P residue 308 ILE 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: 0.4980 chunk 426 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 471 optimal weight: 0.9990 chunk 277 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 311 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 217 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 408 optimal weight: 40.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 225 ASN B 260 HIS ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN D 98 GLN E 168 ASN K 38 HIS ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4270 r_free = 0.4270 target = 0.199127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.117306 restraints weight = 53678.182| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.34 r_work: 0.3014 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4726 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= 0.126 Angle : 0.610 30.630 62182 Z= 0.299 Chirality : 0.043 0.290 6998 Planarity : 0.004 0.081 7607 Dihedral : 15.596 179.614 7113 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.11 % Allowed : 18.52 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.12), residues: 5269 helix: 1.50 (0.12), residues: 2063 sheet: -0.70 (0.19), residues: 708 loop : -0.73 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 99 TYR 0.039 0.001 TYR E 90 PHE 0.023 0.001 PHE B 380 TRP 0.011 0.001 TRP C 40 HIS 0.012 0.001 HIS M 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (45655) covalent geometry : angle 0.57431 / 0.30 (62137) hydrogen bonds : bond 0.03587 / 2.40 ( 1961) hydrogen bonds : angle 4.43243 / 3.16 ( 5558) metal coordination : bond 0.00575 / 0.27 ( 28) metal coordination : angle 7.68451 / 4.39 ( 45) Misc. bond : bond 0.00078 / 0.04 ( 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 817 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 671 time to evaluate : 1.494 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: 0.7317 (pm20) cc_final: 0.6967 (pm20) REVERT: A 89 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7591 (tp30) REVERT: A 131 ARG cc_start: 0.7859 (ptp-110) cc_final: 0.7525 (ptp-170) REVERT: A 216 GLU cc_start: 0.7787 (tt0) cc_final: 0.7440 (tt0) REVERT: A 217 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7006 (t0) REVERT: A 221 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8442 (mt) REVERT: A 233 GLU cc_start: 0.8601 (tp30) cc_final: 0.8349 (tp30) REVERT: A 240 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8967 (mtp) REVERT: A 270 LEU cc_start: 0.0358 (OUTLIER) cc_final: -0.0360 (mp) REVERT: A 278 ASP cc_start: 0.8712 (m-30) cc_final: 0.8501 (m-30) REVERT: A 311 ASP cc_start: 0.8384 (t0) cc_final: 0.8115 (m-30) REVERT: A 312 PHE cc_start: 0.8311 (t80) cc_final: 0.7962 (m-80) REVERT: A 575 LYS cc_start: 0.9122 (ptpt) cc_final: 0.8858 (ptpt) REVERT: A 620 LYS cc_start: 0.7154 (mtmt) cc_final: 0.6267 (mptt) REVERT: A 636 SER cc_start: 0.8986 (m) cc_final: 0.8695 (p) REVERT: A 709 LEU cc_start: 0.8675 (tm) cc_final: 0.8382 (tt) REVERT: A 761 ASP cc_start: 0.8532 (m-30) cc_final: 0.8256 (m-30) REVERT: A 769 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7985 (mtm-85) REVERT: A 814 GLU cc_start: 0.8434 (tt0) cc_final: 0.7974 (tp30) REVERT: A 836 ASN cc_start: 0.9022 (m110) cc_final: 0.8806 (m-40) REVERT: A 947 LEU cc_start: 0.8572 (tt) cc_final: 0.8038 (mt) REVERT: A 954 LYS cc_start: 0.8188 (ptpt) cc_final: 0.7802 (mmtt) REVERT: A 970 LYS cc_start: 0.7746 (mttt) cc_final: 0.7468 (mmtt) REVERT: A 1020 ASP cc_start: 0.8790 (t70) cc_final: 0.8507 (t0) REVERT: A 1024 ARG cc_start: 0.8974 (mtm110) cc_final: 0.8601 (mtm180) REVERT: A 1091 LYS cc_start: 0.7854 (mttt) cc_final: 0.7616 (mmtt) REVERT: A 1112 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8210 (mp0) REVERT: A 1151 TYR cc_start: 0.8352 (t80) cc_final: 0.7904 (t80) REVERT: A 1179 GLU cc_start: 0.8178 (pt0) cc_final: 0.7494 (tm-30) REVERT: A 1206 GLU cc_start: 0.8295 (mp0) cc_final: 0.7877 (mp0) REVERT: B 54 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: B 107 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8761 (ptp) REVERT: B 192 GLU cc_start: 0.7760 (pt0) cc_final: 0.7135 (pm20) REVERT: B 258 GLU cc_start: 0.7991 (mp0) cc_final: 0.7570 (mp0) REVERT: B 290 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7564 (mmmm) REVERT: B 325 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6537 (mm-30) REVERT: B 332 CYS cc_start: 0.8976 (m) cc_final: 0.8502 (m) REVERT: B 374 GLU cc_start: 0.8530 (tt0) cc_final: 0.8127 (tt0) REVERT: B 384 MET cc_start: 0.7145 (ttp) cc_final: 0.6915 (mtp) REVERT: B 408 GLN cc_start: 0.7299 (tt0) cc_final: 0.6791 (tt0) REVERT: B 499 MET cc_start: 0.9016 (ttp) cc_final: 0.8725 (ttp) REVERT: B 506 MET cc_start: 0.8806 (mpp) cc_final: 0.8571 (mpp) REVERT: B 530 GLU cc_start: 0.8033 (mp0) cc_final: 0.7698 (mp0) REVERT: B 554 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8378 (tmtp) REVERT: B 575 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8451 (p) REVERT: B 600 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7837 (mttp) REVERT: B 611 MET cc_start: 0.9029 (mmm) cc_final: 0.8707 (mmp) REVERT: B 612 GLU cc_start: 0.8543 (tp30) cc_final: 0.7565 (mm-30) REVERT: B 616 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7236 (mp10) REVERT: B 623 ASP cc_start: 0.8946 (m-30) cc_final: 0.8679 (m-30) REVERT: B 780 LYS cc_start: 0.7963 (ptmt) cc_final: 0.7669 (pttt) REVERT: B 916 MET cc_start: 0.9405 (mmm) cc_final: 0.8938 (mtp) REVERT: B 1062 MET cc_start: 0.9374 (mmm) cc_final: 0.9053 (mmm) REVERT: C 28 ASP cc_start: 0.9068 (p0) cc_final: 0.8784 (p0) REVERT: C 141 ARG cc_start: 0.8829 (tpt170) cc_final: 0.8309 (tpt90) REVERT: C 145 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8174 (tmt170) REVERT: C 161 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8176 (mm-30) REVERT: D 18 GLN cc_start: 0.7432 (mt0) cc_final: 0.6973 (mt0) REVERT: D 82 GLU cc_start: 0.6541 (mt-10) cc_final: 0.4766 (tm-30) REVERT: D 83 LYS cc_start: 0.7737 (mttt) cc_final: 0.7060 (mttp) REVERT: D 100 MET cc_start: 0.5011 (mmt) cc_final: 0.3005 (mtt) REVERT: E 21 CYS cc_start: 0.8313 (m) cc_final: 0.7752 (m) REVERT: E 33 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7911 (mm) REVERT: E 34 ASP cc_start: 0.7674 (t0) cc_final: 0.6663 (p0) REVERT: E 46 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6871 (t0) REVERT: E 107 GLN cc_start: 0.7877 (tt0) cc_final: 0.7455 (tm-30) REVERT: F 51 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.4709 (mmp-170) REVERT: F 84 GLU cc_start: 0.8481 (pt0) cc_final: 0.8232 (pm20) REVERT: F 100 ARG cc_start: 0.8399 (mtp85) cc_final: 0.7781 (mmt-90) REVERT: G 7 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8530 (mmm) REVERT: G 32 LYS cc_start: 0.8588 (mtpt) cc_final: 0.8145 (mtmt) REVERT: G 36 ASN cc_start: 0.8096 (m-40) cc_final: 0.7710 (m-40) REVERT: G 41 ASN cc_start: 0.8818 (m-40) cc_final: 0.8525 (m-40) REVERT: G 53 LYS cc_start: 0.7999 (tptt) cc_final: 0.7492 (tppp) REVERT: G 197 LEU cc_start: 0.5456 (mt) cc_final: 0.4991 (mm) REVERT: H 52 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8313 (tt) REVERT: H 100 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7602 (mt-10) REVERT: H 146 LYS cc_start: 0.8963 (tttp) cc_final: 0.8679 (tttm) REVERT: I 22 ARG cc_start: 0.6311 (ptt180) cc_final: 0.6058 (ptt180) REVERT: I 45 LYS cc_start: 0.7927 (tptt) cc_final: 0.7569 (tmtt) REVERT: J 26 GLN cc_start: 0.8374 (tp40) cc_final: 0.7962 (tt0) REVERT: K 24 LYS cc_start: 0.7497 (ptpp) cc_final: 0.6936 (ptmm) REVERT: K 50 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8581 (t) REVERT: K 60 MET cc_start: 0.9305 (mmm) cc_final: 0.9007 (mmm) REVERT: K 66 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: K 79 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8990 (ttpt) REVERT: L 42 ARG cc_start: 0.8654 (mtt90) cc_final: 0.8387 (mtp85) REVERT: M 97 MET cc_start: 0.7278 (ttt) cc_final: 0.6542 (ttp) REVERT: M 121 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.6103 (mp10) REVERT: M 209 HIS cc_start: 0.6320 (OUTLIER) cc_final: 0.6089 (p-80) REVERT: M 292 MET cc_start: 0.2595 (ptm) cc_final: 0.2095 (ptm) REVERT: M 389 MET cc_start: 0.4707 (ptp) cc_final: 0.3926 (ptm) REVERT: N 271 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8422 (pp) REVERT: N 341 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8291 (tt) REVERT: N 380 LYS cc_start: 0.7691 (tppp) cc_final: 0.7289 (tptp) REVERT: N 381 HIS cc_start: 0.8400 (m90) cc_final: 0.8101 (m-70) REVERT: N 390 GLU cc_start: 0.7491 (tt0) cc_final: 0.6726 (tm-30) REVERT: O 14 GLN cc_start: 0.7739 (tt0) cc_final: 0.7394 (tm-30) REVERT: O 41 HIS cc_start: 0.7844 (t-90) cc_final: 0.7589 (t-90) REVERT: O 76 GLU cc_start: 0.8217 (tt0) cc_final: 0.7105 (pm20) REVERT: O 259 MET cc_start: 0.7560 (mpt) cc_final: 0.7327 (mmt) REVERT: O 355 GLN cc_start: 0.8397 (tt0) cc_final: 0.7929 (tt0) REVERT: O 394 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7245 (mtp) REVERT: O 402 ASN cc_start: 0.7509 (t160) cc_final: 0.7301 (t0) REVERT: O 404 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7853 (mtm) REVERT: O 419 ARG cc_start: 0.7006 (ptp-170) cc_final: 0.6582 (ptm-80) REVERT: O 490 MET cc_start: 0.3557 (mpp) cc_final: 0.3282 (ptp) REVERT: O 507 ASN cc_start: 0.8038 (m-40) cc_final: 0.7711 (m110) REVERT: Q 54 GLU cc_start: 0.6784 (mp0) cc_final: 0.6527 (mp0) REVERT: Q 56 TYR cc_start: 0.7701 (t80) cc_final: 0.7319 (t80) REVERT: Q 71 MET cc_start: 0.7708 (mmm) cc_final: 0.6747 (ttt) REVERT: Q 73 TYR cc_start: 0.7494 (m-80) cc_final: 0.6841 (m-80) REVERT: Q 77 THR cc_start: 0.5578 (OUTLIER) cc_final: 0.5323 (m) REVERT: Q 110 MET cc_start: 0.6949 (ptp) cc_final: 0.6704 (ptp) outliers start: 146 outliers final: 60 residues processed: 761 average time/residue: 0.6533 time to fit residues: 613.9652 Evaluate side-chains 714 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 632 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 544 ASP 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 1117 ILE Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1225 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 107 MET 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 321 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 575 SER 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 794 MET 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 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 261 VAL 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 117 SER Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 35 PHE 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 K residue 50 THR Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 97 GLN 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 319 MET Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 281 THR 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 163 VAL Chi-restraints excluded: chain O residue 301 TYR Chi-restraints excluded: chain O residue 394 MET Chi-restraints excluded: chain O residue 404 MET 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 46 VAL Chi-restraints excluded: chain Q residue 77 THR 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: 1.9990 chunk 460 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 360 optimal weight: 0.5980 chunk 515 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 347 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 ASN A 316 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 68 ASN M 209 HIS ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.199531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118646 restraints weight = 53430.565| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.38 r_work: 0.3033 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45685 Z= 0.134 Angle : 0.608 28.960 62182 Z= 0.298 Chirality : 0.043 0.376 6998 Planarity : 0.004 0.073 7607 Dihedral : 15.525 179.880 7113 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.92 % Allowed : 19.31 % Favored : 77.77 % 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: 0.28 (0.12), residues: 5269 helix: 1.56 (0.12), residues: 2069 sheet: -0.65 (0.19), residues: 721 loop : -0.70 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 99 TYR 0.029 0.001 TYR E 90 PHE 0.027 0.001 PHE A1191 TRP 0.036 0.001 TRP G 200 HIS 0.022 0.001 HIS M 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (45655) covalent geometry : angle 0.57476 / 0.30 (62137) hydrogen bonds : bond 0.03574 / 2.39 ( 1961) hydrogen bonds : angle 4.39879 / 3.13 ( 5558) metal coordination : bond 0.00578 / 0.29 ( 28) metal coordination : angle 7.37039 / 4.22 ( 45) Misc. bond : bond 0.00196 / 0.10 ( 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: 137 poor density : 647 time to evaluate : 1.075 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: 0.7481 (pm20) cc_final: 0.7142 (pm20) REVERT: A 89 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7607 (tp30) REVERT: A 107 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8403 (mmm) REVERT: A 131 ARG cc_start: 0.7907 (ptp-110) cc_final: 0.7609 (ptp-170) REVERT: A 216 GLU cc_start: 0.7698 (tt0) cc_final: 0.7254 (tt0) REVERT: A 240 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9005 (mtp) REVERT: A 270 LEU cc_start: 0.0487 (OUTLIER) cc_final: -0.0232 (mp) REVERT: A 278 ASP cc_start: 0.8676 (m-30) cc_final: 0.8461 (m-30) REVERT: A 311 ASP cc_start: 0.8454 (t0) cc_final: 0.8207 (m-30) REVERT: A 312 PHE cc_start: 0.8344 (t80) cc_final: 0.8078 (m-80) REVERT: A 575 LYS cc_start: 0.9070 (ptpt) cc_final: 0.8849 (ptpt) REVERT: A 620 LYS cc_start: 0.7216 (mtmt) cc_final: 0.6394 (mptt) REVERT: A 754 LYS cc_start: 0.8199 (tppt) cc_final: 0.7693 (tmmt) REVERT: A 814 GLU cc_start: 0.8458 (tt0) cc_final: 0.8077 (tp30) REVERT: A 836 ASN cc_start: 0.8948 (m110) cc_final: 0.8697 (m-40) REVERT: A 947 LEU cc_start: 0.8624 (tt) cc_final: 0.8133 (mt) REVERT: A 954 LYS cc_start: 0.8130 (ptpt) cc_final: 0.7848 (mmtt) REVERT: A 970 LYS cc_start: 0.7877 (mttt) cc_final: 0.7644 (mmtt) REVERT: A 1020 ASP cc_start: 0.8827 (t70) cc_final: 0.8548 (t0) REVERT: A 1024 ARG cc_start: 0.9049 (mtm110) cc_final: 0.8712 (mtm180) REVERT: A 1084 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8908 (mm) REVERT: A 1091 LYS cc_start: 0.7885 (mttt) cc_final: 0.7646 (mmtt) REVERT: A 1112 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8190 (mp0) REVERT: A 1119 GLU cc_start: 0.7460 (pt0) cc_final: 0.6765 (pt0) REVERT: A 1138 ARG cc_start: 0.8136 (ttp-110) cc_final: 0.7840 (ttp80) REVERT: A 1151 TYR cc_start: 0.8286 (t80) cc_final: 0.7852 (t80) REVERT: A 1179 GLU cc_start: 0.8188 (pt0) cc_final: 0.7409 (tm-30) REVERT: A 1206 GLU cc_start: 0.8382 (mp0) cc_final: 0.8017 (mp0) REVERT: B 54 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: B 107 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8696 (ptp) REVERT: B 139 MET cc_start: 0.9319 (ttm) cc_final: 0.9057 (ttm) REVERT: B 192 GLU cc_start: 0.7858 (pt0) cc_final: 0.7274 (pm20) REVERT: B 258 GLU cc_start: 0.8055 (mp0) cc_final: 0.7565 (mp0) REVERT: B 290 LYS cc_start: 0.8047 (mmtm) cc_final: 0.7578 (mmmm) REVERT: B 325 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6491 (mm-30) REVERT: B 332 CYS cc_start: 0.8971 (m) cc_final: 0.8528 (m) REVERT: B 374 GLU cc_start: 0.8533 (tt0) cc_final: 0.8148 (tt0) REVERT: B 408 GLN cc_start: 0.7287 (tt0) cc_final: 0.6826 (tt0) REVERT: B 499 MET cc_start: 0.9035 (ttp) cc_final: 0.8644 (ttp) REVERT: B 530 GLU cc_start: 0.8302 (mp0) cc_final: 0.8023 (mp0) REVERT: B 554 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8448 (tmtp) REVERT: B 575 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8486 (p) REVERT: B 600 LYS cc_start: 0.8155 (mtpt) cc_final: 0.7860 (mttp) REVERT: B 611 MET cc_start: 0.9094 (mmm) cc_final: 0.8751 (mmp) REVERT: B 612 GLU cc_start: 0.8629 (tp30) cc_final: 0.7684 (mm-30) REVERT: B 616 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7360 (mp10) REVERT: B 623 ASP cc_start: 0.9048 (m-30) cc_final: 0.8804 (m-30) REVERT: B 641 CYS cc_start: 0.8572 (m) cc_final: 0.7823 (m) REVERT: B 916 MET cc_start: 0.9341 (mmm) cc_final: 0.8898 (mtp) REVERT: B 1062 MET cc_start: 0.9328 (mmm) cc_final: 0.9022 (mmm) REVERT: C 28 ASP cc_start: 0.9083 (p0) cc_final: 0.8807 (p0) REVERT: C 141 ARG cc_start: 0.8958 (tpt170) cc_final: 0.8626 (tpt170) REVERT: C 145 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8332 (tmt170) REVERT: C 161 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8401 (mm-30) REVERT: D 18 GLN cc_start: 0.7359 (mt0) cc_final: 0.6936 (mt0) REVERT: D 64 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: D 82 GLU cc_start: 0.6438 (mt-10) cc_final: 0.4866 (tm-30) REVERT: D 83 LYS cc_start: 0.7794 (mttt) cc_final: 0.7103 (mttp) REVERT: D 100 MET cc_start: 0.5089 (mmt) cc_final: 0.2987 (mtt) REVERT: E 21 CYS cc_start: 0.8337 (m) cc_final: 0.7804 (m) REVERT: E 33 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7960 (mm) REVERT: E 34 ASP cc_start: 0.7694 (t0) cc_final: 0.6690 (p0) REVERT: E 46 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6893 (t0) REVERT: E 107 GLN cc_start: 0.7852 (tt0) cc_final: 0.7439 (tm-30) REVERT: F 51 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.5005 (mmp-170) REVERT: F 100 ARG cc_start: 0.8414 (mtp85) cc_final: 0.7834 (mmt-90) REVERT: G 32 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8190 (mtmt) REVERT: G 36 ASN cc_start: 0.8133 (m-40) cc_final: 0.7194 (m-40) REVERT: G 41 ASN cc_start: 0.8825 (m-40) cc_final: 0.8563 (m-40) REVERT: G 53 LYS cc_start: 0.7916 (tptt) cc_final: 0.7598 (tppp) REVERT: H 13 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8570 (mmtm) REVERT: H 52 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8325 (tt) REVERT: H 100 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7685 (mt-10) REVERT: H 146 LYS cc_start: 0.9050 (tttp) cc_final: 0.8781 (tttm) REVERT: I 22 ARG cc_start: 0.6467 (ptt180) cc_final: 0.6210 (ptt180) REVERT: I 45 LYS cc_start: 0.7992 (tptt) cc_final: 0.7714 (tmtt) REVERT: J 26 GLN cc_start: 0.8533 (tp40) cc_final: 0.8174 (tt0) REVERT: K 24 LYS cc_start: 0.7571 (ptpp) cc_final: 0.7063 (ptmm) REVERT: K 50 THR cc_start: 0.9055 (OUTLIER) cc_final: 0.8682 (t) REVERT: K 60 MET cc_start: 0.9227 (mmm) cc_final: 0.8960 (mmm) REVERT: K 66 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: K 79 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9060 (ttpt) REVERT: M 97 MET cc_start: 0.7275 (ttt) cc_final: 0.6548 (ttp) REVERT: M 121 GLN cc_start: 0.6631 (OUTLIER) cc_final: 0.6206 (mp10) REVERT: M 286 MET cc_start: 0.3697 (mmm) cc_final: 0.3044 (mmm) REVERT: M 292 MET cc_start: 0.2605 (ptm) cc_final: 0.1998 (ttt) REVERT: M 389 MET cc_start: 0.4634 (ptp) cc_final: 0.4010 (ptm) REVERT: M 421 MET cc_start: 0.5029 (pp-130) cc_final: 0.4235 (mpp) REVERT: N 157 MET cc_start: 0.0342 (OUTLIER) cc_final: -0.0535 (tmm) REVERT: N 271 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8373 (pp) REVERT: N 341 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8286 (tt) REVERT: N 380 LYS cc_start: 0.7649 (tppp) cc_final: 0.7273 (tptp) REVERT: N 381 HIS cc_start: 0.8424 (m90) cc_final: 0.8157 (m-70) REVERT: N 390 GLU cc_start: 0.7525 (tt0) cc_final: 0.6847 (tm-30) REVERT: O 14 GLN cc_start: 0.7763 (tt0) cc_final: 0.7438 (tm-30) REVERT: O 41 HIS cc_start: 0.7827 (t-90) cc_final: 0.7590 (t-90) REVERT: O 76 GLU cc_start: 0.8267 (tt0) cc_final: 0.7243 (pm20) REVERT: O 355 GLN cc_start: 0.8497 (tt0) cc_final: 0.8042 (tt0) REVERT: O 402 ASN cc_start: 0.7578 (t160) cc_final: 0.7357 (t0) REVERT: O 408 GLU cc_start: 0.7285 (tm-30) cc_final: 0.7027 (tm-30) REVERT: O 419 ARG cc_start: 0.7003 (ptp-170) cc_final: 0.6574 (ptm-80) REVERT: O 474 MET cc_start: 0.0097 (pp-130) cc_final: -0.0304 (ppp) REVERT: Q 54 GLU cc_start: 0.6852 (mp0) cc_final: 0.6564 (mp0) REVERT: Q 56 TYR cc_start: 0.7731 (t80) cc_final: 0.7404 (t80) REVERT: Q 70 ARG cc_start: 0.7614 (mpp80) cc_final: 0.7411 (tpm170) REVERT: Q 71 MET cc_start: 0.7469 (mmm) cc_final: 0.7227 (ttt) REVERT: Q 73 TYR cc_start: 0.7584 (m-80) cc_final: 0.6974 (m-80) REVERT: Q 110 MET cc_start: 0.6928 (ptp) cc_final: 0.6651 (ptp) outliers start: 137 outliers final: 71 residues processed: 737 average time/residue: 0.5990 time to fit residues: 544.2581 Evaluate side-chains 714 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 624 time to evaluate : 1.255 ------------------------------------------------------------------------------- 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 62 THR 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 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 544 ASP 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 778 LEU 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 1225 LEU Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 107 MET 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 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 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 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 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 64 GLU 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 74 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 35 PHE 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 38 GLU Chi-restraints excluded: chain L residue 47 LYS 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 M residue 319 MET 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 363 VAL Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 20 ILE 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 46 VAL 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: 0.0870 chunk 425 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 258 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 361 optimal weight: 2.9990 chunk 368 optimal weight: 0.8980 chunk 453 optimal weight: 10.0000 chunk 115 optimal weight: 0.0870 chunk 403 optimal weight: 20.0000 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 E 168 ASN H 87 GLN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.200581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.118977 restraints weight = 53659.441| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.31 r_work: 0.3081 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 45685 Z= 0.111 Angle : 0.596 27.774 62182 Z= 0.291 Chirality : 0.043 0.277 6998 Planarity : 0.004 0.078 7607 Dihedral : 15.424 179.774 7112 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.47 % Allowed : 19.91 % Favored : 77.62 % 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: 0.39 (0.12), residues: 5269 helix: 1.68 (0.12), residues: 2057 sheet: -0.61 (0.18), residues: 729 loop : -0.65 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 99 TYR 0.024 0.001 TYR E 90 PHE 0.032 0.001 PHE B 278 TRP 0.041 0.001 TRP G 200 HIS 0.006 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (45655) covalent geometry : angle 0.56508 / 0.29 (62137) hydrogen bonds : bond 0.03338 / 2.22 ( 1961) hydrogen bonds : angle 4.31669 / 3.07 ( 5558) metal coordination : bond 0.00451 / 0.22 ( 28) metal coordination : angle 7.07001 / 4.05 ( 45) Misc. bond : bond 0.00167 / 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 773 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 657 time to evaluate : 0.986 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: 0.7368 (pm20) cc_final: 0.7009 (pm20) REVERT: A 89 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7510 (tp30) REVERT: A 107 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8375 (mmm) REVERT: A 173 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7758 (mtmt) REVERT: A 216 GLU cc_start: 0.7890 (tt0) cc_final: 0.7203 (tt0) REVERT: A 221 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8469 (mt) REVERT: A 270 LEU cc_start: 0.0481 (OUTLIER) cc_final: -0.0240 (mp) REVERT: A 311 ASP cc_start: 0.8341 (t0) cc_final: 0.8038 (m-30) REVERT: A 312 PHE cc_start: 0.8360 (t80) cc_final: 0.8007 (m-80) REVERT: A 349 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: A 523 MET cc_start: 0.9425 (mtp) cc_final: 0.9211 (mtp) REVERT: A 575 LYS cc_start: 0.9072 (ptpt) cc_final: 0.8829 (ptpt) REVERT: A 620 LYS cc_start: 0.7186 (mtmt) cc_final: 0.6364 (mptt) REVERT: A 754 LYS cc_start: 0.8094 (tppt) cc_final: 0.7580 (tmmt) REVERT: A 814 GLU cc_start: 0.8391 (tt0) cc_final: 0.7967 (tp30) REVERT: A 836 ASN cc_start: 0.8919 (m110) cc_final: 0.8700 (m-40) REVERT: A 947 LEU cc_start: 0.8546 (tt) cc_final: 0.8051 (mt) REVERT: A 954 LYS cc_start: 0.8180 (ptpt) cc_final: 0.7883 (mmtm) REVERT: A 970 LYS cc_start: 0.7892 (mttt) cc_final: 0.7620 (mmtt) REVERT: A 1020 ASP cc_start: 0.8730 (t70) cc_final: 0.8434 (t0) REVERT: A 1024 ARG cc_start: 0.9032 (mtm110) cc_final: 0.8674 (mtm180) REVERT: A 1065 LEU cc_start: 0.9068 (tp) cc_final: 0.8853 (mt) REVERT: A 1084 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8845 (mm) REVERT: A 1091 LYS cc_start: 0.7874 (mttt) cc_final: 0.7576 (ttmm) REVERT: A 1112 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8150 (mp0) REVERT: A 1138 ARG cc_start: 0.8061 (ttp-110) cc_final: 0.7800 (ttp80) REVERT: A 1151 TYR cc_start: 0.8335 (t80) cc_final: 0.7914 (t80) REVERT: A 1179 GLU cc_start: 0.8184 (pt0) cc_final: 0.7376 (tm-30) REVERT: A 1185 MET cc_start: 0.7254 (pmm) cc_final: 0.6902 (pp-130) REVERT: A 1206 GLU cc_start: 0.8299 (mp0) cc_final: 0.7922 (mp0) REVERT: B 54 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7601 (tt0) REVERT: B 192 GLU cc_start: 0.7810 (pt0) cc_final: 0.7202 (pm20) REVERT: B 258 GLU cc_start: 0.8049 (mp0) cc_final: 0.7524 (mp0) REVERT: B 290 LYS cc_start: 0.8025 (mmtm) cc_final: 0.7540 (mmmm) REVERT: B 325 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6474 (mm-30) REVERT: B 332 CYS cc_start: 0.8948 (m) cc_final: 0.8480 (m) REVERT: B 374 GLU cc_start: 0.8486 (tt0) cc_final: 0.8075 (tt0) REVERT: B 408 GLN cc_start: 0.7212 (tt0) cc_final: 0.6781 (tt0) REVERT: B 499 MET cc_start: 0.9029 (ttp) cc_final: 0.8792 (ttp) REVERT: B 505 ASP cc_start: 0.8010 (m-30) cc_final: 0.7590 (m-30) REVERT: B 530 GLU cc_start: 0.8280 (mp0) cc_final: 0.7964 (mp0) REVERT: B 554 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8401 (tmtp) REVERT: B 600 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7830 (mttp) REVERT: B 611 MET cc_start: 0.9062 (mmm) cc_final: 0.8733 (mmp) REVERT: B 612 GLU cc_start: 0.8572 (tp30) cc_final: 0.7606 (mm-30) REVERT: B 616 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7242 (mp10) REVERT: B 623 ASP cc_start: 0.8991 (m-30) cc_final: 0.8735 (m-30) REVERT: B 879 PHE cc_start: 0.7435 (m-80) cc_final: 0.7211 (t80) REVERT: B 916 MET cc_start: 0.9356 (mmm) cc_final: 0.8923 (mtp) REVERT: B 1062 MET cc_start: 0.9317 (mmm) cc_final: 0.9026 (mmm) REVERT: C 28 ASP cc_start: 0.9014 (p0) cc_final: 0.8743 (p0) REVERT: C 161 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8365 (mm-30) REVERT: D 2 GLU cc_start: 0.7967 (pm20) cc_final: 0.7740 (pm20) REVERT: D 18 GLN cc_start: 0.7327 (mt0) cc_final: 0.6959 (mt0) REVERT: D 64 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: D 82 GLU cc_start: 0.6469 (mt-10) cc_final: 0.4891 (tm-30) REVERT: D 83 LYS cc_start: 0.7830 (mttt) cc_final: 0.7209 (mttp) REVERT: D 100 MET cc_start: 0.4904 (mmt) cc_final: 0.3014 (mtt) REVERT: E 21 CYS cc_start: 0.8243 (m) cc_final: 0.7754 (m) REVERT: E 33 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7692 (mm) REVERT: E 34 ASP cc_start: 0.7689 (t0) cc_final: 0.6689 (p0) REVERT: E 46 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6833 (t0) REVERT: E 107 GLN cc_start: 0.7794 (tt0) cc_final: 0.7389 (tm-30) REVERT: F 51 ARG cc_start: 0.7198 (mtm-85) cc_final: 0.4663 (mmp-170) REVERT: F 100 ARG cc_start: 0.8395 (mtp85) cc_final: 0.7801 (mmt-90) REVERT: G 32 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8055 (mtmt) REVERT: G 36 ASN cc_start: 0.8084 (m-40) cc_final: 0.6844 (m110) REVERT: G 41 ASN cc_start: 0.8829 (m-40) cc_final: 0.8588 (m-40) REVERT: G 53 LYS cc_start: 0.7800 (tptt) cc_final: 0.7452 (tppp) REVERT: H 13 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8540 (mmtm) REVERT: H 52 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8311 (tt) REVERT: H 100 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7529 (mt-10) REVERT: H 146 LYS cc_start: 0.8986 (tttp) cc_final: 0.8683 (tttm) REVERT: I 22 ARG cc_start: 0.6331 (ptt180) cc_final: 0.6089 (ptt180) REVERT: I 45 LYS cc_start: 0.7987 (tptt) cc_final: 0.7709 (tmtt) REVERT: J 26 GLN cc_start: 0.8472 (tp40) cc_final: 0.8095 (tt0) REVERT: K 24 LYS cc_start: 0.7521 (ptpp) cc_final: 0.7002 (ptmm) REVERT: K 60 MET cc_start: 0.9246 (mmm) cc_final: 0.9026 (mmm) REVERT: K 66 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8409 (tm-30) REVERT: K 79 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9066 (ttpt) REVERT: K 124 GLN cc_start: 0.8503 (tt0) cc_final: 0.8154 (tm-30) REVERT: M 97 MET cc_start: 0.7270 (ttt) cc_final: 0.6624 (mmm) REVERT: M 121 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.6290 (mp10) REVERT: M 207 HIS cc_start: 0.7774 (m90) cc_final: 0.7485 (m90) REVERT: M 286 MET cc_start: 0.3679 (mmm) cc_final: 0.3042 (mmm) REVERT: M 292 MET cc_start: 0.2622 (ptm) cc_final: 0.2016 (ttt) REVERT: M 389 MET cc_start: 0.4626 (ptp) cc_final: 0.3995 (ptm) REVERT: M 421 MET cc_start: 0.5029 (pp-130) cc_final: 0.4239 (mpp) REVERT: N 157 MET cc_start: 0.0323 (OUTLIER) cc_final: -0.0529 (tmm) REVERT: N 271 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8438 (pp) REVERT: N 341 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8069 (tt) REVERT: N 380 LYS cc_start: 0.7734 (tppp) cc_final: 0.7272 (tptp) REVERT: N 390 GLU cc_start: 0.7444 (tt0) cc_final: 0.6766 (tm-30) REVERT: O 14 GLN cc_start: 0.7655 (tt0) cc_final: 0.7335 (tm-30) REVERT: O 22 GLU cc_start: 0.8060 (pp20) cc_final: 0.7125 (pt0) REVERT: O 41 HIS cc_start: 0.7824 (t-90) cc_final: 0.7504 (t70) REVERT: O 70 ARG cc_start: 0.6626 (mpp-170) cc_final: 0.6179 (mpp-170) REVERT: O 76 GLU cc_start: 0.8224 (tt0) cc_final: 0.7172 (pm20) REVERT: O 259 MET cc_start: 0.7749 (mpt) cc_final: 0.7471 (mmt) REVERT: O 355 GLN cc_start: 0.8448 (tt0) cc_final: 0.7989 (tt0) REVERT: O 402 ASN cc_start: 0.7594 (t160) cc_final: 0.7393 (t0) REVERT: O 404 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7819 (mtm) REVERT: O 419 ARG cc_start: 0.7000 (ptp-170) cc_final: 0.6550 (ptm-80) REVERT: O 474 MET cc_start: 0.0137 (pp-130) cc_final: -0.0264 (ppp) REVERT: O 531 MET cc_start: 0.6734 (mtm) cc_final: 0.6394 (mtm) REVERT: P 308 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7106 (mp) REVERT: Q 54 GLU cc_start: 0.6816 (mp0) cc_final: 0.6506 (mp0) REVERT: Q 56 TYR cc_start: 0.7646 (t80) cc_final: 0.7377 (t80) REVERT: Q 58 LEU cc_start: 0.7568 (tt) cc_final: 0.7238 (mp) REVERT: Q 70 ARG cc_start: 0.7636 (mpp80) cc_final: 0.7391 (tpm170) REVERT: Q 71 MET cc_start: 0.7464 (mmm) cc_final: 0.7171 (ttt) REVERT: Q 73 TYR cc_start: 0.7554 (m-80) cc_final: 0.6908 (m-80) REVERT: Q 110 MET cc_start: 0.6912 (ptp) cc_final: 0.6698 (ptp) outliers start: 116 outliers final: 55 residues processed: 726 average time/residue: 0.4696 time to fit residues: 421.3065 Evaluate side-chains 700 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 627 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 221 LEU 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 544 ASP 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 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 1130 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 190 ILE 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 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 835 VAL Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 911 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 261 VAL Chi-restraints excluded: chain C residue 265 GLN Chi-restraints excluded: chain D residue 64 GLU 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 74 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain H residue 35 PHE 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 47 LYS 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 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 363 VAL Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 404 MET 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 P residue 308 ILE Chi-restraints excluded: chain Q residue 46 VAL 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: 6.9990 chunk 242 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 498 optimal weight: 1.9990 chunk 465 optimal weight: 8.9990 chunk 494 optimal weight: 10.0000 chunk 431 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 215 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 M 209 HIS ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.198939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.117206 restraints weight = 53573.206| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.63 r_work: 0.3020 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 45685 Z= 0.129 Angle : 0.606 26.540 62182 Z= 0.296 Chirality : 0.043 0.266 6998 Planarity : 0.004 0.075 7607 Dihedral : 15.376 179.600 7112 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.30 % Allowed : 20.48 % Favored : 77.22 % 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: 1.70 (0.12), residues: 2059 sheet: -0.60 (0.18), residues: 731 loop : -0.63 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 99 TYR 0.020 0.001 TYR B 357 PHE 0.030 0.001 PHE A1191 TRP 0.031 0.001 TRP G 200 HIS 0.012 0.001 HIS M 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (45655) covalent geometry : angle 0.57668 / 0.30 (62137) hydrogen bonds : bond 0.03425 / 2.29 ( 1961) hydrogen bonds : angle 4.30580 / 3.06 ( 5558) metal coordination : bond 0.00541 / 0.27 ( 28) metal coordination : angle 6.96460 / 3.98 ( 45) Misc. bond : bond 0.00172 / 0.09 ( 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 741 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 633 time to evaluate : 0.981 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: 0.7386 (pm20) cc_final: 0.6992 (pm20) REVERT: A 53 TYR cc_start: 0.8784 (m-80) cc_final: 0.8574 (m-80) REVERT: A 89 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7492 (tp30) REVERT: A 107 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8383 (mmm) REVERT: A 163 ASN cc_start: 0.7923 (m-40) cc_final: 0.7695 (m110) REVERT: A 173 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7711 (mtmt) REVERT: A 221 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8449 (mt) REVERT: A 270 LEU cc_start: 0.0546 (OUTLIER) cc_final: -0.0188 (mp) REVERT: A 278 ASP cc_start: 0.8565 (m-30) cc_final: 0.8363 (m-30) REVERT: A 307 MET cc_start: 0.8307 (tpp) cc_final: 0.7994 (mmm) REVERT: A 311 ASP cc_start: 0.8401 (t0) cc_final: 0.8116 (m-30) REVERT: A 312 PHE cc_start: 0.8333 (t80) cc_final: 0.7954 (m-80) REVERT: A 349 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: A 575 LYS cc_start: 0.9150 (ptpt) cc_final: 0.8884 (ptpt) REVERT: A 620 LYS cc_start: 0.7171 (mtmt) cc_final: 0.6339 (mptt) REVERT: A 754 LYS cc_start: 0.8118 (tppt) cc_final: 0.7579 (tmmt) REVERT: A 814 GLU cc_start: 0.8474 (tt0) cc_final: 0.8021 (tp30) REVERT: A 836 ASN cc_start: 0.9035 (m110) cc_final: 0.8825 (m-40) REVERT: A 947 LEU cc_start: 0.8576 (tt) cc_final: 0.8086 (mt) REVERT: A 954 LYS cc_start: 0.8249 (ptpt) cc_final: 0.7897 (mmtm) REVERT: A 1020 ASP cc_start: 0.8800 (t70) cc_final: 0.8520 (t0) REVERT: A 1024 ARG cc_start: 0.9031 (mtm110) cc_final: 0.8644 (mtm180) REVERT: A 1065 LEU cc_start: 0.9086 (tp) cc_final: 0.8860 (mt) REVERT: A 1084 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8871 (mm) REVERT: A 1091 LYS cc_start: 0.8011 (mttt) cc_final: 0.7653 (ttmm) REVERT: A 1138 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7947 (ttp80) REVERT: A 1151 TYR cc_start: 0.8354 (t80) cc_final: 0.7928 (t80) REVERT: A 1179 GLU cc_start: 0.8186 (pt0) cc_final: 0.7429 (tm-30) REVERT: A 1206 GLU cc_start: 0.8296 (mp0) cc_final: 0.7911 (mp0) REVERT: B 54 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7575 (tt0) REVERT: B 139 MET cc_start: 0.9330 (ttm) cc_final: 0.9069 (ttm) REVERT: B 192 GLU cc_start: 0.7730 (pt0) cc_final: 0.7121 (pm20) REVERT: B 258 GLU cc_start: 0.7991 (mp0) cc_final: 0.7461 (mp0) REVERT: B 290 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7529 (mmmm) REVERT: B 325 GLU cc_start: 0.6899 (mm-30) cc_final: 0.6428 (mm-30) REVERT: B 332 CYS cc_start: 0.8973 (m) cc_final: 0.8505 (m) REVERT: B 374 GLU cc_start: 0.8512 (tt0) cc_final: 0.8075 (tt0) REVERT: B 408 GLN cc_start: 0.7042 (tt0) cc_final: 0.6654 (tt0) REVERT: B 499 MET cc_start: 0.9101 (ttp) cc_final: 0.8864 (ttp) REVERT: B 505 ASP cc_start: 0.8028 (m-30) cc_final: 0.7580 (m-30) REVERT: B 530 GLU cc_start: 0.8327 (mp0) cc_final: 0.7968 (mp0) REVERT: B 554 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8403 (tmtp) REVERT: B 575 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 600 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7796 (mttp) REVERT: B 611 MET cc_start: 0.9032 (mmm) cc_final: 0.8728 (mmp) REVERT: B 612 GLU cc_start: 0.8534 (tp30) cc_final: 0.7570 (mm-30) REVERT: B 616 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7246 (mp10) REVERT: B 623 ASP cc_start: 0.8961 (m-30) cc_final: 0.8694 (m-30) REVERT: B 879 PHE cc_start: 0.7535 (m-80) cc_final: 0.7258 (t80) REVERT: B 916 MET cc_start: 0.9374 (mmm) cc_final: 0.8963 (mtp) REVERT: B 1031 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8584 (tm) REVERT: B 1062 MET cc_start: 0.9376 (mmm) cc_final: 0.9079 (mmm) REVERT: B 1127 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8666 (tmtm) REVERT: C 28 ASP cc_start: 0.9038 (p0) cc_final: 0.8746 (p0) REVERT: C 143 GLN cc_start: 0.8329 (tt0) cc_final: 0.7996 (mm-40) REVERT: C 161 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8433 (mm-30) REVERT: C 279 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.7811 (ttt90) REVERT: D 2 GLU cc_start: 0.8044 (pm20) cc_final: 0.7807 (pm20) REVERT: D 18 GLN cc_start: 0.7314 (mt0) cc_final: 0.6934 (mt0) REVERT: D 29 GLU cc_start: 0.5869 (mt-10) cc_final: 0.5452 (tm-30) REVERT: D 64 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: D 82 GLU cc_start: 0.6502 (mt-10) cc_final: 0.4978 (tm-30) REVERT: D 83 LYS cc_start: 0.7816 (mttt) cc_final: 0.7187 (mttp) REVERT: D 85 GLN cc_start: 0.7574 (mt0) cc_final: 0.7213 (mp10) REVERT: D 100 MET cc_start: 0.5045 (mmt) cc_final: 0.3151 (mtt) REVERT: E 21 CYS cc_start: 0.8255 (m) cc_final: 0.7736 (m) REVERT: E 33 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7671 (mm) REVERT: E 34 ASP cc_start: 0.7711 (t0) cc_final: 0.6692 (p0) REVERT: E 46 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6844 (t0) REVERT: E 107 GLN cc_start: 0.7919 (tt0) cc_final: 0.7454 (tm-30) REVERT: F 51 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.4898 (mmp-170) REVERT: F 100 ARG cc_start: 0.8432 (mtp85) cc_final: 0.7804 (mmt-90) REVERT: G 32 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8049 (mtmt) REVERT: G 36 ASN cc_start: 0.8094 (m-40) cc_final: 0.6866 (m110) REVERT: G 41 ASN cc_start: 0.8840 (m-40) cc_final: 0.8583 (m-40) REVERT: G 53 LYS cc_start: 0.7790 (tptt) cc_final: 0.7430 (tppp) REVERT: H 13 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8522 (mmtm) REVERT: H 52 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8310 (tt) REVERT: H 100 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7570 (mt-10) REVERT: H 146 LYS cc_start: 0.8942 (tttp) cc_final: 0.8644 (tttm) REVERT: I 22 ARG cc_start: 0.6280 (ptt180) cc_final: 0.6035 (ptt180) REVERT: I 45 LYS cc_start: 0.8029 (tptt) cc_final: 0.7743 (tmtt) REVERT: J 26 GLN cc_start: 0.8446 (tp40) cc_final: 0.8113 (tt0) REVERT: K 24 LYS cc_start: 0.7484 (ptpp) cc_final: 0.6959 (ptmm) REVERT: K 60 MET cc_start: 0.9316 (mmm) cc_final: 0.9082 (mmm) REVERT: K 66 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: K 124 GLN cc_start: 0.8564 (tt0) cc_final: 0.8149 (tm-30) REVERT: M 97 MET cc_start: 0.7304 (ttt) cc_final: 0.6653 (mmm) REVERT: M 121 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6256 (mp10) REVERT: M 207 HIS cc_start: 0.7772 (m90) cc_final: 0.7495 (m90) REVERT: M 286 MET cc_start: 0.3677 (mmm) cc_final: 0.3028 (mmm) REVERT: M 292 MET cc_start: 0.2527 (ptm) cc_final: 0.1927 (ttt) REVERT: M 389 MET cc_start: 0.4555 (ptp) cc_final: 0.3867 (ptm) REVERT: M 421 MET cc_start: 0.5028 (pp-130) cc_final: 0.4260 (mpp) REVERT: N 157 MET cc_start: 0.0305 (OUTLIER) cc_final: -0.0562 (tmm) REVERT: N 271 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8357 (pp) REVERT: N 341 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8061 (tt) REVERT: N 380 LYS cc_start: 0.7736 (tppp) cc_final: 0.7259 (tptp) REVERT: N 390 GLU cc_start: 0.7440 (tt0) cc_final: 0.6738 (tm-30) REVERT: O 14 GLN cc_start: 0.7670 (tt0) cc_final: 0.7368 (tm-30) REVERT: O 22 GLU cc_start: 0.8080 (pp20) cc_final: 0.7062 (pt0) REVERT: O 41 HIS cc_start: 0.7848 (t-90) cc_final: 0.7592 (t-90) REVERT: O 70 ARG cc_start: 0.6633 (mpp-170) cc_final: 0.6354 (mpp-170) REVERT: O 76 GLU cc_start: 0.8180 (tt0) cc_final: 0.7109 (pm20) REVERT: O 259 MET cc_start: 0.7638 (mpt) cc_final: 0.7430 (mmt) REVERT: O 355 GLN cc_start: 0.8425 (tt0) cc_final: 0.7988 (tt0) REVERT: O 419 ARG cc_start: 0.7008 (ptp-170) cc_final: 0.6529 (ptm-80) REVERT: O 531 MET cc_start: 0.6797 (mtm) cc_final: 0.6435 (mtm) REVERT: P 308 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7165 (mp) REVERT: Q 54 GLU cc_start: 0.6859 (mp0) cc_final: 0.6636 (mp0) REVERT: Q 56 TYR cc_start: 0.7587 (t80) cc_final: 0.7364 (t80) REVERT: Q 70 ARG cc_start: 0.7775 (mpp80) cc_final: 0.7172 (tpm170) REVERT: Q 71 MET cc_start: 0.7553 (mmm) cc_final: 0.7255 (ttt) REVERT: Q 73 TYR cc_start: 0.7552 (m-80) cc_final: 0.6860 (m-80) REVERT: Q 77 THR cc_start: 0.5679 (OUTLIER) cc_final: 0.5427 (m) REVERT: Q 110 MET cc_start: 0.7082 (ptp) cc_final: 0.6813 (ptp) outliers start: 108 outliers final: 60 residues processed: 704 average time/residue: 0.4747 time to fit residues: 412.6034 Evaluate side-chains 697 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 616 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 270 LEU Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 544 ASP 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 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 1130 VAL Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain B residue 54 GLU 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 321 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 575 SER 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 906 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LEU 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 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 D residue 64 GLU 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 74 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain G residue 197 LEU 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 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 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 477 THR Chi-restraints excluded: chain P residue 193 GLU Chi-restraints excluded: chain P residue 287 CYS Chi-restraints excluded: chain P residue 308 ILE Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 77 THR 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: 0.4980 chunk 5 optimal weight: 2.9990 chunk 529 optimal weight: 40.0000 chunk 30 optimal weight: 4.9990 chunk 451 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 200 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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** K 38 HIS ** M 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 209 HIS P 207 ASN ** P 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.196289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.112947 restraints weight = 53565.372| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.48 r_work: 0.2961 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 45685 Z= 0.198 Angle : 0.667 26.684 62182 Z= 0.329 Chirality : 0.045 0.242 6998 Planarity : 0.005 0.083 7607 Dihedral : 15.409 179.876 7112 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.15 % Allowed : 20.74 % Favored : 77.11 % 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: 0.25 (0.12), residues: 5269 helix: 1.51 (0.12), residues: 2070 sheet: -0.61 (0.18), residues: 729 loop : -0.72 (0.12), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 99 TYR 0.022 0.002 TYR B 357 PHE 0.027 0.002 PHE B 380 TRP 0.032 0.002 TRP G 200 HIS 0.013 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (45655) covalent geometry : angle 0.63743 / 0.33 (62137) hydrogen bonds : bond 0.03938 / 2.65 ( 1961) hydrogen bonds : angle 4.46713 / 3.18 ( 5558) metal coordination : bond 0.00856 / 0.46 ( 28) metal coordination : angle 7.30727 / 4.13 ( 45) Misc. bond : bond 0.00209 / 0.11 ( 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 742 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 641 time to evaluate : 0.944 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: 0.7498 (pm20) cc_final: 0.7074 (pm20) REVERT: A 53 TYR cc_start: 0.8853 (m-80) cc_final: 0.8542 (m-80) REVERT: A 89 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7558 (tp30) REVERT: A 107 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8465 (mmm) REVERT: A 131 ARG cc_start: 0.7877 (ptp-110) cc_final: 0.7539 (ptp90) REVERT: A 173 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7807 (mtmt) REVERT: A 221 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8415 (mt) REVERT: A 262 ILE cc_start: 0.8848 (mp) cc_final: 0.8618 (mt) REVERT: A 270 LEU cc_start: 0.0899 (OUTLIER) cc_final: 0.0168 (mp) REVERT: A 278 ASP cc_start: 0.8654 (m-30) cc_final: 0.8447 (m-30) REVERT: A 307 MET cc_start: 0.8349 (tpp) cc_final: 0.8092 (mmm) REVERT: A 312 PHE cc_start: 0.8388 (t80) cc_final: 0.7989 (m-80) REVERT: A 406 LYS cc_start: 0.9245 (ttpt) cc_final: 0.8600 (mmtm) REVERT: A 575 LYS cc_start: 0.9177 (ptpt) cc_final: 0.8900 (ptpt) REVERT: A 620 LYS cc_start: 0.7215 (mtmt) cc_final: 0.6274 (mptt) REVERT: A 754 LYS cc_start: 0.8149 (tppt) cc_final: 0.7704 (tmmt) REVERT: A 947 LEU cc_start: 0.8611 (tt) cc_final: 0.8125 (mt) REVERT: A 1020 ASP cc_start: 0.8790 (t70) cc_final: 0.8499 (t0) REVERT: A 1024 ARG cc_start: 0.9024 (mtm110) cc_final: 0.8627 (mtm180) REVERT: A 1065 LEU cc_start: 0.9105 (tp) cc_final: 0.8866 (mt) REVERT: A 1091 LYS cc_start: 0.8021 (mttt) cc_final: 0.7696 (mmtt) REVERT: A 1151 TYR cc_start: 0.8340 (t80) cc_final: 0.7928 (t80) REVERT: A 1179 GLU cc_start: 0.8198 (pt0) cc_final: 0.7343 (tm-30) REVERT: A 1211 VAL cc_start: 0.8712 (m) cc_final: 0.8494 (t) REVERT: B 54 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: B 192 GLU cc_start: 0.7729 (pt0) cc_final: 0.7070 (pm20) REVERT: B 233 ASP cc_start: 0.8665 (p0) cc_final: 0.8398 (p0) REVERT: B 258 GLU cc_start: 0.8026 (mp0) cc_final: 0.7506 (mp0) REVERT: B 285 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7829 (tmtt) REVERT: B 290 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7541 (mmmm) REVERT: B 325 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6567 (mm-30) REVERT: B 332 CYS cc_start: 0.9042 (m) cc_final: 0.8600 (m) REVERT: B 374 GLU cc_start: 0.8619 (tt0) cc_final: 0.8173 (tt0) REVERT: B 408 GLN cc_start: 0.7084 (tt0) cc_final: 0.6718 (tt0) REVERT: B 499 MET cc_start: 0.9216 (ttp) cc_final: 0.8809 (ttp) REVERT: B 530 GLU cc_start: 0.8489 (mp0) cc_final: 0.8112 (mp0) REVERT: B 554 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8487 (tmtp) REVERT: B 575 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8549 (p) REVERT: B 600 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7771 (mttp) REVERT: B 611 MET cc_start: 0.9025 (mmm) cc_final: 0.8768 (mmp) REVERT: B 612 GLU cc_start: 0.8546 (tp30) cc_final: 0.7580 (mm-30) REVERT: B 616 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7259 (mp10) REVERT: B 622 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8245 (mp0) REVERT: B 623 ASP cc_start: 0.8978 (m-30) cc_final: 0.8658 (m-30) REVERT: B 641 CYS cc_start: 0.8720 (m) cc_final: 0.7904 (m) REVERT: B 781 ARG cc_start: 0.8058 (mtp85) cc_final: 0.7496 (mtt180) REVERT: B 879 PHE cc_start: 0.7697 (m-80) cc_final: 0.7360 (t80) REVERT: B 916 MET cc_start: 0.9433 (mmm) cc_final: 0.9001 (mtp) REVERT: B 1127 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8640 (tmtm) REVERT: C 28 ASP cc_start: 0.9089 (p0) cc_final: 0.8793 (p0) REVERT: C 143 GLN cc_start: 0.8318 (tt0) cc_final: 0.7909 (mm-40) REVERT: C 161 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8493 (mm-30) REVERT: C 279 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7911 (ttt90) REVERT: C 311 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8784 (pt0) REVERT: D 18 GLN cc_start: 0.7408 (mt0) cc_final: 0.7044 (mt0) REVERT: D 29 GLU cc_start: 0.6173 (mt-10) cc_final: 0.5508 (tm-30) REVERT: D 64 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: D 82 GLU cc_start: 0.6516 (mt-10) cc_final: 0.4982 (tm-30) REVERT: D 83 LYS cc_start: 0.7821 (mttt) cc_final: 0.7242 (mttp) REVERT: D 100 MET cc_start: 0.5078 (mmt) cc_final: 0.3175 (mtt) REVERT: E 33 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7869 (mm) REVERT: E 34 ASP cc_start: 0.7873 (t0) cc_final: 0.7069 (p0) REVERT: E 46 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7003 (t0) REVERT: E 107 GLN cc_start: 0.8045 (tt0) cc_final: 0.7538 (tm-30) REVERT: F 51 ARG cc_start: 0.7253 (mtm-85) cc_final: 0.4659 (mmp-170) REVERT: F 100 ARG cc_start: 0.8392 (mtp85) cc_final: 0.7747 (mmt-90) REVERT: G 32 LYS cc_start: 0.8587 (mtpt) cc_final: 0.8134 (mtmt) REVERT: G 36 ASN cc_start: 0.8432 (m-40) cc_final: 0.7846 (m110) REVERT: G 41 ASN cc_start: 0.8793 (m-40) cc_final: 0.8519 (m-40) REVERT: G 53 LYS cc_start: 0.7813 (tptt) cc_final: 0.7514 (tppp) REVERT: H 13 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8542 (mmtm) REVERT: H 52 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8309 (tt) REVERT: H 100 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7680 (mt-10) REVERT: H 146 LYS cc_start: 0.8962 (tttp) cc_final: 0.8694 (tttm) REVERT: I 22 ARG cc_start: 0.6370 (ptt180) cc_final: 0.6136 (ptt180) REVERT: J 26 GLN cc_start: 0.8458 (tp40) cc_final: 0.8158 (tt0) REVERT: K 24 LYS cc_start: 0.7637 (ptpp) cc_final: 0.7025 (ptmm) REVERT: K 50 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8650 (t) REVERT: K 60 MET cc_start: 0.9347 (mmm) cc_final: 0.9064 (mmm) REVERT: K 66 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: K 124 GLN cc_start: 0.8631 (tt0) cc_final: 0.8210 (tm-30) REVERT: L 25 GLU cc_start: 0.8837 (mp0) cc_final: 0.8210 (mt-10) REVERT: M 68 ASN cc_start: 0.6394 (m110) cc_final: 0.6115 (m110) REVERT: M 97 MET cc_start: 0.7419 (ttt) cc_final: 0.6641 (mmm) REVERT: M 121 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6535 (mp10) REVERT: M 207 HIS cc_start: 0.7813 (m90) cc_final: 0.7484 (m90) REVERT: M 286 MET cc_start: 0.3492 (mmm) cc_final: 0.2858 (mmm) REVERT: M 292 MET cc_start: 0.2514 (ptm) cc_final: 0.1916 (ttt) REVERT: M 389 MET cc_start: 0.4538 (ptp) cc_final: 0.3846 (ptm) REVERT: M 421 MET cc_start: 0.5022 (pp-130) cc_final: 0.4274 (mpp) REVERT: N 150 GLU cc_start: 0.3944 (mt-10) cc_final: 0.3253 (tp30) REVERT: N 157 MET cc_start: 0.0269 (OUTLIER) cc_final: -0.0566 (tmm) REVERT: N 271 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8373 (pp) REVERT: N 341 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8035 (tt) REVERT: N 380 LYS cc_start: 0.7773 (tppp) cc_final: 0.7421 (tptp) REVERT: N 390 GLU cc_start: 0.7512 (tt0) cc_final: 0.6769 (tm-30) REVERT: O 14 GLN cc_start: 0.7680 (tt0) cc_final: 0.7372 (tm-30) REVERT: O 22 GLU cc_start: 0.8173 (pp20) cc_final: 0.7134 (pt0) REVERT: O 41 HIS cc_start: 0.7850 (t-90) cc_final: 0.7596 (t-90) REVERT: O 70 ARG cc_start: 0.6533 (mpp-170) cc_final: 0.6300 (mpp-170) REVERT: O 76 GLU cc_start: 0.8183 (tt0) cc_final: 0.7097 (pm20) REVERT: O 259 MET cc_start: 0.7527 (mpt) cc_final: 0.7290 (mmt) REVERT: O 355 GLN cc_start: 0.8419 (tt0) cc_final: 0.8022 (tt0) REVERT: O 404 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7977 (mtm) REVERT: O 419 ARG cc_start: 0.7007 (ptp-170) cc_final: 0.6497 (ptm-80) REVERT: O 474 MET cc_start: 0.0508 (pp-130) cc_final: 0.0073 (ppp) REVERT: O 524 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7675 (tm-30) REVERT: P 308 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7442 (mp) REVERT: Q 54 GLU cc_start: 0.6899 (mp0) cc_final: 0.6619 (mp0) REVERT: Q 70 ARG cc_start: 0.7750 (mpp80) cc_final: 0.7132 (tpm170) REVERT: Q 71 MET cc_start: 0.7487 (mmm) cc_final: 0.7043 (ttt) REVERT: Q 77 THR cc_start: 0.5680 (OUTLIER) cc_final: 0.5440 (m) REVERT: Q 110 MET cc_start: 0.6988 (ptp) cc_final: 0.6737 (ptp) outliers start: 101 outliers final: 62 residues processed: 709 average time/residue: 0.4786 time to fit residues: 417.4637 Evaluate side-chains 700 residues out of total 4699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 617 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 62 THR 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 221 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 544 ASP 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 778 LEU 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 1303 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 185 SER 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 573 SER Chi-restraints excluded: chain B residue 575 SER Chi-restraints excluded: chain B residue 625 LEU 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 794 MET Chi-restraints excluded: chain B residue 906 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 929 MET Chi-restraints excluded: chain B residue 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 258 SER Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 279 ARG Chi-restraints excluded: chain C residue 311 GLU Chi-restraints excluded: chain D residue 64 GLU 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 74 VAL Chi-restraints excluded: chain E residue 117 SER 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 59 ILE Chi-restraints excluded: chain K residue 66 GLU 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 341 LEU Chi-restraints excluded: chain N residue 363 VAL Chi-restraints excluded: chain N residue 374 THR Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 163 VAL Chi-restraints excluded: chain O residue 404 MET 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 P residue 308 ILE Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 77 THR 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: 0.7980 chunk 0 optimal weight: 10.0000 chunk 413 optimal weight: 0.0470 chunk 110 optimal weight: 1.9990 chunk 462 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 353 optimal weight: 8.9990 chunk 532 optimal weight: 50.0000 chunk 68 optimal weight: 0.7980 chunk 395 optimal weight: 10.0000 chunk 272 optimal weight: 0.1980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 154 ASN A 163 ASN A 225 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 ** both conformations clash, **PLEASE CHECK MANUALLY** M 209 HIS O 402 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 = 0.4264 r_free = 0.4264 target = 0.198721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115977 restraints weight = 53860.869| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.29 r_work: 0.3049 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 45685 Z= 0.115 Angle : 0.613 26.901 62182 Z= 0.300 Chirality : 0.042 0.222 6998 Planarity : 0.004 0.086 7607 Dihedral : 15.336 179.646 7112 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.72 % Allowed : 21.55 % Favored : 76.73 % 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: 0.41 (0.12), residues: 5269 helix: 1.67 (0.12), residues: 2061 sheet: -0.61 (0.18), residues: 730 loop : -0.62 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 99 TYR 0.020 0.001 TYR M 210 PHE 0.033 0.001 PHE B 278 TRP 0.027 0.001 TRP G 200 HIS 0.007 0.001 HIS M 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (45655) covalent geometry : angle 0.58375 / 0.30 (62137) hydrogen bonds : bond 0.03395 / 2.26 ( 1961) hydrogen bonds : angle 4.33959 / 3.09 ( 5558) metal coordination : bond 0.00465 / 0.22 ( 28) metal coordination : angle 6.98023 / 3.95 ( 45) Misc. bond : bond 0.00151 / 0.08 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19594.04 seconds wall clock time: 332 minutes 26.74 seconds (19946.74 seconds total)