Starting phenix.real_space_refine on Mon Apr 15 20:20:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cen_16610/04_2024/8cen_16610_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cen_16610/04_2024/8cen_16610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cen_16610/04_2024/8cen_16610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cen_16610/04_2024/8cen_16610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cen_16610/04_2024/8cen_16610_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cen_16610/04_2024/8cen_16610_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 17 6.06 5 P 145 5.49 5 Mg 1 5.21 5 S 502 5.16 5 C 64238 2.51 5 N 17489 2.21 5 O 19547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 119": "OE1" <-> "OE2" Residue "0 PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 644": "OE1" <-> "OE2" Residue "3 GLU 112": "OE1" <-> "OE2" Residue "3 GLU 131": "OE1" <-> "OE2" Residue "5 GLU 53": "OE1" <-> "OE2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 100": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "M GLU 141": "OE1" <-> "OE2" Residue "M TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "O PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "Q GLU 410": "OE1" <-> "OE2" Residue "a GLU 25": "OE1" <-> "OE2" Residue "b GLU 53": "OE1" <-> "OE2" Residue "b ASP 152": "OD1" <-> "OD2" Residue "d ASP 257": "OD1" <-> "OD2" Residue "g GLU 11": "OE1" <-> "OE2" Residue "n PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 101943 Number of models: 1 Model: "" Number of chains: 58 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4214 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 503} Chain breaks: 6 Chain: "2" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3647 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 17, 'TRANS': 434} Chain breaks: 1 Chain: "3" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2338 Classifications: {'peptide': 302} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3019 Classifications: {'peptide': 383} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 361} Chain breaks: 1 Chain: "7" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4954 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 24, 'TRANS': 590} Chain breaks: 2 Chain: "A" Number of atoms: 11815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1508, 11815 Classifications: {'peptide': 1508} Link IDs: {'PCIS': 3, 'PTRANS': 87, 'TRANS': 1417} Chain breaks: 6 Chain: "B" Number of atoms: 9404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9404 Classifications: {'peptide': 1180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "C" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2092 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1343 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 983 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2379 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 297} Chain breaks: 1 Chain: "N" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1495 Classifications: {'DNA': 73} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 72} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 172} Chain: "Q" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1871 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 2 Chain: "R" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2230 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "T" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1495 Classifications: {'DNA': 73} Link IDs: {'rna3p': 72} Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 885 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain breaks: 2 Chain: "V" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'TRANS': 103} Chain breaks: 1 Chain: "W" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2473 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 3 Chain: "X" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1708 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain breaks: 1 Chain: "a" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1495 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain breaks: 3 Chain: "b" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1414 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain breaks: 1 Chain: "c" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 902 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "d" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4063 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 19, 'TRANS': 481} Chain breaks: 9 Chain: "e" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Chain breaks: 1 Chain: "f" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1578 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Chain: "g" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 815 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Chain: "h" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1394 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "i" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1512 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 13, 'TRANS': 167} Chain breaks: 2 Chain: "j" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 852 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain breaks: 1 Chain: "k" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1259 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain: "l" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4385 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 22, 'TRANS': 512} Chain breaks: 6 Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1068 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "n" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1095 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "o" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 922 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 101} Chain: "p" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1863 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 1 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 938 SG CYS 0 115 73.003 92.545 185.935 1.00 31.43 S ATOM 1265 SG CYS 0 156 67.953 92.154 190.123 1.00 31.15 S ATOM 1080 SG CYS 0 133 70.314 97.968 187.963 1.00 32.25 S ATOM 1566 SG CYS 0 191 72.868 94.674 192.365 1.00 31.27 S ATOM 13991 SG CYS 3 13 61.032 124.996 142.688 1.00 38.19 S ATOM 14012 SG CYS 3 16 62.028 124.524 139.124 1.00 35.89 S ATOM 14207 SG CYS 3 39 63.446 127.505 140.819 1.00 35.89 S ATOM 14228 SG CYS 3 42 59.852 127.475 139.866 1.00 35.13 S ATOM 14160 SG CYS 3 34 53.070 128.610 152.065 1.00 36.86 S ATOM 14318 SG CYS 3 54 52.525 128.848 148.110 1.00 39.96 S ATOM 14356 SG CYS 3 59 49.542 128.836 150.563 1.00 38.59 S ATOM 17084 SG CYS 4 289 118.075 49.214 203.946 1.00 27.56 S ATOM 17103 SG CYS 4 292 121.373 50.040 205.519 1.00 30.10 S ATOM 17195 SG CYS 4 305 118.696 48.388 207.498 1.00 36.56 S ATOM 17213 SG CYS 4 308 118.381 52.244 206.429 1.00 36.14 S ATOM 20040 SG CYS 6 349 119.694 32.631 190.146 1.00 26.85 S ATOM 20061 SG CYS 6 352 117.706 30.153 187.892 1.00 30.64 S ATOM 20140 SG CYS 6 363 118.142 33.642 186.732 1.00 27.68 S ATOM 20159 SG CYS 6 366 115.879 32.934 189.639 1.00 30.98 S ATOM 20461 SG CYS 6 403 149.818 64.045 201.549 1.00 27.30 S ATOM 20484 SG CYS 6 406 151.409 63.278 197.876 1.00 29.51 S ATOM 20743 SG CYS 6 437 149.124 66.042 198.313 1.00 26.02 S ATOM 20764 SG CYS 6 440 147.821 62.542 198.754 1.00 30.03 S ATOM 20676 SG CYS 6 429 139.598 63.512 207.973 1.00 27.81 S ATOM 20699 SG CYS 6 432 142.554 61.767 209.585 1.00 27.59 S ATOM 20857 SG CYS 6 451 141.474 60.685 206.186 1.00 25.33 S ATOM 20874 SG CYS 6 454 139.232 59.909 209.146 1.00 29.67 S ATOM 19939 SG CYS 6 336 123.293 33.296 176.510 1.00 31.57 S ATOM 19951 SG CYS 6 338 122.299 36.201 178.849 1.00 31.86 S ATOM 20099 SG CYS 6 357 125.964 35.597 178.003 1.00 30.75 S ATOM 26686 SG CYS A 107 98.491 118.271 115.820 1.00 36.72 S ATOM 26710 SG CYS A 110 97.888 119.732 119.216 1.00 36.38 S ATOM 27015 SG CYS A 148 101.467 118.730 118.082 1.00 36.71 S ATOM 27153 SG CYS A 167 98.850 116.056 118.862 1.00 38.05 S ATOM 26381 SG CYS A 67 61.957 144.543 101.114 1.00 33.20 S ATOM 26403 SG CYS A 70 62.668 148.189 101.945 1.00 34.30 S ATOM 26456 SG CYS A 77 64.683 146.465 99.185 1.00 23.21 S ATOM 46591 SG CYS B1163 75.330 148.577 112.115 1.00 28.77 S ATOM 46609 SG CYS B1166 76.526 145.568 110.601 1.00 24.19 S ATOM 46734 SG CYS B1182 72.622 146.127 111.306 1.00 32.34 S ATOM 46753 SG CYS B1185 75.256 145.137 113.997 1.00 33.18 S ATOM 47738 SG CYS C 86 47.437 183.872 48.211 1.00 21.83 S ATOM 47755 SG CYS C 88 46.748 180.305 49.407 1.00 24.44 S ATOM 47788 SG CYS C 92 45.457 181.598 46.060 1.00 14.36 S ATOM 47811 SG CYS C 95 49.162 180.700 46.689 1.00 10.54 S ATOM 55767 SG CYS I 7 129.889 91.889 59.765 1.00 20.66 S ATOM 55792 SG CYS I 10 126.393 92.148 61.514 1.00 23.88 S ATOM 55958 SG CYS I 29 129.340 92.841 63.623 1.00 22.62 S ATOM 55982 SG CYS I 32 128.908 89.377 62.171 1.00 24.64 S ATOM 56309 SG CYS I 75 134.323 124.755 30.839 1.00 30.42 S ATOM 56331 SG CYS I 78 133.719 122.142 27.834 1.00 33.30 S ATOM 56547 SG CYS I 103 130.845 123.584 30.056 1.00 28.73 S ATOM 56567 SG CYS I 106 133.374 120.904 30.911 1.00 31.02 S ATOM 56712 SG CYS J 7 76.115 169.701 35.176 1.00 4.02 S ATOM 56735 SG CYS J 10 75.720 173.408 34.171 1.00 1.18 S ATOM 57015 SG CYS J 45 79.156 171.335 34.112 1.00 26.24 S ATOM 57021 SG CYS J 46 76.373 171.171 31.528 1.00 3.73 S ATOM 58201 SG CYS L 31 50.194 135.626 44.938 1.00 24.43 S ATOM 58221 SG CYS L 34 48.341 135.557 41.763 1.00 26.23 S ATOM 58325 SG CYS L 48 46.837 133.885 44.951 1.00 26.17 S ATOM 58348 SG CYS L 51 49.682 132.272 43.084 1.00 30.27 S ATOM 58592 SG CYS M 24 49.638 164.839 90.704 1.00 23.70 S ATOM 58614 SG CYS M 27 47.076 166.772 88.682 1.00 27.01 S ATOM 58758 SG CYS M 45 49.271 164.139 87.009 1.00 17.53 S ATOM 58777 SG CYS M 48 50.738 167.485 88.181 1.00 15.86 S ATOM 72112 SG CYS W 124 47.828 142.854 110.556 1.00 39.54 S ATOM 72133 SG CYS W 127 51.146 141.822 109.204 1.00 35.11 S ATOM 72318 SG CYS W 149 50.439 145.573 109.902 1.00 40.24 S ATOM 72338 SG CYS W 152 48.834 143.732 106.970 1.00 36.36 S Time building chain proxies: 39.15, per 1000 atoms: 0.38 Number of scatterers: 101943 At special positions: 0 Unit cell: (211.05, 282.45, 262.5, 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 17 29.99 Fe 4 26.01 S 502 16.00 P 145 15.00 Mg 1 11.99 O 19547 8.00 N 17489 7.00 C 64238 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.84 Conformation dependent library (CDL) restraints added in 13.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" NE2 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " Number of angles added : 93 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23524 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 445 helices and 104 sheets defined 50.9% alpha, 13.7% beta 61 base pairs and 124 stacking pairs defined. Time for finding SS restraints: 71.60 Creating SS restraints... Processing helix chain '0' and resid 18 through 35 Processing helix chain '0' and resid 47 through 63 Processing helix chain '0' and resid 75 through 98 Processing helix chain '0' and resid 110 through 115 Processing helix chain '0' and resid 125 through 138 Processing helix chain '0' and resid 139 through 149 Proline residue: 0 149 - end of helix Processing helix chain '0' and resid 156 through 166 removed outlier: 3.850A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE 0 165 " --> pdb=" O ASN 0 161 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N GLU 0 166 " --> pdb=" O LEU 0 162 " (cutoff:3.500A) Processing helix chain '0' and resid 177 through 189 Processing helix chain '0' and resid 191 through 200 Processing helix chain '0' and resid 209 through 214 removed outlier: 4.213A pdb=" N LEU 0 213 " --> pdb=" O SER 0 209 " (cutoff:3.500A) Processing helix chain '0' and resid 218 through 227 removed outlier: 4.093A pdb=" N VAL 0 222 " --> pdb=" O ILE 0 218 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN 0 224 " --> pdb=" O GLU 0 220 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU 0 225 " --> pdb=" O ARG 0 221 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER 0 227 " --> pdb=" O SER 0 223 " (cutoff:3.500A) Processing helix chain '0' and resid 239 through 249 removed outlier: 3.856A pdb=" N VAL 0 243 " --> pdb=" O ASN 0 239 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 253 through 278 Processing helix chain '0' and resid 279 through 292 removed outlier: 4.267A pdb=" N GLU 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) Processing helix chain '0' and resid 294 through 299 Processing helix chain '0' and resid 312 through 317 removed outlier: 5.445A pdb=" N LEU 0 317 " --> pdb=" O PRO 0 313 " (cutoff:3.500A) Processing helix chain '0' and resid 322 through 327 removed outlier: 6.776A pdb=" N ARG 0 326 " --> pdb=" O PRO 0 322 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG 0 327 " --> pdb=" O GLY 0 323 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 322 through 327' Processing helix chain '0' and resid 328 through 348 removed outlier: 3.555A pdb=" N LYS 0 347 " --> pdb=" O LYS 0 343 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL 0 348 " --> pdb=" O THR 0 344 " (cutoff:3.500A) Processing helix chain '0' and resid 355 through 367 Processing helix chain '0' and resid 370 through 389 removed outlier: 3.638A pdb=" N LEU 0 374 " --> pdb=" O GLU 0 370 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS 0 377 " --> pdb=" O PRO 0 373 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 394 through 412 removed outlier: 5.117A pdb=" N ALA 0 398 " --> pdb=" O GLU 0 394 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU 0 399 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) Processing helix chain '0' and resid 441 through 453 removed outlier: 4.788A pdb=" N ALA 0 445 " --> pdb=" O ASP 0 441 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE 0 446 " --> pdb=" O ALA 0 442 " (cutoff:3.500A) Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 465 through 474 removed outlier: 4.448A pdb=" N TYR 0 469 " --> pdb=" O PRO 0 465 " (cutoff:3.500A) Proline residue: 0 470 - end of helix removed outlier: 4.489A pdb=" N ASN 0 474 " --> pdb=" O PRO 0 470 " (cutoff:3.500A) Processing helix chain '0' and resid 515 through 533 Processing helix chain '0' and resid 543 through 558 Processing helix chain '0' and resid 559 through 567 removed outlier: 3.730A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 593 Processing helix chain '0' and resid 604 through 610 removed outlier: 3.929A pdb=" N GLU 0 608 " --> pdb=" O GLY 0 604 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLY 0 609 " --> pdb=" O LYS 0 605 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE 0 610 " --> pdb=" O VAL 0 606 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 604 through 610' Processing helix chain '0' and resid 632 through 645 Processing helix chain '0' and resid 649 through 669 removed outlier: 3.967A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 685 through 690 removed outlier: 4.013A pdb=" N LYS 0 689 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG 0 690 " --> pdb=" O PHE 0 686 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 685 through 690' Processing helix chain '0' and resid 694 through 702 removed outlier: 5.039A pdb=" N SER 0 702 " --> pdb=" O ALA 0 698 " (cutoff:3.500A) Processing helix chain '0' and resid 709 through 726 removed outlier: 3.966A pdb=" N GLN 0 726 " --> pdb=" O ARG 0 722 " (cutoff:3.500A) Processing helix chain '0' and resid 729 through 734 Processing helix chain '0' and resid 740 through 752 Processing helix chain '1' and resid 93 through 121 Processing helix chain '1' and resid 170 through 177 Processing helix chain '1' and resid 178 through 189 removed outlier: 5.082A pdb=" N LYS 1 189 " --> pdb=" O LEU 1 185 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 198 removed outlier: 4.005A pdb=" N VAL 1 194 " --> pdb=" O VAL 1 190 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLU 1 197 " --> pdb=" O LYS 1 193 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR 1 198 " --> pdb=" O VAL 1 194 " (cutoff:3.500A) Processing helix chain '1' and resid 205 through 214 removed outlier: 4.036A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) Processing helix chain '1' and resid 215 through 226 removed outlier: 3.814A pdb=" N THR 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN 1 226 " --> pdb=" O LEU 1 222 " (cutoff:3.500A) Processing helix chain '1' and resid 232 through 238 removed outlier: 5.134A pdb=" N LYS 1 238 " --> pdb=" O LEU 1 234 " (cutoff:3.500A) Processing helix chain '1' and resid 252 through 263 Processing helix chain '1' and resid 264 through 276 removed outlier: 3.710A pdb=" N ASP 1 272 " --> pdb=" O LYS 1 268 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN 1 273 " --> pdb=" O ALA 1 269 " (cutoff:3.500A) Proline residue: 1 275 - end of helix Processing helix chain '1' and resid 279 through 290 Processing helix chain '1' and resid 291 through 298 Processing helix chain '1' and resid 309 through 330 removed outlier: 4.110A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR 1 314 " --> pdb=" O ILE 1 310 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU 1 315 " --> pdb=" O ILE 1 311 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR 1 316 " --> pdb=" O ASP 1 312 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU 1 317 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET 1 328 " --> pdb=" O LYS 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 347 removed outlier: 5.055A pdb=" N ASP 1 346 " --> pdb=" O ASN 1 342 " (cutoff:3.500A) Proline residue: 1 347 - end of helix Processing helix chain '1' and resid 355 through 360 removed outlier: 3.993A pdb=" N GLN 1 359 " --> pdb=" O ASP 1 355 " (cutoff:3.500A) Proline residue: 1 360 - end of helix No H-bonds generated for 'chain '1' and resid 355 through 360' Processing helix chain '1' and resid 370 through 391 removed outlier: 3.582A pdb=" N ILE 1 374 " --> pdb=" O GLY 1 370 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU 1 375 " --> pdb=" O THR 1 371 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU 1 389 " --> pdb=" O MET 1 385 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS 1 390 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN 1 391 " --> pdb=" O MET 1 387 " (cutoff:3.500A) Processing helix chain '1' and resid 413 through 420 removed outlier: 3.545A pdb=" N ASN 1 417 " --> pdb=" O ASN 1 413 " (cutoff:3.500A) Processing helix chain '1' and resid 421 through 426 removed outlier: 3.675A pdb=" N ASN 1 425 " --> pdb=" O ILE 1 421 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU 1 426 " --> pdb=" O ASP 1 422 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 421 through 426' Processing helix chain '1' and resid 465 through 483 removed outlier: 4.126A pdb=" N LYS 1 483 " --> pdb=" O ASN 1 479 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 490 removed outlier: 4.567A pdb=" N VAL 1 489 " --> pdb=" O ASP 1 485 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL 1 490 " --> pdb=" O LEU 1 486 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 485 through 490' Processing helix chain '1' and resid 492 through 515 removed outlier: 6.153A pdb=" N SER 1 496 " --> pdb=" O ASN 1 492 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN 1 497 " --> pdb=" O ASN 1 493 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 571 removed outlier: 4.522A pdb=" N GLY 1 571 " --> pdb=" O HIS 1 567 " (cutoff:3.500A) Processing helix chain '1' and resid 572 through 604 removed outlier: 3.998A pdb=" N ALA 1 576 " --> pdb=" O GLU 1 572 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SER 1 577 " --> pdb=" O GLN 1 573 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N THR 1 578 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) Processing helix chain '1' and resid 605 through 617 removed outlier: 6.385A pdb=" N SER 1 609 " --> pdb=" O GLY 1 605 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN 1 610 " --> pdb=" O GLU 1 606 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N THR 1 611 " --> pdb=" O SER 1 607 " (cutoff:3.500A) Processing helix chain '1' and resid 618 through 639 Processing helix chain '2' and resid 5 through 18 removed outlier: 3.932A pdb=" N SER 2 9 " --> pdb=" O SER 2 5 " (cutoff:3.500A) Proline residue: 2 18 - end of helix Processing helix chain '2' and resid 19 through 28 removed outlier: 4.046A pdb=" N THR 2 27 " --> pdb=" O ASN 2 23 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 40 removed outlier: 3.582A pdb=" N LEU 2 39 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) Proline residue: 2 40 - end of helix Processing helix chain '2' and resid 41 through 52 removed outlier: 4.397A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 58 through 67 removed outlier: 3.729A pdb=" N LEU 2 62 " --> pdb=" O PRO 2 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASN 2 67 " --> pdb=" O ASP 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 85 Processing helix chain '2' and resid 101 through 114 Processing helix chain '2' and resid 134 through 152 Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 185 through 195 removed outlier: 5.498A pdb=" N GLU 2 195 " --> pdb=" O PHE 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 196 through 212 removed outlier: 5.503A pdb=" N GLU 2 212 " --> pdb=" O LEU 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 217 through 232 removed outlier: 5.461A pdb=" N GLU 2 232 " --> pdb=" O LEU 2 228 " (cutoff:3.500A) Processing helix chain '2' and resid 238 through 243 removed outlier: 5.177A pdb=" N LEU 2 242 " --> pdb=" O LYS 2 238 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER 2 243 " --> pdb=" O ILE 2 239 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 238 through 243' Processing helix chain '2' and resid 244 through 257 Processing helix chain '2' and resid 272 through 281 removed outlier: 3.661A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER 2 280 " --> pdb=" O LEU 2 276 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP 2 281 " --> pdb=" O MET 2 277 " (cutoff:3.500A) Processing helix chain '2' and resid 353 through 364 removed outlier: 4.461A pdb=" N PHE 2 363 " --> pdb=" O VAL 2 359 " (cutoff:3.500A) Processing helix chain '2' and resid 379 through 390 Processing helix chain '2' and resid 392 through 404 Processing helix chain '2' and resid 405 through 423 Processing helix chain '2' and resid 434 through 450 Processing helix chain '2' and resid 464 through 479 removed outlier: 3.722A pdb=" N TYR 2 468 " --> pdb=" O THR 2 464 " (cutoff:3.500A) Processing helix chain '2' and resid 494 through 507 removed outlier: 4.506A pdb=" N SER 2 499 " --> pdb=" O LYS 2 495 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN 2 500 " --> pdb=" O GLU 2 496 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL 2 501 " --> pdb=" O GLY 2 497 " (cutoff:3.500A) Processing helix chain '3' and resid 39 through 50 removed outlier: 4.047A pdb=" N SER 3 48 " --> pdb=" O ASP 3 44 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU 3 49 " --> pdb=" O ARG 3 45 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY 3 50 " --> pdb=" O ILE 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 75 through 93 removed outlier: 4.913A pdb=" N VAL 3 91 " --> pdb=" O ARG 3 87 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN 3 93 " --> pdb=" O PHE 3 89 " (cutoff:3.500A) Processing helix chain '3' and resid 95 through 100 Processing helix chain '3' and resid 102 through 123 Processing helix chain '3' and resid 125 through 139 removed outlier: 4.346A pdb=" N LEU 3 139 " --> pdb=" O THR 3 135 " (cutoff:3.500A) Processing helix chain '4' and resid 33 through 45 removed outlier: 4.765A pdb=" N ASN 4 45 " --> pdb=" O ASP 4 41 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 69 removed outlier: 3.919A pdb=" N LYS 4 52 " --> pdb=" O GLY 4 48 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN 4 68 " --> pdb=" O HIS 4 64 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER 4 69 " --> pdb=" O LEU 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 90 through 97 Processing helix chain '4' and resid 116 through 140 removed outlier: 4.323A pdb=" N VAL 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 167 Processing helix chain '4' and resid 189 through 207 removed outlier: 4.271A pdb=" N TYR 4 193 " --> pdb=" O GLU 4 189 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE 4 194 " --> pdb=" O ILE 4 190 " (cutoff:3.500A) Proline residue: 4 195 - end of helix Processing helix chain '4' and resid 221 through 232 Processing helix chain '4' and resid 243 through 251 removed outlier: 3.678A pdb=" N TYR 4 247 " --> pdb=" O GLY 4 243 " (cutoff:3.500A) Processing helix chain '4' and resid 255 through 260 Proline residue: 4 260 - end of helix Processing helix chain '4' and resid 313 through 322 Processing helix chain '5' and resid 13 through 28 Processing helix chain '5' and resid 46 through 63 removed outlier: 4.100A pdb=" N LYS 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASN 5 61 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE 5 62 " --> pdb=" O LEU 5 58 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR 5 63 " --> pdb=" O SER 5 59 " (cutoff:3.500A) Processing helix chain '6' and resid 82 through 87 removed outlier: 3.946A pdb=" N VAL 6 87 " --> pdb=" O SER 6 83 " (cutoff:3.500A) Processing helix chain '6' and resid 96 through 114 removed outlier: 3.866A pdb=" N GLU 6 104 " --> pdb=" O ALA 6 100 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ASN 6 114 " --> pdb=" O THR 6 110 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 4.221A pdb=" N LEU 6 137 " --> pdb=" O SER 6 133 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU 6 138 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 133 through 138' Processing helix chain '6' and resid 144 through 164 Processing helix chain '6' and resid 188 through 203 removed outlier: 3.892A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS 6 201 " --> pdb=" O LYS 6 197 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN 6 202 " --> pdb=" O SER 6 198 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU 6 203 " --> pdb=" O ILE 6 199 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 225 Proline residue: 6 223 - end of helix Processing helix chain '6' and resid 246 through 258 removed outlier: 3.959A pdb=" N THR 6 250 " --> pdb=" O ASP 6 246 " (cutoff:3.500A) Processing helix chain '6' and resid 270 through 282 Processing helix chain '6' and resid 293 through 306 removed outlier: 3.910A pdb=" N VAL 6 305 " --> pdb=" O PHE 6 301 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR 6 306 " --> pdb=" O ASN 6 302 " (cutoff:3.500A) Processing helix chain '6' and resid 372 through 385 removed outlier: 4.752A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) Proline residue: 6 385 - end of helix Processing helix chain '6' and resid 437 through 446 removed outlier: 3.520A pdb=" N HIS 6 445 " --> pdb=" O ASP 6 441 " (cutoff:3.500A) Processing helix chain '6' and resid 451 through 458 Proline residue: 6 458 - end of helix Processing helix chain '6' and resid 284 through 289 removed outlier: 4.141A pdb=" N PHE 6 287 " --> pdb=" O ASP 6 284 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR 6 288 " --> pdb=" O GLU 6 285 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LYS 6 289 " --> pdb=" O SER 6 286 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 284 through 289' Processing helix chain '7' and resid 109 through 114 removed outlier: 4.835A pdb=" N PHE 7 113 " --> pdb=" O VAL 7 109 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ARG 7 114 " --> pdb=" O SER 7 110 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 109 through 114' Processing helix chain '7' and resid 126 through 131 removed outlier: 3.712A pdb=" N ARG 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) Proline residue: 7 131 - end of helix No H-bonds generated for 'chain '7' and resid 126 through 131' Processing helix chain '7' and resid 149 through 161 removed outlier: 3.583A pdb=" N ALA 7 153 " --> pdb=" O LEU 7 149 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 176 through 187 Processing helix chain '7' and resid 189 through 201 Processing helix chain '7' and resid 206 through 218 Processing helix chain '7' and resid 238 through 246 removed outlier: 4.316A pdb=" N LEU 7 242 " --> pdb=" O GLN 7 238 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN 7 243 " --> pdb=" O ALA 7 239 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU 7 245 " --> pdb=" O ILE 7 241 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU 7 246 " --> pdb=" O LEU 7 242 " (cutoff:3.500A) Processing helix chain '7' and resid 322 through 334 removed outlier: 4.579A pdb=" N ASP 7 334 " --> pdb=" O CYS 7 330 " (cutoff:3.500A) Processing helix chain '7' and resid 342 through 347 removed outlier: 5.625A pdb=" N HIS 7 347 " --> pdb=" O PHE 7 343 " (cutoff:3.500A) Processing helix chain '7' and resid 363 through 375 Processing helix chain '7' and resid 391 through 404 Processing helix chain '7' and resid 413 through 428 Processing helix chain '7' and resid 431 through 436 removed outlier: 5.036A pdb=" N ALA 7 436 " --> pdb=" O PRO 7 432 " (cutoff:3.500A) Processing helix chain '7' and resid 456 through 462 Processing helix chain '7' and resid 467 through 481 removed outlier: 5.357A pdb=" N GLU 7 481 " --> pdb=" O LEU 7 477 " (cutoff:3.500A) Processing helix chain '7' and resid 489 through 494 removed outlier: 4.369A pdb=" N VAL 7 493 " --> pdb=" O GLU 7 489 " (cutoff:3.500A) Proline residue: 7 494 - end of helix No H-bonds generated for 'chain '7' and resid 489 through 494' Processing helix chain '7' and resid 496 through 504 removed outlier: 5.295A pdb=" N ARG 7 500 " --> pdb=" O ALA 7 496 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL 7 501 " --> pdb=" O MET 7 497 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL 7 502 " --> pdb=" O PHE 7 498 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER 7 503 " --> pdb=" O ARG 7 499 " (cutoff:3.500A) Processing helix chain '7' and resid 525 through 531 removed outlier: 4.628A pdb=" N PHE 7 529 " --> pdb=" O GLY 7 525 " (cutoff:3.500A) Processing helix chain '7' and resid 539 through 547 Processing helix chain '7' and resid 562 through 572 removed outlier: 3.559A pdb=" N GLU 7 572 " --> pdb=" O GLU 7 568 " (cutoff:3.500A) Processing helix chain '7' and resid 573 through 584 removed outlier: 3.697A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN 7 584 " --> pdb=" O LEU 7 580 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 602 Processing helix chain '7' and resid 611 through 623 Processing helix chain '7' and resid 632 through 646 Processing helix chain '7' and resid 655 through 661 removed outlier: 4.417A pdb=" N ASP 7 659 " --> pdb=" O SER 7 655 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR 7 660 " --> pdb=" O LYS 7 656 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER 7 661 " --> pdb=" O VAL 7 657 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 655 through 661' Processing helix chain '7' and resid 679 through 692 removed outlier: 3.959A pdb=" N ILE 7 690 " --> pdb=" O ARG 7 686 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG 7 692 " --> pdb=" O GLY 7 688 " (cutoff:3.500A) Processing helix chain '7' and resid 713 through 727 removed outlier: 4.053A pdb=" N TYR 7 717 " --> pdb=" O THR 7 713 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE 7 725 " --> pdb=" O LYS 7 721 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU 7 726 " --> pdb=" O ARG 7 722 " (cutoff:3.500A) Processing helix chain '7' and resid 752 through 767 removed outlier: 4.257A pdb=" N ASN 7 767 " --> pdb=" O VAL 7 763 " (cutoff:3.500A) Processing helix chain '7' and resid 830 through 835 removed outlier: 4.744A pdb=" N ARG 7 834 " --> pdb=" O HIS 7 830 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS 7 835 " --> pdb=" O PRO 7 831 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 830 through 835' Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 107 removed outlier: 5.027A pdb=" N CYS A 107 " --> pdb=" O CYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 removed outlier: 4.060A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 230 through 236 removed outlier: 4.076A pdb=" N MET A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 236' Processing helix chain 'A' and resid 243 through 248 Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 367 through 375 removed outlier: 5.232A pdb=" N THR A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.124A pdb=" N SER A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ALA A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.173A pdb=" N MET A 455 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.967A pdb=" N THR A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Proline residue: A 477 - end of helix No H-bonds generated for 'chain 'A' and resid 471 through 479' Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.725A pdb=" N ILE A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL A 512 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 542 through 554 Proline residue: A 554 - end of helix Processing helix chain 'A' and resid 573 through 583 removed outlier: 3.674A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 671 removed outlier: 4.141A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA A 671 " --> pdb=" O GLY A 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 671' Processing helix chain 'A' and resid 672 through 700 Processing helix chain 'A' and resid 709 through 738 removed outlier: 5.383A pdb=" N LYS A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 762 Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 846 Processing helix chain 'A' and resid 874 through 879 removed outlier: 3.869A pdb=" N ILE A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLU A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 874 through 879' Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.140A pdb=" N GLY A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLY A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 888' Processing helix chain 'A' and resid 889 through 897 Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.409A pdb=" N LEU A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU A 914 " --> pdb=" O PRO A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 914' Processing helix chain 'A' and resid 915 through 920 removed outlier: 4.321A pdb=" N ILE A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 922 through 948 removed outlier: 4.129A pdb=" N GLN A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 998 removed outlier: 5.561A pdb=" N LEU A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1016 Processing helix chain 'A' and resid 1017 through 1027 removed outlier: 3.764A pdb=" N ALA A1027 " --> pdb=" O ARG A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1038 through 1058 removed outlier: 6.115A pdb=" N VAL A1058 " --> pdb=" O LEU A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix removed outlier: 3.637A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1107 removed outlier: 4.677A pdb=" N VAL A1107 " --> pdb=" O GLU A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1147 removed outlier: 3.918A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1177 removed outlier: 3.775A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1251 through 1270 removed outlier: 3.972A pdb=" N GLU A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N HIS A1258 " --> pdb=" O ALA A1254 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1319 removed outlier: 4.009A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.647A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.948A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1403 removed outlier: 3.777A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 4.292A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.619A pdb=" N GLY A 342 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 41 removed outlier: 3.767A pdb=" N SER B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 67 removed outlier: 4.682A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.780A pdb=" N GLU B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 185' Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 370 through 391 Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.774A pdb=" N LYS B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ARG B 405 " --> pdb=" O PHE B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 405' Processing helix chain 'B' and resid 410 through 439 Processing helix chain 'B' and resid 443 through 464 removed outlier: 4.891A pdb=" N ASN B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ALA B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N LYS B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 565 through 570 removed outlier: 3.740A pdb=" N TYR B 569 " --> pdb=" O PRO B 565 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 565 through 570' Processing helix chain 'B' and resid 592 through 607 removed outlier: 3.894A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 694 through 702 removed outlier: 3.642A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 701 " --> pdb=" O GLU B 697 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 4.652A pdb=" N ILE B 748 " --> pdb=" O HIS B 744 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 744 through 749' Processing helix chain 'B' and resid 750 through 757 removed outlier: 3.621A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Proline residue: B 757 - end of helix Processing helix chain 'B' and resid 758 through 763 removed outlier: 3.838A pdb=" N ASN B 762 " --> pdb=" O PHE B 758 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLN B 763 " --> pdb=" O PRO B 759 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 758 through 763' Processing helix chain 'B' and resid 764 through 777 removed outlier: 4.564A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 777 " --> pdb=" O MET B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 789 removed outlier: 5.151A pdb=" N MET B 789 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 813 removed outlier: 4.535A pdb=" N GLU B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 849 Processing helix chain 'B' and resid 995 through 1000 Proline residue: B1000 - end of helix Processing helix chain 'B' and resid 1013 through 1021 removed outlier: 4.378A pdb=" N ILE B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.900A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1063 Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.530A pdb=" N LYS B1102 " --> pdb=" O MET B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1211 Processing helix chain 'C' and resid 26 through 39 Processing helix chain 'C' and resid 59 through 71 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.592A pdb=" N LEU C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 76 through 81' Processing helix chain 'C' and resid 82 through 87 removed outlier: 5.379A pdb=" N PHE C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 removed outlier: 4.403A pdb=" N GLY C 171 " --> pdb=" O HIS C 167 " (cutoff:3.500A) Proline residue: C 172 - end of helix No H-bonds generated for 'chain 'C' and resid 167 through 172' Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 211 removed outlier: 4.014A pdb=" N GLU C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ASP C 211 " --> pdb=" O CYS C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 211' Processing helix chain 'C' and resid 239 through 268 removed outlier: 3.676A pdb=" N ASP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.519A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.849A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 196 Proline residue: D 196 - end of helix Processing helix chain 'D' and resid 203 through 219 removed outlier: 5.633A pdb=" N THR D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'E' and resid 31 through 37 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 4.210A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 73 Proline residue: E 73 - end of helix Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 125 removed outlier: 4.668A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 25 through 33 Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 69 through 74 removed outlier: 4.389A pdb=" N ALA F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE F 74 " --> pdb=" O LYS F 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 69 through 74' Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'F' and resid 147 through 152 removed outlier: 5.435A pdb=" N ILE F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 19 removed outlier: 4.387A pdb=" N PHE G 18 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLY G 19 " --> pdb=" O PRO G 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 14 through 19' Processing helix chain 'G' and resid 21 through 37 removed outlier: 7.847A pdb=" N GLY G 36 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER G 37 " --> pdb=" O GLU G 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 48 Proline residue: H 48 - end of helix Processing helix chain 'H' and resid 88 through 94 removed outlier: 4.741A pdb=" N ASP H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYR H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASP H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 94' Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.568A pdb=" N LEU H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.614A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 63 removed outlier: 4.352A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 11 removed outlier: 4.493A pdb=" N LEU K 9 " --> pdb=" O ASP K 5 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE K 10 " --> pdb=" O ARG K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 54 removed outlier: 3.929A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG K 54 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 5.077A pdb=" N THR K 113 " --> pdb=" O TRP K 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 117 removed outlier: 3.756A pdb=" N THR M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN M 114 " --> pdb=" O LEU M 110 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN M 117 " --> pdb=" O ALA M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 141 Processing helix chain 'M' and resid 143 through 158 Processing helix chain 'M' and resid 167 through 184 Processing helix chain 'M' and resid 188 through 197 removed outlier: 4.199A pdb=" N HIS M 197 " --> pdb=" O GLN M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 221 Processing helix chain 'M' and resid 234 through 247 removed outlier: 3.776A pdb=" N TYR M 238 " --> pdb=" O GLN M 234 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE M 239 " --> pdb=" O ASN M 235 " (cutoff:3.500A) Proline residue: M 240 - end of helix Processing helix chain 'M' and resid 249 through 267 removed outlier: 3.924A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS M 267 " --> pdb=" O CYS M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 290 Processing helix chain 'M' and resid 294 through 303 Processing helix chain 'M' and resid 305 through 320 removed outlier: 4.631A pdb=" N GLU M 318 " --> pdb=" O LYS M 314 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N HIS M 319 " --> pdb=" O ILE M 315 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG M 320 " --> pdb=" O LEU M 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 332 removed outlier: 3.760A pdb=" N ILE M 329 " --> pdb=" O ASP M 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 147 Processing helix chain 'O' and resid 171 through 180 Processing helix chain 'O' and resid 219 through 235 removed outlier: 3.876A pdb=" N ILE O 223 " --> pdb=" O GLN O 219 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N GLN O 225 " --> pdb=" O GLU O 221 " (cutoff:3.500A) Proline residue: O 232 - end of helix Processing helix chain 'Q' and resid 23 through 35 removed outlier: 4.670A pdb=" N MET Q 27 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 112 removed outlier: 4.008A pdb=" N LEU Q 111 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 107 through 112' Processing helix chain 'Q' and resid 152 through 168 Processing helix chain 'Q' and resid 336 through 347 Processing helix chain 'Q' and resid 405 through 415 removed outlier: 5.881A pdb=" N LYS Q 415 " --> pdb=" O LYS Q 411 " (cutoff:3.500A) Processing helix chain 'Q' and resid 423 through 432 Processing helix chain 'Q' and resid 436 through 451 removed outlier: 4.500A pdb=" N GLN Q 451 " --> pdb=" O ALA Q 447 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 removed outlier: 3.888A pdb=" N PHE Q 133 " --> pdb=" O ASN Q 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 128 through 133' Processing helix chain 'R' and resid 47 through 53 removed outlier: 4.625A pdb=" N LYS R 51 " --> pdb=" O ASN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 82 Processing helix chain 'R' and resid 232 through 246 removed outlier: 3.761A pdb=" N VAL R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 265 removed outlier: 4.781A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 287 removed outlier: 3.684A pdb=" N LYS R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N SER R 287 " --> pdb=" O GLU R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 311 removed outlier: 3.811A pdb=" N ASP R 311 " --> pdb=" O PHE R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 323 Processing helix chain 'R' and resid 325 through 337 removed outlier: 4.265A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 352 through 358 removed outlier: 3.991A pdb=" N LYS R 357 " --> pdb=" O PRO R 353 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU R 358 " --> pdb=" O GLU R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 66 removed outlier: 4.336A pdb=" N ASN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 29 removed outlier: 4.662A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 50 removed outlier: 4.913A pdb=" N LEU U 35 " --> pdb=" O ASP U 31 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN U 36 " --> pdb=" O GLU U 32 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP U 37 " --> pdb=" O GLN U 33 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS U 50 " --> pdb=" O LEU U 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 30 removed outlier: 4.157A pdb=" N THR V 25 " --> pdb=" O ASP V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 55 removed outlier: 4.688A pdb=" N LYS V 53 " --> pdb=" O ALA V 49 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP V 54 " --> pdb=" O GLU V 50 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN V 55 " --> pdb=" O THR V 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 20 Processing helix chain 'W' and resid 22 through 36 removed outlier: 4.039A pdb=" N SER W 36 " --> pdb=" O ILE W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 47 Processing helix chain 'W' and resid 52 through 65 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 90 through 119 Proline residue: W 119 - end of helix Processing helix chain 'W' and resid 132 through 140 removed outlier: 3.766A pdb=" N VAL W 137 " --> pdb=" O GLN W 133 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 180 removed outlier: 4.049A pdb=" N LYS W 164 " --> pdb=" O ASP W 160 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN W 165 " --> pdb=" O SER W 161 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS W 166 " --> pdb=" O GLY W 162 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU W 167 " --> pdb=" O LYS W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 181 through 193 removed outlier: 4.803A pdb=" N ARG W 193 " --> pdb=" O ILE W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 206 removed outlier: 4.321A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG W 205 " --> pdb=" O ILE W 201 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU W 206 " --> pdb=" O ALA W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 289 removed outlier: 6.529A pdb=" N GLU W 270 " --> pdb=" O THR W 266 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL W 271 " --> pdb=" O ALA W 267 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA W 272 " --> pdb=" O SER W 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 291 through 296 Processing helix chain 'W' and resid 349 through 369 Processing helix chain 'X' and resid 106 through 116 removed outlier: 4.240A pdb=" N GLN X 116 " --> pdb=" O LEU X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 139 removed outlier: 4.415A pdb=" N LYS X 127 " --> pdb=" O HIS X 123 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY X 139 " --> pdb=" O ILE X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 152 removed outlier: 3.649A pdb=" N LEU X 147 " --> pdb=" O LEU X 143 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 167 removed outlier: 4.142A pdb=" N GLU X 161 " --> pdb=" O ASP X 157 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP X 167 " --> pdb=" O LEU X 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 199 Processing helix chain 'X' and resid 206 through 214 removed outlier: 3.967A pdb=" N LEU X 210 " --> pdb=" O SER X 206 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP X 212 " --> pdb=" O LYS X 208 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLY X 213 " --> pdb=" O ASP X 209 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TRP X 214 " --> pdb=" O LEU X 210 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 228 removed outlier: 5.654A pdb=" N THR X 220 " --> pdb=" O GLN X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 266 removed outlier: 4.388A pdb=" N VAL X 266 " --> pdb=" O MET X 262 " (cutoff:3.500A) Processing helix chain 'X' and resid 272 through 282 removed outlier: 4.662A pdb=" N ARG X 276 " --> pdb=" O ALA X 272 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLN X 279 " --> pdb=" O PRO X 275 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP X 280 " --> pdb=" O ARG X 276 " (cutoff:3.500A) Processing helix chain 'X' and resid 290 through 295 removed outlier: 4.578A pdb=" N LYS X 294 " --> pdb=" O PRO X 290 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG X 295 " --> pdb=" O ALA X 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 290 through 295' Processing helix chain 'a' and resid 13 through 20 Processing helix chain 'a' and resid 23 through 35 removed outlier: 3.629A pdb=" N VAL a 27 " --> pdb=" O ARG a 23 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU a 28 " --> pdb=" O THR a 24 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP a 29 " --> pdb=" O GLU a 25 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU a 33 " --> pdb=" O ASP a 29 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER a 34 " --> pdb=" O TYR a 30 " (cutoff:3.500A) Proline residue: a 35 - end of helix Processing helix chain 'a' and resid 41 through 52 Processing helix chain 'a' and resid 87 through 98 removed outlier: 3.588A pdb=" N ILE a 93 " --> pdb=" O ALA a 89 " (cutoff:3.500A) Proline residue: a 98 - end of helix Processing helix chain 'a' and resid 99 through 111 removed outlier: 4.213A pdb=" N LYS a 109 " --> pdb=" O GLU a 105 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP a 111 " --> pdb=" O LEU a 107 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 193 removed outlier: 3.802A pdb=" N LEU a 191 " --> pdb=" O SER a 187 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE a 192 " --> pdb=" O LEU a 188 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLU a 193 " --> pdb=" O TYR a 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 288 Processing helix chain 'b' and resid 30 through 56 removed outlier: 5.163A pdb=" N LYS b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 87 Processing helix chain 'b' and resid 88 through 93 removed outlier: 5.968A pdb=" N SER b 92 " --> pdb=" O GLU b 88 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR b 93 " --> pdb=" O THR b 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 88 through 93' Processing helix chain 'b' and resid 106 through 115 Processing helix chain 'b' and resid 119 through 134 removed outlier: 4.663A pdb=" N GLY b 134 " --> pdb=" O ARG b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 171 removed outlier: 3.713A pdb=" N HIS b 170 " --> pdb=" O GLU b 166 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP b 171 " --> pdb=" O TYR b 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 197 through 207 Processing helix chain 'c' and resid 3 through 40 removed outlier: 4.077A pdb=" N LEU c 24 " --> pdb=" O LEU c 20 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN c 25 " --> pdb=" O CYS c 21 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 77 removed outlier: 3.841A pdb=" N VAL c 77 " --> pdb=" O LEU c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 92 through 111 Proline residue: c 111 - end of helix Processing helix chain 'd' and resid 89 through 98 removed outlier: 3.674A pdb=" N ILE d 93 " --> pdb=" O ASN d 89 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR d 94 " --> pdb=" O PRO d 90 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER d 96 " --> pdb=" O GLU d 92 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET d 97 " --> pdb=" O ILE d 93 " (cutoff:3.500A) Proline residue: d 98 - end of helix Processing helix chain 'd' and resid 99 through 111 Proline residue: d 104 - end of helix Processing helix chain 'd' and resid 120 through 130 removed outlier: 3.879A pdb=" N LYS d 129 " --> pdb=" O GLN d 125 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN d 130 " --> pdb=" O ASN d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 233 removed outlier: 3.917A pdb=" N SER d 231 " --> pdb=" O LEU d 227 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL d 232 " --> pdb=" O LEU d 228 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 241 removed outlier: 4.922A pdb=" N MET d 238 " --> pdb=" O GLU d 234 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER d 239 " --> pdb=" O SER d 235 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER d 240 " --> pdb=" O THR d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 242 through 249 Processing helix chain 'd' and resid 265 through 316 Processing helix chain 'd' and resid 424 through 453 removed outlier: 3.852A pdb=" N ALA d 450 " --> pdb=" O LYS d 446 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU d 451 " --> pdb=" O LYS d 447 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU d 452 " --> pdb=" O GLU d 448 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE d 453 " --> pdb=" O CYS d 449 " (cutoff:3.500A) Processing helix chain 'd' and resid 497 through 526 Processing helix chain 'd' and resid 540 through 570 Proline residue: d 544 - end of helix removed outlier: 4.200A pdb=" N ASP d 568 " --> pdb=" O ASP d 564 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE d 569 " --> pdb=" O TYR d 565 " (cutoff:3.500A) Processing helix chain 'd' and resid 593 through 611 removed outlier: 4.359A pdb=" N PHE d 606 " --> pdb=" O GLU d 602 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS d 608 " --> pdb=" O ARG d 604 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU d 609 " --> pdb=" O ALA d 605 " (cutoff:3.500A) Processing helix chain 'd' and resid 666 through 681 removed outlier: 3.983A pdb=" N VAL d 670 " --> pdb=" O ASP d 666 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP d 672 " --> pdb=" O LYS d 668 " (cutoff:3.500A) Processing helix chain 'd' and resid 534 through 539 removed outlier: 3.761A pdb=" N ILE d 539 " --> pdb=" O ASN d 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 534 through 539' Processing helix chain 'e' and resid 12 through 28 removed outlier: 3.605A pdb=" N TYR e 16 " --> pdb=" O GLY e 12 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP e 17 " --> pdb=" O ASP e 13 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU e 18 " --> pdb=" O ASP e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 77 removed outlier: 3.741A pdb=" N LEU e 75 " --> pdb=" O PRO e 71 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ASP e 77 " --> pdb=" O SER e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 94 removed outlier: 4.800A pdb=" N LEU e 90 " --> pdb=" O ASN e 86 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS e 91 " --> pdb=" O PHE e 87 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER e 92 " --> pdb=" O ARG e 88 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE e 93 " --> pdb=" O ILE e 89 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N THR e 94 " --> pdb=" O LEU e 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 86 through 94' Processing helix chain 'e' and resid 101 through 111 Processing helix chain 'e' and resid 199 through 208 Processing helix chain 'e' and resid 264 through 283 Processing helix chain 'e' and resid 292 through 297 Processing helix chain 'f' and resid 15 through 25 Processing helix chain 'f' and resid 88 through 95 removed outlier: 3.814A pdb=" N VAL f 92 " --> pdb=" O PRO f 88 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY f 95 " --> pdb=" O LEU f 91 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 111 Processing helix chain 'f' and resid 162 through 178 removed outlier: 5.586A pdb=" N LYS f 166 " --> pdb=" O GLU f 162 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG f 178 " --> pdb=" O LEU f 174 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 210 removed outlier: 5.300A pdb=" N LEU f 210 " --> pdb=" O ARG f 206 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 29 removed outlier: 4.253A pdb=" N LEU g 21 " --> pdb=" O LEU g 17 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA g 22 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR g 28 " --> pdb=" O LEU g 24 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N THR g 29 " --> pdb=" O ILE g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 86 removed outlier: 3.729A pdb=" N VAL g 58 " --> pdb=" O SER g 54 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR g 62 " --> pdb=" O VAL g 58 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET g 63 " --> pdb=" O ASN g 59 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN g 64 " --> pdb=" O ASN g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 117 Processing helix chain 'h' and resid 40 through 63 removed outlier: 4.396A pdb=" N GLU h 44 " --> pdb=" O VAL h 40 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP h 45 " --> pdb=" O GLN h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 66 through 75 removed outlier: 3.837A pdb=" N ALA h 70 " --> pdb=" O ASN h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 127 removed outlier: 3.684A pdb=" N ASN h 92 " --> pdb=" O ALA h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 148 removed outlier: 3.520A pdb=" N ARG h 145 " --> pdb=" O ILE h 141 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER h 146 " --> pdb=" O LEU h 142 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS h 147 " --> pdb=" O GLN h 143 " (cutoff:3.500A) Processing helix chain 'h' and resid 149 through 162 removed outlier: 4.845A pdb=" N LYS h 162 " --> pdb=" O THR h 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 171 through 176 removed outlier: 6.868A pdb=" N VAL h 175 " --> pdb=" O ASP h 171 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY h 176 " --> pdb=" O LYS h 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 171 through 176' Processing helix chain 'h' and resid 184 through 191 Processing helix chain 'h' and resid 192 through 200 Processing helix chain 'i' and resid 17 through 24 removed outlier: 4.853A pdb=" N LYS i 21 " --> pdb=" O PRO i 17 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE i 22 " --> pdb=" O PRO i 18 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE i 23 " --> pdb=" O TYR i 19 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N THR i 24 " --> pdb=" O VAL i 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 17 through 24' Processing helix chain 'i' and resid 25 through 37 Proline residue: i 32 - end of helix removed outlier: 3.526A pdb=" N LYS i 37 " --> pdb=" O LYS i 33 " (cutoff:3.500A) Processing helix chain 'i' and resid 60 through 67 removed outlier: 4.779A pdb=" N TYR i 64 " --> pdb=" O CYS i 60 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU i 65 " --> pdb=" O ALA i 61 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE i 66 " --> pdb=" O LEU i 62 " (cutoff:3.500A) Proline residue: i 67 - end of helix No H-bonds generated for 'chain 'i' and resid 60 through 67' Processing helix chain 'i' and resid 91 through 96 Processing helix chain 'i' and resid 112 through 140 Processing helix chain 'i' and resid 145 through 150 Processing helix chain 'i' and resid 152 through 157 Processing helix chain 'i' and resid 164 through 214 removed outlier: 4.698A pdb=" N HIS i 168 " --> pdb=" O GLU i 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 16 Processing helix chain 'j' and resid 64 through 80 removed outlier: 6.752A pdb=" N HIS j 68 " --> pdb=" O GLU j 64 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS j 78 " --> pdb=" O HIS j 74 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP j 79 " --> pdb=" O GLN j 75 " (cutoff:3.500A) Proline residue: j 80 - end of helix Processing helix chain 'j' and resid 89 through 109 removed outlier: 4.791A pdb=" N SER j 93 " --> pdb=" O THR j 89 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE j 94 " --> pdb=" O LEU j 90 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN j 108 " --> pdb=" O LEU j 104 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLU j 109 " --> pdb=" O ILE j 105 " (cutoff:3.500A) Processing helix chain 'j' and resid 110 through 117 removed outlier: 3.806A pdb=" N SER j 116 " --> pdb=" O LYS j 112 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS j 117 " --> pdb=" O ASP j 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 118 through 148 removed outlier: 4.200A pdb=" N GLN j 131 " --> pdb=" O HIS j 127 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLU j 132 " --> pdb=" O GLN j 128 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU j 133 " --> pdb=" O ARG j 129 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU j 143 " --> pdb=" O VAL j 139 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR j 144 " --> pdb=" O LEU j 140 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ARG j 145 " --> pdb=" O ASP j 141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN j 148 " --> pdb=" O TYR j 144 " (cutoff:3.500A) Processing helix chain 'k' and resid 1 through 39 Processing helix chain 'k' and resid 42 through 69 Processing helix chain 'k' and resid 73 through 78 removed outlier: 5.922A pdb=" N ASP k 78 " --> pdb=" O LEU k 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 80 through 90 removed outlier: 3.935A pdb=" N VAL k 84 " --> pdb=" O PRO k 80 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY k 90 " --> pdb=" O TYR k 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 133 removed outlier: 3.743A pdb=" N TYR k 96 " --> pdb=" O ASN k 92 " (cutoff:3.500A) Processing helix chain 'k' and resid 136 through 149 Proline residue: k 149 - end of helix Processing helix chain 'l' and resid 91 through 115 Processing helix chain 'l' and resid 122 through 155 removed outlier: 3.989A pdb=" N ILE l 154 " --> pdb=" O TRP l 150 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS l 155 " --> pdb=" O THR l 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 158 through 194 removed outlier: 4.164A pdb=" N VAL l 176 " --> pdb=" O THR l 172 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN l 177 " --> pdb=" O ASN l 173 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET l 190 " --> pdb=" O SER l 186 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR l 191 " --> pdb=" O LEU l 187 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN l 192 " --> pdb=" O ASN l 188 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA l 193 " --> pdb=" O SER l 189 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS l 194 " --> pdb=" O MET l 190 " (cutoff:3.500A) Processing helix chain 'l' and resid 199 through 209 Processing helix chain 'l' and resid 238 through 261 removed outlier: 3.658A pdb=" N ALA l 258 " --> pdb=" O SER l 254 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU l 259 " --> pdb=" O ILE l 255 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET l 260 " --> pdb=" O LYS l 256 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASN l 261 " --> pdb=" O ILE l 257 " (cutoff:3.500A) Processing helix chain 'l' and resid 344 through 359 Processing helix chain 'l' and resid 361 through 390 removed outlier: 3.875A pdb=" N ALA l 390 " --> pdb=" O PHE l 386 " (cutoff:3.500A) Processing helix chain 'l' and resid 396 through 401 removed outlier: 3.970A pdb=" N LEU l 400 " --> pdb=" O SER l 396 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE l 401 " --> pdb=" O LYS l 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 396 through 401' Processing helix chain 'l' and resid 444 through 450 Processing helix chain 'l' and resid 463 through 487 Processing helix chain 'l' and resid 530 through 543 removed outlier: 6.995A pdb=" N ASN l 535 " --> pdb=" O PRO l 531 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR l 536 " --> pdb=" O LEU l 532 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER l 538 " --> pdb=" O SER l 534 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA l 543 " --> pdb=" O LYS l 539 " (cutoff:3.500A) Processing helix chain 'l' and resid 545 through 571 removed outlier: 3.681A pdb=" N ILE l 561 " --> pdb=" O LYS l 557 " (cutoff:3.500A) Processing helix chain 'l' and resid 679 through 684 removed outlier: 5.784A pdb=" N THR l 684 " --> pdb=" O LEU l 680 " (cutoff:3.500A) Processing helix chain 'l' and resid 685 through 703 removed outlier: 3.814A pdb=" N LEU l 696 " --> pdb=" O GLN l 692 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASN l 697 " --> pdb=" O ARG l 693 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET l 703 " --> pdb=" O ILE l 699 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 3.515A pdb=" N ASN l 267 " --> pdb=" O LYS l 264 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER l 268 " --> pdb=" O PRO l 265 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR l 269 " --> pdb=" O LEU l 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 264 through 269' Processing helix chain 'm' and resid 33 through 39 Processing helix chain 'm' and resid 40 through 48 Processing helix chain 'm' and resid 64 through 69 Processing helix chain 'm' and resid 89 through 95 Processing helix chain 'm' and resid 112 through 123 Processing helix chain 'm' and resid 134 through 145 removed outlier: 3.728A pdb=" N GLN m 144 " --> pdb=" O SER m 140 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE m 145 " --> pdb=" O VAL m 141 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 29 Processing helix chain 'n' and resid 51 through 80 Processing helix chain 'n' and resid 86 through 138 removed outlier: 3.967A pdb=" N MET n 96 " --> pdb=" O ARG n 92 " (cutoff:3.500A) Processing helix chain 'o' and resid 21 through 36 removed outlier: 3.625A pdb=" N LEU o 33 " --> pdb=" O PHE o 29 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA o 34 " --> pdb=" O ILE o 30 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN o 35 " --> pdb=" O GLN o 31 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE o 36 " --> pdb=" O SER o 32 " (cutoff:3.500A) Processing helix chain 'o' and resid 37 through 45 removed outlier: 3.874A pdb=" N GLN o 45 " --> pdb=" O TYR o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 51 removed outlier: 3.705A pdb=" N LYS o 50 " --> pdb=" O GLN o 46 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER o 51 " --> pdb=" O GLN o 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 46 through 51' Processing helix chain 'o' and resid 52 through 67 removed outlier: 4.014A pdb=" N GLU o 62 " --> pdb=" O LEU o 58 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TYR o 63 " --> pdb=" O LYS o 59 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TRP o 64 " --> pdb=" O TYR o 60 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N CYS o 65 " --> pdb=" O LEU o 61 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ASN o 66 " --> pdb=" O GLU o 62 " (cutoff:3.500A) Proline residue: o 67 - end of helix Processing helix chain 'o' and resid 68 through 74 removed outlier: 4.138A pdb=" N CYS o 72 " --> pdb=" O PRO o 68 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE o 73 " --> pdb=" O TYR o 69 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL o 74 " --> pdb=" O SER o 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 68 through 74' Processing helix chain 'o' and resid 75 through 92 removed outlier: 4.270A pdb=" N LEU o 79 " --> pdb=" O TYR o 75 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE o 88 " --> pdb=" O LEU o 84 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET o 89 " --> pdb=" O LEU o 85 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU o 90 " --> pdb=" O ASN o 86 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER o 91 " --> pdb=" O GLY o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 126 Proline residue: o 107 - end of helix Proline residue: o 115 - end of helix Processing helix chain 'p' and resid 6 through 22 removed outlier: 4.574A pdb=" N THR p 10 " --> pdb=" O SER p 6 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS p 22 " --> pdb=" O PHE p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 27 through 39 removed outlier: 4.664A pdb=" N LEU p 38 " --> pdb=" O LEU p 34 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY p 39 " --> pdb=" O CYS p 35 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 110 Processing helix chain 'p' and resid 114 through 131 removed outlier: 3.790A pdb=" N TYR p 130 " --> pdb=" O LEU p 126 " (cutoff:3.500A) Processing helix chain 'p' and resid 164 through 183 removed outlier: 3.952A pdb=" N SER p 172 " --> pdb=" O PHE p 168 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N HIS p 173 " --> pdb=" O THR p 169 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP p 181 " --> pdb=" O GLN p 177 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN p 182 " --> pdb=" O CYS p 178 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N CYS p 183 " --> pdb=" O PHE p 179 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 1 through 4 Processing sheet with id= 2, first strand: chain '0' and resid 104 through 108 removed outlier: 4.745A pdb=" N SER 0 455 " --> pdb=" O SER 0 230 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL 0 456 " --> pdb=" O GLY 0 36 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 0 479 " --> pdb=" O ASN 0 37 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '0' and resid 350 through 354 removed outlier: 7.397A pdb=" N HIS 0 350 " --> pdb=" O PRO 0 422 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '0' and resid 491 through 498 removed outlier: 3.741A pdb=" N GLY 0 677 " --> pdb=" O SER 0 491 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU 0 493 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG 0 618 " --> pdb=" O TYR 0 676 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR 0 619 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL 0 601 " --> pdb=" O GLU 0 572 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '1' and resid 3 through 8 removed outlier: 6.536A pdb=" N HIS 1 3 " --> pdb=" O ILE 1 18 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS 1 36 " --> pdb=" O SER 1 31 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '1' and resid 46 through 50 removed outlier: 4.689A pdb=" N MET 1 58 " --> pdb=" O PHE 1 91 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN 1 85 " --> pdb=" O GLY 1 64 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '2' and resid 87 through 91 Processing sheet with id= 8, first strand: chain '2' and resid 173 through 177 Processing sheet with id= 9, first strand: chain '2' and resid 338 through 342 removed outlier: 4.068A pdb=" N SER 2 338 " --> pdb=" O TYR 2 350 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS 2 346 " --> pdb=" O GLU 2 342 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE 2 345 " --> pdb=" O ILE 2 378 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '2' and resid 482 through 486 removed outlier: 3.914A pdb=" N TRP 2 483 " --> pdb=" O PHE 2 492 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '4' and resid 23 through 31 removed outlier: 4.837A pdb=" N CYS 4 181 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL 4 234 " --> pdb=" O ILE 4 210 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '4' and resid 75 through 78 removed outlier: 6.438A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '4' and resid 286 through 289 removed outlier: 4.333A pdb=" N CYS 4 294 " --> pdb=" O CYS 4 289 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '4' and resid 303 through 306 removed outlier: 6.687A pdb=" N ASN 4 303 " --> pdb=" O PHE 4 312 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER 4 310 " --> pdb=" O CYS 4 305 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '5' and resid 7 through 11 No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain '6' and resid 179 through 182 removed outlier: 6.687A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG 6 124 " --> pdb=" O ILE 6 166 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '6' and resid 325 through 329 removed outlier: 4.057A pdb=" N GLY 6 346 " --> pdb=" O ILE 6 328 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER 6 354 " --> pdb=" O CYS 6 349 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '6' and resid 360 through 363 removed outlier: 3.949A pdb=" N LEU 6 368 " --> pdb=" O CYS 6 363 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '6' and resid 427 through 430 removed outlier: 4.376A pdb=" N GLN 6 434 " --> pdb=" O CYS 6 429 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '7' and resid 132 through 136 removed outlier: 3.812A pdb=" N ARG 7 140 " --> pdb=" O SER 7 135 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY 7 139 " --> pdb=" O ILE 7 175 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '7' and resid 222 through 227 removed outlier: 9.061A pdb=" N LYS 7 222 " --> pdb=" O THR 7 237 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR 7 237 " --> pdb=" O LYS 7 222 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR 7 232 " --> pdb=" O ILE 7 318 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS 7 314 " --> pdb=" O THR 7 236 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '7' and resid 451 through 455 Processing sheet with id= 23, first strand: chain '7' and resid 650 through 654 Processing sheet with id= 24, first strand: chain 'A' and resid 16 through 19 removed outlier: 4.266A pdb=" N GLU A1417 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'A' and resid 81 through 86 removed outlier: 6.574A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'A' and resid 150 through 154 removed outlier: 5.949A pdb=" N THR A 150 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLN A 160 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.002A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.094A pdb=" N PHE A 347 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 440 " --> pdb=" O VAL A 460 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP A 362 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'A' and resid 376 through 380 removed outlier: 4.831A pdb=" N TRP A 430 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'A' and resid 588 through 591 Processing sheet with id= 31, first strand: chain 'A' and resid 1148 through 1155 removed outlier: 6.675A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE A1237 " --> pdb=" O SER A1229 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP A1223 " --> pdb=" O VAL A1243 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'A' and resid 1281 through 1293 removed outlier: 3.908A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLU A1297 " --> pdb=" O SER A1293 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER A1115 " --> pdb=" O ASN A1330 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 68 through 74 removed outlier: 5.233A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'B' and resid 100 through 103 Processing sheet with id= 35, first strand: chain 'B' and resid 209 through 213 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'B' and resid 221 through 228 removed outlier: 5.428A pdb=" N ILE B 222 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG B 241 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER B 235 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 543 through 546 removed outlier: 4.539A pdb=" N ARG B 632 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 587 through 591 removed outlier: 3.717A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS B 622 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 791 through 797 removed outlier: 5.456A pdb=" N THR B 791 " --> pdb=" O SER B 858 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ARG B 852 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 11.106A pdb=" N GLN B 862 " --> pdb=" O PHE B 874 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE B 874 " --> pdb=" O GLN B 862 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS B 864 " --> pdb=" O GLU B 872 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 870 " --> pdb=" O TYR B 866 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 871 " --> pdb=" O PRO B 917 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY B 913 " --> pdb=" O GLU B 875 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS B 914 " --> pdb=" O ALA B 937 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER B 933 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 821 through 827 removed outlier: 4.139A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASP B 978 " --> pdb=" O ILE B 990 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN B 986 " --> pdb=" O SER B 982 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 902 through 907 removed outlier: 4.260A pdb=" N VAL B 903 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLU B 945 " --> pdb=" O GLY B 907 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 1158 through 1164 removed outlier: 8.712A pdb=" N ASP B1190 " --> pdb=" O GLY B1164 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 1171 through 1175 Processing sheet with id= 44, first strand: chain 'B' and resid 128 through 131 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'B' and resid 124 through 128 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'B' and resid 635 through 639 No H-bonds generated for sheet with id= 46 Processing sheet with id= 47, first strand: chain 'B' and resid 852 through 862 Processing sheet with id= 48, first strand: chain 'B' and resid 1068 through 1071 removed outlier: 6.084A pdb=" N GLY B1068 " --> pdb=" O PHE B1087 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 8 through 11 removed outlier: 6.805A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.608A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLN C 151 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 98 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= 52, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.861A pdb=" N THR E 107 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'E' and resid 151 through 156 removed outlier: 5.066A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLU E 194 " --> pdb=" O CYS E 214 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'F' and resid 134 through 138 removed outlier: 4.210A pdb=" N SER F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'G' and resid 6 through 13 removed outlier: 4.344A pdb=" N SER G 67 " --> pdb=" O LEU G 62 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'G' and resid 84 through 89 Processing sheet with id= 57, first strand: chain 'G' and resid 98 through 102 Processing sheet with id= 58, first strand: chain 'G' and resid 120 through 123 Processing sheet with id= 59, first strand: chain 'G' and resid 149 through 152 removed outlier: 3.742A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'H' and resid 5 through 11 Processing sheet with id= 61, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.422A pdb=" N CYS H 36 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'I' and resid 14 through 18 removed outlier: 4.637A pdb=" N TYR I 34 " --> pdb=" O CYS I 29 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'I' and resid 83 through 87 removed outlier: 5.963A pdb=" N LEU I 99 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS I 108 " --> pdb=" O CYS I 103 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.802A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'L' and resid 36 through 41 removed outlier: 4.713A pdb=" N SER L 36 " --> pdb=" O CYS L 31 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LYS L 28 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE L 55 " --> pdb=" O ALA L 32 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'M' and resid 34 through 38 Processing sheet with id= 67, first strand: chain 'O' and resid 101 through 105 removed outlier: 4.124A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL O 71 " --> pdb=" O GLN O 158 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'O' and resid 161 through 165 removed outlier: 4.036A pdb=" N LYS O 211 " --> pdb=" O PHE O 207 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE O 202 " --> pdb=" O MET O 197 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N PHE O 182 " --> pdb=" O ARG O 196 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Q' and resid 102 through 105 removed outlier: 4.549A pdb=" N SER Q 383 " --> pdb=" O GLU Q 379 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TYR Q 373 " --> pdb=" O ALA Q 389 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Q' and resid 117 through 122 removed outlier: 4.933A pdb=" N ALA Q 397 " --> pdb=" O GLN Q 122 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL Q 392 " --> pdb=" O GLU Q 366 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASN Q 359 " --> pdb=" O ASP Q 354 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'R' and resid 69 through 73 removed outlier: 6.908A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU R 124 " --> pdb=" O SER R 102 " (cutoff:3.500A) removed outlier: 11.060A pdb=" N SER R 102 " --> pdb=" O LEU R 124 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'R' and resid 134 through 139 removed outlier: 6.451A pdb=" N VAL R 134 " --> pdb=" O VAL R 215 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'R' and resid 338 through 341 removed outlier: 4.054A pdb=" N LYS R 348 " --> pdb=" O VAL R 340 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'U' and resid 242 through 247 removed outlier: 4.000A pdb=" N LEU U 247 " --> pdb=" O ASP U 264 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP U 264 " --> pdb=" O LEU U 247 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY U 265 " --> pdb=" O PHE U 276 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE U 276 " --> pdb=" O GLY U 265 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'U' and resid 250 through 254 removed outlier: 3.757A pdb=" N ARG U 257 " --> pdb=" O THR U 254 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA U 256 " --> pdb=" O TRP U 285 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'V' and resid 59 through 64 removed outlier: 5.593A pdb=" N LYS V 59 " --> pdb=" O GLU V 88 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER V 104 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'V' and resid 68 through 71 Processing sheet with id= 78, first strand: chain 'W' and resid 67 through 71 Processing sheet with id= 79, first strand: chain 'W' and resid 122 through 125 removed outlier: 3.604A pdb=" N THR W 129 " --> pdb=" O CYS W 124 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'X' and resid 168 through 173 removed outlier: 5.422A pdb=" N ARG X 168 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR X 177 " --> pdb=" O ASP X 172 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'X' and resid 229 through 232 removed outlier: 6.281A pdb=" N LYS X 229 " --> pdb=" O ASN X 247 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'a' and resid 112 through 118 removed outlier: 6.613A pdb=" N VAL a 127 " --> pdb=" O SER a 118 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLN a 151 " --> pdb=" O LYS a 130 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP a 152 " --> pdb=" O SER a 163 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'd' and resid 321 through 326 removed outlier: 4.616A pdb=" N VAL d 321 " --> pdb=" O LYS d 338 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'd' and resid 354 through 361 removed outlier: 7.052A pdb=" N ILE d 354 " --> pdb=" O HIS d 371 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'd' and resid 393 through 396 removed outlier: 6.747A pdb=" N ILE d 393 " --> pdb=" O SER d 406 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'd' and resid 456 through 460 removed outlier: 5.210A pdb=" N GLY d 456 " --> pdb=" O GLU d 468 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS d 464 " --> pdb=" O GLU d 460 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN d 463 " --> pdb=" O LEU d 478 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'd' and resid 573 through 579 removed outlier: 4.015A pdb=" N SER d 574 " --> pdb=" O ASN d 620 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU d 631 " --> pdb=" O ILE d 619 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU d 621 " --> pdb=" O PRO d 629 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER d 628 " --> pdb=" O GLY d 652 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY d 652 " --> pdb=" O SER d 628 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'e' and resid 209 through 212 removed outlier: 7.091A pdb=" N VAL e 40 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG e 63 " --> pdb=" O SER e 169 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER e 169 " --> pdb=" O ARG e 63 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N GLU e 69 " --> pdb=" O PRO e 163 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLN e 214 " --> pdb=" O ILE e 238 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'e' and resid 32 through 40 removed outlier: 3.610A pdb=" N THR e 217 " --> pdb=" O SER e 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE e 213 " --> pdb=" O VAL e 40 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'e' and resid 235 through 239 No H-bonds generated for sheet with id= 90 Processing sheet with id= 91, first strand: chain 'f' and resid 76 through 81 removed outlier: 6.029A pdb=" N SER f 36 " --> pdb=" O HIS f 63 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR f 41 " --> pdb=" O ARG f 119 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE f 115 " --> pdb=" O SER f 45 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'f' and resid 127 through 132 removed outlier: 3.772A pdb=" N LEU f 135 " --> pdb=" O LEU f 132 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR f 136 " --> pdb=" O LEU f 155 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU f 155 " --> pdb=" O THR f 136 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG f 138 " --> pdb=" O ILE f 153 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE f 153 " --> pdb=" O ARG f 138 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL f 140 " --> pdb=" O LEU f 151 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU f 151 " --> pdb=" O VAL f 140 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU f 142 " --> pdb=" O LYS f 149 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'f' and resid 36 through 41 removed outlier: 3.751A pdb=" N GLN f 120 " --> pdb=" O THR f 41 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'i' and resid 74 through 77 removed outlier: 9.040A pdb=" N GLN i 74 " --> pdb=" O VAL i 85 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'l' and resid 275 through 280 removed outlier: 6.694A pdb=" N GLN l 287 " --> pdb=" O VAL l 300 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'l' and resid 402 through 405 removed outlier: 4.299A pdb=" N LYS l 426 " --> pdb=" O ASP l 443 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL l 455 " --> pdb=" O TRP l 442 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'l' and resid 498 through 502 No H-bonds generated for sheet with id= 97 Processing sheet with id= 98, first strand: chain 'l' and resid 621 through 628 removed outlier: 3.545A pdb=" N LEU l 621 " --> pdb=" O SER l 644 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET l 676 " --> pdb=" O LYS l 653 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'l' and resid 284 through 287 Processing sheet with id=100, first strand: chain 'p' and resid 42 through 47 removed outlier: 6.581A pdb=" N LEU p 51 " --> pdb=" O LEU p 47 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLU p 50 " --> pdb=" O LYS p 69 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP p 66 " --> pdb=" O GLN p 75 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'p' and resid 186 through 190 Processing sheet with id=102, first strand: chain 'p' and resid 213 through 219 Processing sheet with id=103, first strand: chain 'p' and resid 229 through 235 No H-bonds generated for sheet with id=103 Processing sheet with id=104, first strand: chain 'p' and resid 61 through 66 removed outlier: 4.153A pdb=" N ASP p 76 " --> pdb=" O ASP p 66 " (cutoff:3.500A) 4851 hydrogen bonds defined for protein. 14415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 146 hydrogen bonds 292 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 124 stacking parallelities Total time for adding SS restraints: 51.69 Time building geometry restraints manager: 35.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.38: 36223 1.38 - 1.60: 66889 1.60 - 1.83: 946 1.83 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 104070 Sorted by residual: bond pdb=" CG PRO p 211 " pdb=" CD PRO p 211 " ideal model delta sigma weight residual 1.503 1.153 0.350 3.40e-02 8.65e+02 1.06e+02 bond pdb=" C LEU d 493 " pdb=" N PRO d 494 " ideal model delta sigma weight residual 1.333 1.373 -0.040 1.01e-02 9.80e+03 1.56e+01 bond pdb=" CA VAL A 507 " pdb=" CB VAL A 507 " ideal model delta sigma weight residual 1.534 1.560 -0.025 6.80e-03 2.16e+04 1.38e+01 bond pdb=" CB PRO 7 106 " pdb=" CG PRO 7 106 " ideal model delta sigma weight residual 1.492 1.631 -0.139 5.00e-02 4.00e+02 7.73e+00 bond pdb=" N PRO p 211 " pdb=" CD PRO p 211 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.34e+00 ... (remaining 104065 not shown) Histogram of bond angle deviations from ideal: 73.66 - 86.33: 14 86.33 - 99.00: 23 99.00 - 111.67: 48659 111.67 - 124.34: 89974 124.34 - 137.00: 2482 Bond angle restraints: 141152 Sorted by residual: angle pdb=" N PRO p 211 " pdb=" CD PRO p 211 " pdb=" CG PRO p 211 " ideal model delta sigma weight residual 103.20 78.57 24.63 1.50e+00 4.44e-01 2.70e+02 angle pdb=" CA PRO p 211 " pdb=" CB PRO p 211 " pdb=" CG PRO p 211 " ideal model delta sigma weight residual 104.50 77.37 27.13 1.90e+00 2.77e-01 2.04e+02 angle pdb=" CA PRO 7 106 " pdb=" N PRO 7 106 " pdb=" CD PRO 7 106 " ideal model delta sigma weight residual 112.00 100.23 11.77 1.40e+00 5.10e-01 7.07e+01 angle pdb=" CA PRO k 80 " pdb=" N PRO k 80 " pdb=" CD PRO k 80 " ideal model delta sigma weight residual 112.00 101.10 10.90 1.40e+00 5.10e-01 6.06e+01 angle pdb=" N PRO p 211 " pdb=" CA PRO p 211 " pdb=" CB PRO p 211 " ideal model delta sigma weight residual 103.36 97.45 5.91 8.80e-01 1.29e+00 4.51e+01 ... (remaining 141147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 62226 35.46 - 70.92: 1320 70.92 - 106.37: 106 106.37 - 141.83: 0 141.83 - 177.29: 2 Dihedral angle restraints: 63654 sinusoidal: 27504 harmonic: 36150 Sorted by residual: dihedral pdb=" CA ILE o 36 " pdb=" C ILE o 36 " pdb=" N GLN o 37 " pdb=" CA GLN o 37 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA TRP B 561 " pdb=" C TRP B 561 " pdb=" N GLY B 562 " pdb=" CA GLY B 562 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA LEU A 597 " pdb=" C LEU A 597 " pdb=" N LEU A 598 " pdb=" CA LEU A 598 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 63651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 14945 0.098 - 0.197: 1030 0.197 - 0.295: 33 0.295 - 0.394: 5 0.394 - 0.492: 2 Chirality restraints: 16015 Sorted by residual: chirality pdb=" CG LEU 6 319 " pdb=" CB LEU 6 319 " pdb=" CD1 LEU 6 319 " pdb=" CD2 LEU 6 319 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CB ILE 0 463 " pdb=" CA ILE 0 463 " pdb=" CG1 ILE 0 463 " pdb=" CG2 ILE 0 463 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" CB ILE l 271 " pdb=" CA ILE l 271 " pdb=" CG1 ILE l 271 " pdb=" CG2 ILE l 271 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 16012 not shown) Planarity restraints: 17567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL 7 105 " -0.111 5.00e-02 4.00e+02 1.58e-01 4.00e+01 pdb=" N PRO 7 106 " 0.273 5.00e-02 4.00e+02 pdb=" CA PRO 7 106 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO 7 106 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR f 13 " -0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO f 14 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO f 14 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO f 14 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE j 70 " 0.029 2.00e-02 2.50e+03 3.30e-02 1.90e+01 pdb=" CG PHE j 70 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 PHE j 70 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE j 70 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE j 70 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE j 70 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE j 70 " 0.000 2.00e-02 2.50e+03 ... (remaining 17564 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 3077 2.71 - 3.26: 98277 3.26 - 3.80: 172143 3.80 - 4.35: 220855 4.35 - 4.90: 359969 Nonbonded interactions: 854321 Sorted by model distance: nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.160 2.170 nonbonded pdb=" OH TYR A1640 " pdb=" OD2 ASP a 124 " model vdw 2.181 2.440 nonbonded pdb=" OD1 ASP A 485 " pdb="MG MG A1803 " model vdw 2.185 2.170 nonbonded pdb=" O HIS A 451 " pdb=" OG SER A 454 " model vdw 2.214 2.440 nonbonded pdb=" O LYS b 203 " pdb=" OG1 THR b 207 " model vdw 2.227 2.440 ... (remaining 854316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.080 Extract box with map and model: 16.470 Check model and map are aligned: 1.150 Set scattering table: 0.690 Process input model: 312.400 Find NCS groups from input model: 2.870 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 349.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5146 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 : 0.004 0.350 104070 Z= 0.265 Angle : 0.795 27.130 141152 Z= 0.420 Chirality : 0.051 0.492 16015 Planarity : 0.006 0.158 17567 Dihedral : 14.488 177.288 40130 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.06 % Rotamer: Outliers : 0.05 % Allowed : 0.39 % Favored : 99.56 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.07), residues: 12095 helix: -0.02 (0.07), residues: 5432 sheet: -0.43 (0.12), residues: 1704 loop : -0.72 (0.08), residues: 4959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP b 158 HIS 0.018 0.001 HIS i 200 PHE 0.075 0.002 PHE j 70 TYR 0.059 0.002 TYR 7 581 ARG 0.014 0.001 ARG 3 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1407 time to evaluate : 8.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 472 MET cc_start: -0.1095 (ttt) cc_final: -0.2002 (tmt) REVERT: 0 485 MET cc_start: -0.1077 (ptm) cc_final: -0.1553 (ptm) REVERT: 0 642 MET cc_start: 0.0075 (mmt) cc_final: -0.0451 (mmp) REVERT: 2 81 MET cc_start: -0.3199 (mtm) cc_final: -0.4280 (mmm) REVERT: 2 216 MET cc_start: 0.1305 (mmt) cc_final: 0.0923 (mmp) REVERT: 2 227 MET cc_start: -0.1815 (ttp) cc_final: -0.4975 (mtt) REVERT: 2 253 MET cc_start: -0.2156 (mmp) cc_final: -0.3656 (mmt) REVERT: 2 408 MET cc_start: -0.1029 (mtp) cc_final: -0.1302 (mpp) REVERT: 6 95 MET cc_start: 0.0867 (ppp) cc_final: -0.0243 (tmt) REVERT: 6 384 MET cc_start: -0.0946 (pmm) cc_final: -0.1429 (pp-130) REVERT: 7 244 MET cc_start: 0.2907 (ppp) cc_final: 0.2575 (pp-130) REVERT: 7 445 MET cc_start: 0.0719 (mmm) cc_final: 0.0245 (tpt) REVERT: 7 622 MET cc_start: -0.1716 (mtt) cc_final: -0.3034 (mtt) REVERT: B 484 ASN cc_start: 0.7965 (m-40) cc_final: 0.7761 (m-40) REVERT: B 841 MET cc_start: 0.8518 (ttm) cc_final: 0.8278 (ttm) REVERT: B 1192 TYR cc_start: 0.8756 (m-80) cc_final: 0.8553 (m-80) REVERT: X 153 MET cc_start: 0.0211 (pmm) cc_final: -0.0653 (pp-130) REVERT: e 231 GLU cc_start: 0.5723 (mt-10) cc_final: 0.5327 (mt-10) REVERT: h 206 ILE cc_start: 0.0138 (mm) cc_final: -0.0100 (mm) REVERT: i 95 MET cc_start: -0.1616 (mtp) cc_final: -0.4320 (ptt) REVERT: l 190 MET cc_start: -0.0301 (mmt) cc_final: -0.1480 (mtp) outliers start: 6 outliers final: 6 residues processed: 1413 average time/residue: 1.9240 time to fit residues: 3654.9402 Evaluate side-chains 782 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 776 time to evaluate : 8.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 46 ILE Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain e residue 216 LEU Chi-restraints excluded: chain f residue 176 GLU Chi-restraints excluded: chain m residue 95 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 1037 optimal weight: 0.9990 chunk 931 optimal weight: 20.0000 chunk 516 optimal weight: 3.9990 chunk 318 optimal weight: 30.0000 chunk 628 optimal weight: 10.0000 chunk 497 optimal weight: 0.8980 chunk 963 optimal weight: 7.9990 chunk 372 optimal weight: 2.9990 chunk 585 optimal weight: 1.9990 chunk 716 optimal weight: 0.5980 chunk 1116 optimal weight: 50.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 23 ASN ** 0 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 365 ASN ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 232 ASN 6 353 HIS 7 471 GLN ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 ASN A 515 GLN A 959 ASN A 994 GLN A1059 HIS ** A1258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1330 ASN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 ASN B1093 GLN B1112 GLN B1178 ASN B1179 GLN C 252 GLN C 267 GLN D 138 ASN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN I 12 ASN J 26 GLN M 193 GLN O 158 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 88 HIS R 265 HIS W 72 GLN X 222 ASN X 267 GLN ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 2 GLN d 255 ASN d 364 GLN d 371 HIS d 646 HIS e 243 ASN f 141 ASN g 64 GLN j 96 HIS ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 217 HIS m 29 ASN m 95 GLN n 74 ASN ** o 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5293 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 104070 Z= 0.235 Angle : 0.607 12.325 141152 Z= 0.316 Chirality : 0.043 0.278 16015 Planarity : 0.005 0.086 17567 Dihedral : 11.562 179.786 14945 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.70 % Favored : 97.29 % Rotamer: Outliers : 1.30 % Allowed : 8.15 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.07), residues: 12095 helix: 0.72 (0.07), residues: 5459 sheet: -0.30 (0.12), residues: 1696 loop : -0.54 (0.09), residues: 4940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP o 117 HIS 0.013 0.001 HIS j 96 PHE 0.043 0.001 PHE j 70 TYR 0.032 0.001 TYR 7 581 ARG 0.018 0.001 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 837 time to evaluate : 9.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: -0.0750 (mmm) cc_final: -0.1399 (mmm) REVERT: 0 42 MET cc_start: -0.0708 (mtp) cc_final: -0.1544 (ttp) REVERT: 0 61 MET cc_start: 0.0391 (mpt) cc_final: 0.0003 (mpt) REVERT: 0 90 MET cc_start: -0.1177 (mmt) cc_final: -0.2479 (mpt) REVERT: 0 468 MET cc_start: -0.1199 (tpp) cc_final: -0.1842 (tmt) REVERT: 0 472 MET cc_start: 0.0043 (ttt) cc_final: -0.0743 (tmt) REVERT: 0 485 MET cc_start: -0.1162 (ptm) cc_final: -0.3565 (mtm) REVERT: 0 642 MET cc_start: 0.0271 (mmt) cc_final: -0.0269 (mmp) REVERT: 1 1 MET cc_start: -0.0510 (tpt) cc_final: -0.0782 (tpt) REVERT: 1 58 MET cc_start: -0.1225 (mtm) cc_final: -0.1436 (mtm) REVERT: 1 469 MET cc_start: -0.2427 (tpt) cc_final: -0.2736 (tpt) REVERT: 2 50 MET cc_start: 0.0502 (tmt) cc_final: 0.0117 (tmt) REVERT: 2 81 MET cc_start: -0.3297 (mtm) cc_final: -0.3619 (mmm) REVERT: 2 194 GLN cc_start: -0.2151 (OUTLIER) cc_final: -0.2713 (pp30) REVERT: 2 227 MET cc_start: -0.1773 (ttp) cc_final: -0.4932 (mtt) REVERT: 2 253 MET cc_start: -0.2196 (mmt) cc_final: -0.3813 (mmt) REVERT: 2 408 MET cc_start: -0.1199 (mtp) cc_final: -0.1488 (mpp) REVERT: 4 114 MET cc_start: -0.1032 (tpt) cc_final: -0.1854 (tpt) REVERT: 4 252 MET cc_start: -0.0239 (OUTLIER) cc_final: -0.0519 (tpt) REVERT: 6 384 MET cc_start: -0.1018 (pmm) cc_final: -0.1425 (pp-130) REVERT: 7 244 MET cc_start: 0.2888 (ppp) cc_final: 0.2434 (pp-130) REVERT: 7 445 MET cc_start: 0.0638 (mmm) cc_final: 0.0405 (tpt) REVERT: 7 622 MET cc_start: -0.2403 (mtt) cc_final: -0.3179 (mtt) REVERT: A 618 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7242 (pp20) REVERT: A 1373 ASP cc_start: 0.7840 (m-30) cc_final: 0.7480 (m-30) REVERT: B 484 ASN cc_start: 0.8071 (m-40) cc_final: 0.7779 (m-40) REVERT: B 1178 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8409 (t0) REVERT: C 179 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: H 14 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6913 (tp30) REVERT: X 153 MET cc_start: 0.0296 (pmm) cc_final: -0.0556 (pp-130) REVERT: X 317 MET cc_start: -0.2979 (ptt) cc_final: -0.3194 (ptt) REVERT: d 411 MET cc_start: 0.5060 (tpp) cc_final: 0.4647 (mmp) REVERT: i 95 MET cc_start: -0.1535 (mtp) cc_final: -0.4336 (ptt) REVERT: l 104 MET cc_start: -0.1011 (mpp) cc_final: -0.2394 (mpt) REVERT: l 190 MET cc_start: -0.0606 (mmt) cc_final: -0.1618 (mpp) REVERT: p 256 MET cc_start: 0.2885 (tpp) cc_final: 0.2657 (tpt) outliers start: 145 outliers final: 43 residues processed: 923 average time/residue: 1.8520 time to fit residues: 2327.0705 Evaluate side-chains 758 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 709 time to evaluate : 8.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 943 SER Chi-restraints excluded: chain B residue 1178 ASN Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 342 LEU Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 96 ASP Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain h residue 90 TYR Chi-restraints excluded: chain h residue 151 THR Chi-restraints excluded: chain m residue 118 GLU Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain o residue 21 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 620 optimal weight: 30.0000 chunk 346 optimal weight: 0.9990 chunk 928 optimal weight: 20.0000 chunk 759 optimal weight: 10.0000 chunk 307 optimal weight: 50.0000 chunk 1118 optimal weight: 30.0000 chunk 1207 optimal weight: 40.0000 chunk 995 optimal weight: 9.9990 chunk 1108 optimal weight: 50.0000 chunk 381 optimal weight: 3.9990 chunk 896 optimal weight: 50.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 356 GLN ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN A 959 ASN A1258 HIS ** A1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1330 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1097 HIS B1112 GLN C 131 HIS C 252 GLN D 138 ASN D 179 GLN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN M 114 GLN M 300 GLN Q 17 ASN Q 134 HIS ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 ASN R 265 HIS ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 GLN W 93 HIS X 222 ASN X 267 GLN ** a 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN d 255 ASN d 285 ASN d 371 HIS d 428 GLN d 595 ASN ** e 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 64 HIS g 64 GLN g 68 ASN ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 29 ASN ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 45 GLN ** o 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5479 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.185 104070 Z= 0.898 Angle : 0.810 13.305 141152 Z= 0.423 Chirality : 0.057 0.420 16015 Planarity : 0.006 0.116 17567 Dihedral : 11.730 177.832 14931 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.22 % Favored : 96.77 % Rotamer: Outliers : 2.13 % Allowed : 10.26 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.07), residues: 12095 helix: 0.74 (0.07), residues: 5450 sheet: -0.29 (0.12), residues: 1666 loop : -0.69 (0.08), residues: 4979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 519 HIS 0.017 0.002 HIS A 451 PHE 0.042 0.003 PHE A 219 TYR 0.047 0.002 TYR 3 136 ARG 0.026 0.001 ARG A 469 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 812 time to evaluate : 8.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: -0.0924 (mmm) cc_final: -0.1338 (tpt) REVERT: 0 42 MET cc_start: -0.0856 (mtp) cc_final: -0.1606 (ttp) REVERT: 0 61 MET cc_start: 0.0803 (mpt) cc_final: 0.0407 (mpt) REVERT: 0 90 MET cc_start: -0.1171 (mmt) cc_final: -0.2432 (mpt) REVERT: 0 472 MET cc_start: 0.0095 (ttt) cc_final: -0.1156 (tmt) REVERT: 0 485 MET cc_start: -0.1267 (ptm) cc_final: -0.3670 (mtm) REVERT: 0 642 MET cc_start: 0.0187 (mmt) cc_final: -0.0424 (mmp) REVERT: 0 724 MET cc_start: -0.1127 (OUTLIER) cc_final: -0.1651 (ptt) REVERT: 1 1 MET cc_start: -0.0594 (tpt) cc_final: -0.0855 (tpt) REVERT: 1 58 MET cc_start: -0.1120 (mtm) cc_final: -0.1413 (mtm) REVERT: 1 469 MET cc_start: -0.2446 (tpt) cc_final: -0.2760 (tpt) REVERT: 2 81 MET cc_start: -0.3244 (mtm) cc_final: -0.3685 (mmm) REVERT: 2 150 MET cc_start: -0.1698 (mmt) cc_final: -0.1912 (mmt) REVERT: 2 194 GLN cc_start: -0.1800 (OUTLIER) cc_final: -0.2493 (pp30) REVERT: 2 227 MET cc_start: -0.1593 (ttp) cc_final: -0.5275 (mtt) REVERT: 2 253 MET cc_start: -0.2136 (mmt) cc_final: -0.3817 (mmt) REVERT: 2 408 MET cc_start: -0.1134 (mtp) cc_final: -0.1413 (mpp) REVERT: 4 114 MET cc_start: -0.1072 (tpt) cc_final: -0.1809 (tpt) REVERT: 4 252 MET cc_start: -0.0154 (OUTLIER) cc_final: -0.0511 (tpt) REVERT: 6 106 ARG cc_start: -0.0339 (mmp-170) cc_final: -0.1223 (mmt180) REVERT: 6 384 MET cc_start: -0.1145 (pmm) cc_final: -0.1385 (pp-130) REVERT: 7 112 MET cc_start: -0.1221 (OUTLIER) cc_final: -0.1604 (ppp) REVERT: 7 244 MET cc_start: 0.2807 (ppp) cc_final: 0.2356 (pp-130) REVERT: 7 561 MET cc_start: 0.0105 (mmt) cc_final: -0.0603 (mmt) REVERT: 7 622 MET cc_start: -0.2367 (mtt) cc_final: -0.3284 (mtt) REVERT: A 22 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: A 63 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7988 (mtm110) REVERT: A 129 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6670 (pmtt) REVERT: A 688 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7358 (tttp) REVERT: A 1039 LYS cc_start: 0.8064 (tptp) cc_final: 0.7856 (tptp) REVERT: A 1062 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: A 1386 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7720 (ptp90) REVERT: B 173 MET cc_start: 0.9055 (ttm) cc_final: 0.8677 (ttm) REVERT: B 836 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: B 1028 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: C 179 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: C 265 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7411 (ptm) REVERT: K 14 GLU cc_start: 0.6486 (mm-30) cc_final: 0.6214 (mm-30) REVERT: M 95 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7315 (ptp-170) REVERT: W 227 MET cc_start: 0.2108 (mmt) cc_final: 0.1231 (mpm) REVERT: X 153 MET cc_start: -0.0273 (pmm) cc_final: -0.0723 (pp-130) REVERT: X 317 MET cc_start: -0.3054 (ptt) cc_final: -0.3288 (ptt) REVERT: d 411 MET cc_start: 0.5265 (tpp) cc_final: 0.4931 (mmp) REVERT: f 102 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6589 (tp30) REVERT: i 95 MET cc_start: -0.1441 (mtp) cc_final: -0.4166 (ptt) REVERT: k 115 MET cc_start: -0.2267 (OUTLIER) cc_final: -0.3016 (ptp) REVERT: l 190 MET cc_start: -0.0706 (mmt) cc_final: -0.1768 (mpp) REVERT: l 676 MET cc_start: 0.4953 (ppp) cc_final: 0.4732 (ppp) outliers start: 237 outliers final: 105 residues processed: 969 average time/residue: 1.8668 time to fit residues: 2478.1996 Evaluate side-chains 808 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 687 time to evaluate : 8.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 724 MET Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 364 ILE Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 3 residue 96 ILE Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 7 residue 112 MET Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 688 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 899 VAL Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1336 MET Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 836 GLU Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1028 GLU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 95 ARG Chi-restraints excluded: chain M residue 135 MET Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 406 ILE Chi-restraints excluded: chain V residue 50 GLU Chi-restraints excluded: chain a residue 167 PHE Chi-restraints excluded: chain b residue 68 GLN Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 216 LEU Chi-restraints excluded: chain e residue 217 THR Chi-restraints excluded: chain e residue 273 THR Chi-restraints excluded: chain f residue 102 GLU Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 187 ASP Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain h residue 90 TYR Chi-restraints excluded: chain k residue 115 MET Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 697 ASN Chi-restraints excluded: chain m residue 118 GLU Chi-restraints excluded: chain n residue 4 ARG Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain n residue 121 HIS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 66 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 1104 optimal weight: 50.0000 chunk 840 optimal weight: 7.9990 chunk 580 optimal weight: 0.5980 chunk 123 optimal weight: 40.0000 chunk 533 optimal weight: 2.9990 chunk 750 optimal weight: 0.7980 chunk 1122 optimal weight: 30.0000 chunk 1187 optimal weight: 30.0000 chunk 586 optimal weight: 0.9990 chunk 1063 optimal weight: 50.0000 chunk 320 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 106 GLN ** 2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 HIS A 515 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 706 GLN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN H 83 GLN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN M 114 GLN M 303 GLN Q 134 HIS ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 ASN b 85 HIS ** c 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 371 HIS e 3 GLN ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 160 HIS ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 217 HIS ** n 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 119 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5366 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 104070 Z= 0.210 Angle : 0.589 12.538 141152 Z= 0.307 Chirality : 0.042 0.237 16015 Planarity : 0.004 0.092 17567 Dihedral : 11.611 178.235 14931 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.75 % Favored : 97.24 % Rotamer: Outliers : 1.71 % Allowed : 12.45 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.08), residues: 12095 helix: 1.12 (0.07), residues: 5453 sheet: -0.20 (0.12), residues: 1636 loop : -0.54 (0.09), residues: 5006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP l 665 HIS 0.022 0.001 HIS A 286 PHE 0.047 0.002 PHE a 95 TYR 0.040 0.001 TYR 3 136 ARG 0.011 0.000 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 754 time to evaluate : 9.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: -0.0970 (mmm) cc_final: -0.1603 (mmt) REVERT: 0 42 MET cc_start: -0.0750 (OUTLIER) cc_final: -0.1580 (ttp) REVERT: 0 61 MET cc_start: 0.0871 (mpt) cc_final: 0.0494 (mpt) REVERT: 0 90 MET cc_start: -0.1235 (mmt) cc_final: -0.2487 (mpt) REVERT: 0 136 MET cc_start: 0.0210 (ptt) cc_final: -0.0564 (ppp) REVERT: 0 472 MET cc_start: 0.0073 (ttt) cc_final: -0.1230 (tmt) REVERT: 0 485 MET cc_start: -0.1049 (ptm) cc_final: -0.3496 (mtm) REVERT: 0 642 MET cc_start: 0.0215 (mmt) cc_final: -0.0371 (mmp) REVERT: 0 724 MET cc_start: -0.1136 (OUTLIER) cc_final: -0.2276 (ptt) REVERT: 1 1 MET cc_start: -0.0563 (tpt) cc_final: -0.0809 (tpt) REVERT: 1 58 MET cc_start: -0.1233 (mtm) cc_final: -0.1476 (mtm) REVERT: 1 469 MET cc_start: -0.2346 (tpt) cc_final: -0.2795 (tpt) REVERT: 2 50 MET cc_start: 0.0185 (tmt) cc_final: -0.0187 (tmt) REVERT: 2 81 MET cc_start: -0.3193 (mtm) cc_final: -0.3552 (mmm) REVERT: 2 194 GLN cc_start: -0.1485 (OUTLIER) cc_final: -0.2186 (pp30) REVERT: 2 227 MET cc_start: -0.1603 (ttp) cc_final: -0.5272 (mtt) REVERT: 2 253 MET cc_start: -0.1974 (mmt) cc_final: -0.3658 (mmt) REVERT: 2 408 MET cc_start: -0.1138 (mtp) cc_final: -0.1344 (mpp) REVERT: 3 133 LEU cc_start: 0.5036 (pp) cc_final: 0.4741 (mm) REVERT: 4 114 MET cc_start: -0.1224 (tpt) cc_final: -0.1946 (tpt) REVERT: 4 252 MET cc_start: -0.0128 (OUTLIER) cc_final: -0.0503 (tpt) REVERT: 6 95 MET cc_start: 0.0007 (ppp) cc_final: -0.1771 (tmt) REVERT: 6 106 ARG cc_start: -0.0504 (mmp-170) cc_final: -0.1336 (mmt180) REVERT: 6 384 MET cc_start: -0.1070 (pmm) cc_final: -0.1271 (pp-130) REVERT: 7 112 MET cc_start: -0.1341 (ppp) cc_final: -0.1577 (ppp) REVERT: 7 244 MET cc_start: 0.2699 (ppp) cc_final: 0.2216 (pp-130) REVERT: 7 497 MET cc_start: 0.1047 (pp-130) cc_final: 0.0709 (ptt) REVERT: 7 561 MET cc_start: 0.0167 (mmt) cc_final: -0.0371 (mmt) REVERT: 7 622 MET cc_start: -0.2200 (mtt) cc_final: -0.3075 (mtt) REVERT: A 22 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.7943 (m-80) REVERT: A 63 ARG cc_start: 0.8212 (ttp-110) cc_final: 0.7884 (mtm110) REVERT: A 1386 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7648 (ptp90) REVERT: C 265 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7134 (ptm) REVERT: K 14 GLU cc_start: 0.5927 (mm-30) cc_final: 0.5587 (mm-30) REVERT: X 153 MET cc_start: -0.0117 (pmm) cc_final: -0.0433 (pp-130) REVERT: X 317 MET cc_start: -0.2614 (ptt) cc_final: -0.2874 (ptt) REVERT: d 411 MET cc_start: 0.5295 (tpp) cc_final: 0.5070 (mmp) REVERT: f 86 ASP cc_start: 0.5538 (p0) cc_final: 0.5328 (p0) REVERT: i 95 MET cc_start: -0.1067 (mtp) cc_final: -0.1586 (mtt) REVERT: k 114 LYS cc_start: 0.1462 (OUTLIER) cc_final: 0.0804 (tmmt) REVERT: l 190 MET cc_start: -0.0792 (mmt) cc_final: -0.1851 (mpp) REVERT: m 25 TYR cc_start: -0.0415 (OUTLIER) cc_final: -0.0817 (t80) REVERT: p 14 MET cc_start: 0.3188 (tmm) cc_final: 0.2108 (tpp) REVERT: p 256 MET cc_start: 0.2243 (OUTLIER) cc_final: 0.1987 (tpt) outliers start: 190 outliers final: 71 residues processed: 874 average time/residue: 1.8515 time to fit residues: 2217.1877 Evaluate side-chains 752 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 671 time to evaluate : 8.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 724 MET Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 949 ASP Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 406 ILE Chi-restraints excluded: chain V residue 50 GLU Chi-restraints excluded: chain V residue 112 ARG Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain b residue 68 GLN Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 96 ASP Chi-restraints excluded: chain e residue 216 LEU Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain h residue 46 LEU Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain h residue 90 TYR Chi-restraints excluded: chain j residue 10 GLN Chi-restraints excluded: chain k residue 11 LEU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain k residue 115 MET Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 697 ASN Chi-restraints excluded: chain m residue 15 TYR Chi-restraints excluded: chain m residue 25 TYR Chi-restraints excluded: chain n residue 83 VAL Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 256 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 989 optimal weight: 7.9990 chunk 674 optimal weight: 0.0570 chunk 17 optimal weight: 10.0000 chunk 884 optimal weight: 10.0000 chunk 490 optimal weight: 5.9990 chunk 1013 optimal weight: 20.0000 chunk 821 optimal weight: 5.9990 chunk 1 optimal weight: 40.0000 chunk 606 optimal weight: 0.9990 chunk 1066 optimal weight: 20.0000 chunk 299 optimal weight: 9.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN ** A1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 706 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN L 66 GLN M 114 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 265 HIS ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 54 GLN d 371 HIS e 214 GLN ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** i 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 72 GLN ** n 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5429 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 104070 Z= 0.470 Angle : 0.654 14.815 141152 Z= 0.340 Chirality : 0.046 0.310 16015 Planarity : 0.005 0.180 17567 Dihedral : 11.640 177.065 14931 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.16 % Favored : 96.83 % Rotamer: Outliers : 2.12 % Allowed : 13.33 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.08), residues: 12095 helix: 1.16 (0.07), residues: 5459 sheet: -0.25 (0.13), residues: 1620 loop : -0.53 (0.09), residues: 5016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP o 125 HIS 0.013 0.001 HIS A 286 PHE 0.050 0.002 PHE n 19 TYR 0.028 0.002 TYR G 51 ARG 0.012 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 715 time to evaluate : 8.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: -0.1042 (mmm) cc_final: -0.2062 (mmt) REVERT: 0 42 MET cc_start: -0.0535 (OUTLIER) cc_final: -0.1327 (ttt) REVERT: 0 61 MET cc_start: 0.0939 (mpt) cc_final: 0.0376 (mpt) REVERT: 0 90 MET cc_start: -0.1213 (mmt) cc_final: -0.2465 (mpt) REVERT: 0 136 MET cc_start: 0.0208 (OUTLIER) cc_final: -0.0691 (ppp) REVERT: 0 468 MET cc_start: -0.0411 (ttt) cc_final: -0.0711 (ttt) REVERT: 0 472 MET cc_start: 0.0047 (ttt) cc_final: -0.1172 (tmt) REVERT: 0 485 MET cc_start: -0.1260 (ptm) cc_final: -0.3569 (mtm) REVERT: 0 642 MET cc_start: 0.0119 (mmt) cc_final: -0.0528 (mmp) REVERT: 0 724 MET cc_start: -0.1034 (OUTLIER) cc_final: -0.2087 (ptt) REVERT: 1 1 MET cc_start: -0.0500 (tpt) cc_final: -0.0753 (tpt) REVERT: 1 58 MET cc_start: -0.1012 (mtm) cc_final: -0.1394 (mtm) REVERT: 1 469 MET cc_start: -0.2257 (tpt) cc_final: -0.2826 (tpt) REVERT: 1 608 MET cc_start: -0.0543 (tmm) cc_final: -0.1278 (tpt) REVERT: 2 50 MET cc_start: 0.0397 (tmt) cc_final: -0.0083 (tmt) REVERT: 2 81 MET cc_start: -0.3242 (mtm) cc_final: -0.3690 (mmm) REVERT: 2 194 GLN cc_start: -0.1427 (OUTLIER) cc_final: -0.2064 (pp30) REVERT: 2 210 MET cc_start: 0.1086 (ptm) cc_final: 0.0643 (ptp) REVERT: 2 227 MET cc_start: -0.1396 (ttp) cc_final: -0.5340 (mtt) REVERT: 2 253 MET cc_start: -0.1997 (mmt) cc_final: -0.3472 (mmt) REVERT: 4 114 MET cc_start: -0.1292 (OUTLIER) cc_final: -0.1990 (tpt) REVERT: 4 252 MET cc_start: -0.0115 (OUTLIER) cc_final: -0.0523 (tpt) REVERT: 5 27 MET cc_start: -0.3482 (ptt) cc_final: -0.3890 (pp-130) REVERT: 6 95 MET cc_start: -0.0143 (ppp) cc_final: -0.2080 (tmt) REVERT: 6 106 ARG cc_start: -0.0451 (mmp-170) cc_final: -0.1328 (mmt180) REVERT: 6 322 MET cc_start: 0.1616 (pp-130) cc_final: -0.0174 (ppp) REVERT: 7 112 MET cc_start: -0.1502 (ppp) cc_final: -0.1756 (ppp) REVERT: 7 561 MET cc_start: 0.0333 (mmt) cc_final: -0.0506 (mmt) REVERT: 7 622 MET cc_start: -0.2323 (mtt) cc_final: -0.2898 (mtt) REVERT: A 22 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: A 63 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7956 (mtm110) REVERT: A 383 TYR cc_start: 0.8294 (m-80) cc_final: 0.8014 (m-80) REVERT: A 1062 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: A 1386 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7644 (ptp90) REVERT: B 545 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8911 (mt) REVERT: B 763 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: C 179 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: C 265 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7248 (ptm) REVERT: K 14 GLU cc_start: 0.6342 (mm-30) cc_final: 0.6014 (mm-30) REVERT: W 227 MET cc_start: 0.2051 (mmt) cc_final: 0.0973 (mpm) REVERT: X 317 MET cc_start: -0.2705 (ptt) cc_final: -0.2962 (ptt) REVERT: f 86 ASP cc_start: 0.5353 (OUTLIER) cc_final: 0.5121 (p0) REVERT: i 95 MET cc_start: -0.0984 (mtp) cc_final: -0.1463 (mtt) REVERT: k 114 LYS cc_start: 0.1263 (OUTLIER) cc_final: 0.0658 (tmmt) REVERT: l 190 MET cc_start: -0.0691 (mmt) cc_final: -0.1719 (mpp) REVERT: m 25 TYR cc_start: -0.0363 (OUTLIER) cc_final: -0.0852 (t80) REVERT: m 60 LEU cc_start: -0.3013 (OUTLIER) cc_final: -0.4474 (tt) REVERT: p 256 MET cc_start: 0.2212 (OUTLIER) cc_final: 0.1915 (tpt) outliers start: 236 outliers final: 119 residues processed: 883 average time/residue: 1.7451 time to fit residues: 2127.5783 Evaluate side-chains 801 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 664 time to evaluate : 8.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 724 MET Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 3 residue 96 ILE Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1006 ILE Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1448 GLU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 598 GLU Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 872 GLU Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 406 ILE Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain U residue 245 LEU Chi-restraints excluded: chain V residue 50 GLU Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain b residue 68 GLN Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 51 ASN Chi-restraints excluded: chain e residue 96 ASP Chi-restraints excluded: chain e residue 216 LEU Chi-restraints excluded: chain e residue 217 THR Chi-restraints excluded: chain e residue 260 SER Chi-restraints excluded: chain f residue 86 ASP Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 187 ASP Chi-restraints excluded: chain h residue 90 TYR Chi-restraints excluded: chain j residue 10 GLN Chi-restraints excluded: chain k residue 11 LEU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 697 ASN Chi-restraints excluded: chain m residue 15 TYR Chi-restraints excluded: chain m residue 25 TYR Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain n residue 83 VAL Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain n residue 121 HIS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 29 PHE Chi-restraints excluded: chain p residue 256 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 399 optimal weight: 0.9980 chunk 1069 optimal weight: 50.0000 chunk 234 optimal weight: 40.0000 chunk 697 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 1189 optimal weight: 50.0000 chunk 987 optimal weight: 10.0000 chunk 550 optimal weight: 0.8980 chunk 98 optimal weight: 50.0000 chunk 393 optimal weight: 0.5980 chunk 624 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 19 GLN ** 2 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 395 GLN A 517 ASN A1106 ASN ** A1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 706 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN M 114 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 138 GLN ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 265 ASN ** b 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 371 HIS ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 119 ASN i 150 ASN ** i 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 5 ASN ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 ASN ** n 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 104070 Z= 0.225 Angle : 0.594 12.403 141152 Z= 0.306 Chirality : 0.042 0.269 16015 Planarity : 0.004 0.109 17567 Dihedral : 11.564 176.605 14931 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.77 % Favored : 97.22 % Rotamer: Outliers : 1.79 % Allowed : 14.68 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.08), residues: 12095 helix: 1.35 (0.07), residues: 5443 sheet: -0.19 (0.13), residues: 1618 loop : -0.46 (0.09), residues: 5034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP o 125 HIS 0.007 0.001 HIS A 659 PHE 0.033 0.001 PHE j 70 TYR 0.041 0.001 TYR 3 136 ARG 0.013 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 698 time to evaluate : 8.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: -0.1079 (mmm) cc_final: -0.2201 (mmt) REVERT: 0 42 MET cc_start: -0.0625 (OUTLIER) cc_final: -0.1153 (ttt) REVERT: 0 61 MET cc_start: 0.0873 (mpt) cc_final: 0.0334 (mpt) REVERT: 0 90 MET cc_start: -0.1284 (mmt) cc_final: -0.2437 (mpt) REVERT: 0 136 MET cc_start: 0.0290 (OUTLIER) cc_final: -0.0608 (ppp) REVERT: 0 472 MET cc_start: -0.0054 (ttt) cc_final: -0.0993 (tmm) REVERT: 0 485 MET cc_start: -0.1192 (ptm) cc_final: -0.1999 (ptp) REVERT: 0 557 MET cc_start: 0.1876 (OUTLIER) cc_final: 0.0969 (pmt) REVERT: 0 642 MET cc_start: 0.0096 (mmt) cc_final: -0.0543 (mmp) REVERT: 0 724 MET cc_start: -0.1188 (OUTLIER) cc_final: -0.2163 (ptt) REVERT: 1 1 MET cc_start: -0.0619 (tpt) cc_final: -0.0860 (tpt) REVERT: 1 58 MET cc_start: -0.1074 (mtm) cc_final: -0.1431 (mtm) REVERT: 1 469 MET cc_start: -0.2417 (tpt) cc_final: -0.2934 (tpt) REVERT: 1 608 MET cc_start: -0.0517 (tmm) cc_final: -0.1090 (tpt) REVERT: 2 50 MET cc_start: 0.0535 (tmt) cc_final: -0.0207 (tmt) REVERT: 2 81 MET cc_start: -0.3089 (mtm) cc_final: -0.3520 (mmm) REVERT: 2 194 GLN cc_start: -0.1553 (OUTLIER) cc_final: -0.2208 (pp30) REVERT: 2 227 MET cc_start: -0.1365 (ttp) cc_final: -0.5307 (mtt) REVERT: 2 253 MET cc_start: -0.2039 (mmt) cc_final: -0.3402 (mmt) REVERT: 4 114 MET cc_start: -0.1371 (OUTLIER) cc_final: -0.2057 (tpt) REVERT: 4 252 MET cc_start: -0.0069 (OUTLIER) cc_final: -0.0488 (tpt) REVERT: 5 27 MET cc_start: -0.3530 (ptt) cc_final: -0.3965 (pp-130) REVERT: 6 95 MET cc_start: -0.0218 (ppp) cc_final: -0.2182 (tmt) REVERT: 6 106 ARG cc_start: -0.0447 (mmp-170) cc_final: -0.1343 (mmt180) REVERT: 6 322 MET cc_start: 0.0574 (pp-130) cc_final: -0.0107 (ppp) REVERT: 7 112 MET cc_start: -0.1552 (ppp) cc_final: -0.1923 (ppp) REVERT: 7 561 MET cc_start: 0.0114 (mmt) cc_final: -0.0518 (mmt) REVERT: 7 622 MET cc_start: -0.2147 (mtt) cc_final: -0.2911 (mtt) REVERT: A 22 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: A 63 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7895 (mtm110) REVERT: A 1320 PRO cc_start: 0.8844 (Cg_endo) cc_final: 0.8553 (Cg_exo) REVERT: A 1386 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7697 (ptp90) REVERT: B 545 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8844 (mp) REVERT: B 763 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: C 179 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: K 14 GLU cc_start: 0.5950 (mm-30) cc_final: 0.5637 (mm-30) REVERT: L 34 CYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8345 (p) REVERT: W 227 MET cc_start: 0.2272 (mmt) cc_final: 0.1208 (mpm) REVERT: X 317 MET cc_start: -0.2503 (ptt) cc_final: -0.2758 (ptt) REVERT: a 281 ASP cc_start: 0.4178 (OUTLIER) cc_final: 0.3848 (p0) REVERT: c 1 MET cc_start: 0.2942 (tmt) cc_final: 0.2445 (tmm) REVERT: d 411 MET cc_start: 0.4672 (OUTLIER) cc_final: 0.4078 (tpp) REVERT: f 86 ASP cc_start: 0.5449 (OUTLIER) cc_final: 0.5242 (p0) REVERT: i 95 MET cc_start: -0.1026 (mtp) cc_final: -0.1479 (mtt) REVERT: j 87 LEU cc_start: 0.3097 (tt) cc_final: 0.2869 (mt) REVERT: k 114 LYS cc_start: 0.1256 (OUTLIER) cc_final: 0.0604 (tmmt) REVERT: l 190 MET cc_start: -0.0867 (mmt) cc_final: -0.1904 (mpp) REVERT: m 25 TYR cc_start: -0.0168 (OUTLIER) cc_final: -0.0795 (t80) REVERT: m 60 LEU cc_start: -0.3091 (OUTLIER) cc_final: -0.4496 (tt) REVERT: p 14 MET cc_start: 0.3241 (tmm) cc_final: 0.2415 (tpp) REVERT: p 256 MET cc_start: 0.2369 (OUTLIER) cc_final: 0.2086 (tpt) outliers start: 199 outliers final: 87 residues processed: 844 average time/residue: 1.7952 time to fit residues: 2083.7280 Evaluate side-chains 761 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 654 time to evaluate : 8.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 557 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 724 MET Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 3 residue 96 ILE Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 7 residue 445 MET Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 336 ASP Chi-restraints excluded: chain Q residue 406 ILE Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain U residue 245 LEU Chi-restraints excluded: chain V residue 50 GLU Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain a residue 281 ASP Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain b residue 212 ILE Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain d residue 411 MET Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 170 ASP Chi-restraints excluded: chain e residue 217 THR Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 86 ASP Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 187 ASP Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain h residue 90 TYR Chi-restraints excluded: chain h residue 186 ASP Chi-restraints excluded: chain i residue 153 THR Chi-restraints excluded: chain j residue 10 GLN Chi-restraints excluded: chain k residue 11 LEU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain m residue 15 TYR Chi-restraints excluded: chain m residue 25 TYR Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain n residue 83 VAL Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain n residue 110 GLU Chi-restraints excluded: chain n residue 121 HIS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 256 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 1146 optimal weight: 50.0000 chunk 134 optimal weight: 10.0000 chunk 677 optimal weight: 0.8980 chunk 868 optimal weight: 1.9990 chunk 672 optimal weight: 4.9990 chunk 1000 optimal weight: 6.9990 chunk 664 optimal weight: 5.9990 chunk 1184 optimal weight: 10.0000 chunk 741 optimal weight: 0.9980 chunk 722 optimal weight: 4.9990 chunk 546 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN A1312 ASN B 395 GLN B 706 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN M 114 GLN ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 371 HIS e 3 GLN ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 160 HIS ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 104070 Z= 0.284 Angle : 0.620 16.827 141152 Z= 0.316 Chirality : 0.043 0.323 16015 Planarity : 0.004 0.119 17567 Dihedral : 11.541 176.032 14931 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.94 % Favored : 97.05 % Rotamer: Outliers : 1.78 % Allowed : 15.13 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.08), residues: 12095 helix: 1.39 (0.07), residues: 5441 sheet: -0.19 (0.13), residues: 1636 loop : -0.42 (0.09), residues: 5018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP o 49 HIS 0.009 0.001 HIS A 659 PHE 0.058 0.002 PHE n 19 TYR 0.040 0.001 TYR 3 136 ARG 0.013 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 699 time to evaluate : 9.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: -0.0988 (mmm) cc_final: -0.1993 (mmt) REVERT: 0 42 MET cc_start: -0.0661 (mtp) cc_final: -0.1347 (ttt) REVERT: 0 61 MET cc_start: 0.0839 (mpt) cc_final: -0.0014 (mpt) REVERT: 0 136 MET cc_start: 0.0304 (OUTLIER) cc_final: -0.0613 (ppp) REVERT: 0 468 MET cc_start: -0.1129 (ttt) cc_final: -0.1828 (tmm) REVERT: 0 472 MET cc_start: 0.0390 (ttt) cc_final: -0.0525 (tmm) REVERT: 0 557 MET cc_start: 0.1902 (OUTLIER) cc_final: 0.0894 (pmt) REVERT: 0 642 MET cc_start: 0.0103 (mmt) cc_final: -0.0576 (mmp) REVERT: 0 724 MET cc_start: -0.1098 (OUTLIER) cc_final: -0.1947 (ptt) REVERT: 1 1 MET cc_start: -0.0523 (tpt) cc_final: -0.0780 (tpt) REVERT: 1 58 MET cc_start: -0.1383 (mtm) cc_final: -0.1939 (ptm) REVERT: 1 469 MET cc_start: -0.2428 (tpt) cc_final: -0.2921 (tpt) REVERT: 1 608 MET cc_start: -0.0842 (tmm) cc_final: -0.1284 (tpt) REVERT: 2 50 MET cc_start: 0.0658 (tmt) cc_final: -0.0105 (tmt) REVERT: 2 81 MET cc_start: -0.3129 (mtm) cc_final: -0.3531 (mmm) REVERT: 2 194 GLN cc_start: -0.1547 (OUTLIER) cc_final: -0.2195 (pp30) REVERT: 2 210 MET cc_start: 0.0760 (ptm) cc_final: 0.0135 (ptp) REVERT: 2 227 MET cc_start: -0.1403 (ttp) cc_final: -0.5324 (mtt) REVERT: 2 253 MET cc_start: -0.2398 (mmt) cc_final: -0.4770 (mtm) REVERT: 4 114 MET cc_start: -0.1100 (OUTLIER) cc_final: -0.1754 (tpt) REVERT: 4 252 MET cc_start: -0.0001 (OUTLIER) cc_final: -0.0420 (tpt) REVERT: 5 27 MET cc_start: -0.3344 (ptt) cc_final: -0.3878 (pp-130) REVERT: 6 95 MET cc_start: -0.0294 (ppp) cc_final: -0.2178 (tmt) REVERT: 6 106 ARG cc_start: -0.0444 (mmp-170) cc_final: -0.1358 (mmt180) REVERT: 6 322 MET cc_start: 0.0876 (pp-130) cc_final: 0.0389 (tmt) REVERT: 7 112 MET cc_start: -0.1642 (ppp) cc_final: -0.2034 (ppp) REVERT: 7 561 MET cc_start: 0.0025 (mmt) cc_final: -0.0676 (mmt) REVERT: 7 622 MET cc_start: -0.2144 (mtt) cc_final: -0.2895 (mtt) REVERT: A 22 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: A 63 ARG cc_start: 0.8163 (ttp-110) cc_final: 0.7900 (mtm110) REVERT: A 1386 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7722 (ptp90) REVERT: B 545 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 763 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: C 179 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: L 34 CYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8336 (p) REVERT: X 317 MET cc_start: -0.2663 (ptt) cc_final: -0.2906 (ptt) REVERT: a 281 ASP cc_start: 0.4075 (OUTLIER) cc_final: 0.3726 (p0) REVERT: c 1 MET cc_start: 0.2881 (tmt) cc_final: 0.2460 (tmm) REVERT: d 411 MET cc_start: 0.4315 (mmp) cc_final: 0.4015 (tpp) REVERT: f 86 ASP cc_start: 0.5495 (OUTLIER) cc_final: 0.5277 (p0) REVERT: h 69 ILE cc_start: 0.1992 (OUTLIER) cc_final: 0.1221 (mm) REVERT: i 95 MET cc_start: -0.1129 (mtp) cc_final: -0.1572 (mtt) REVERT: k 114 LYS cc_start: 0.1423 (OUTLIER) cc_final: 0.0780 (tmmt) REVERT: l 104 MET cc_start: -0.0878 (mpp) cc_final: -0.2373 (mpt) REVERT: l 190 MET cc_start: -0.0826 (mmt) cc_final: -0.2182 (mpp) REVERT: m 25 TYR cc_start: -0.0288 (OUTLIER) cc_final: -0.0907 (t80) REVERT: m 60 LEU cc_start: -0.3097 (OUTLIER) cc_final: -0.4485 (tt) REVERT: p 14 MET cc_start: 0.3223 (tmm) cc_final: 0.2437 (tpp) REVERT: p 256 MET cc_start: 0.2512 (OUTLIER) cc_final: 0.2080 (tpt) outliers start: 198 outliers final: 104 residues processed: 842 average time/residue: 1.7831 time to fit residues: 2089.4291 Evaluate side-chains 783 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 660 time to evaluate : 8.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 557 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 724 MET Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 364 ILE Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 3 residue 96 ILE Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 336 ASP Chi-restraints excluded: chain Q residue 406 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain V residue 50 GLU Chi-restraints excluded: chain V residue 111 LEU Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 157 VAL Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain a residue 281 ASP Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 170 ASP Chi-restraints excluded: chain e residue 216 LEU Chi-restraints excluded: chain e residue 217 THR Chi-restraints excluded: chain e residue 260 SER Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 86 ASP Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 187 ASP Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain h residue 69 ILE Chi-restraints excluded: chain h residue 90 TYR Chi-restraints excluded: chain h residue 186 ASP Chi-restraints excluded: chain j residue 10 GLN Chi-restraints excluded: chain k residue 11 LEU Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 95 VAL Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain m residue 15 TYR Chi-restraints excluded: chain m residue 25 TYR Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain n residue 83 VAL Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain n residue 110 GLU Chi-restraints excluded: chain n residue 121 HIS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 256 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 732 optimal weight: 10.0000 chunk 473 optimal weight: 0.6980 chunk 707 optimal weight: 0.7980 chunk 356 optimal weight: 0.6980 chunk 232 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 753 optimal weight: 9.9990 chunk 807 optimal weight: 9.9990 chunk 585 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 931 optimal weight: 50.0000 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 138 ASN ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 356 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN A1312 ASN ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 706 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 270 GLN ** b 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 371 HIS ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 99 GLN i 160 HIS ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 104070 Z= 0.281 Angle : 0.628 13.976 141152 Z= 0.319 Chirality : 0.043 0.363 16015 Planarity : 0.004 0.123 17567 Dihedral : 11.549 176.043 14931 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.94 % Favored : 97.05 % Rotamer: Outliers : 1.72 % Allowed : 15.71 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.08), residues: 12095 helix: 1.39 (0.07), residues: 5454 sheet: -0.17 (0.13), residues: 1644 loop : -0.39 (0.09), residues: 4997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP o 49 HIS 0.010 0.001 HIS A 659 PHE 0.029 0.002 PHE j 70 TYR 0.037 0.001 TYR 3 136 ARG 0.015 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 683 time to evaluate : 8.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: -0.1089 (mmm) cc_final: -0.2152 (mmt) REVERT: 0 42 MET cc_start: -0.0594 (mtp) cc_final: -0.1388 (ttt) REVERT: 0 61 MET cc_start: 0.0642 (mpt) cc_final: -0.0186 (mpt) REVERT: 0 90 MET cc_start: -0.1628 (mmt) cc_final: -0.2827 (mpt) REVERT: 0 136 MET cc_start: 0.0333 (OUTLIER) cc_final: -0.0634 (ppp) REVERT: 0 468 MET cc_start: -0.1311 (ttt) cc_final: -0.2054 (tmm) REVERT: 0 472 MET cc_start: 0.0402 (ttt) cc_final: -0.0699 (tmm) REVERT: 0 485 MET cc_start: -0.1150 (ptm) cc_final: -0.1391 (ptm) REVERT: 0 642 MET cc_start: 0.0101 (mmt) cc_final: -0.0565 (mmp) REVERT: 0 724 MET cc_start: -0.1230 (OUTLIER) cc_final: -0.2107 (ptt) REVERT: 1 1 MET cc_start: -0.0624 (tpt) cc_final: -0.0941 (tpt) REVERT: 1 469 MET cc_start: -0.2502 (tpt) cc_final: -0.3019 (tpt) REVERT: 1 608 MET cc_start: -0.0997 (tmm) cc_final: -0.1344 (tpt) REVERT: 2 50 MET cc_start: 0.0725 (tmt) cc_final: -0.0034 (tmt) REVERT: 2 81 MET cc_start: -0.3143 (mtm) cc_final: -0.3536 (mmm) REVERT: 2 173 MET cc_start: -0.1669 (mmt) cc_final: -0.2276 (mmt) REVERT: 2 194 GLN cc_start: -0.1538 (OUTLIER) cc_final: -0.2187 (pp30) REVERT: 2 210 MET cc_start: 0.0898 (ptm) cc_final: 0.0206 (ptp) REVERT: 2 227 MET cc_start: -0.1477 (ttp) cc_final: -0.5312 (mtt) REVERT: 2 253 MET cc_start: -0.2315 (mmt) cc_final: -0.4657 (mtm) REVERT: 4 114 MET cc_start: -0.0939 (OUTLIER) cc_final: -0.1597 (tpt) REVERT: 4 252 MET cc_start: 0.0019 (OUTLIER) cc_final: -0.0401 (tpt) REVERT: 5 27 MET cc_start: -0.3356 (ptt) cc_final: -0.3928 (pp-130) REVERT: 6 106 ARG cc_start: -0.0449 (mmp-170) cc_final: -0.1380 (mmt180) REVERT: 6 322 MET cc_start: 0.0849 (pp-130) cc_final: 0.0407 (tmt) REVERT: 7 112 MET cc_start: -0.1532 (ppp) cc_final: -0.1944 (ppp) REVERT: 7 561 MET cc_start: -0.0069 (mmt) cc_final: -0.0665 (mmt) REVERT: 7 622 MET cc_start: -0.2565 (mtt) cc_final: -0.3287 (mtt) REVERT: A 22 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: A 63 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7919 (mtm110) REVERT: A 1202 MET cc_start: 0.4059 (mmm) cc_final: 0.3818 (mmm) REVERT: A 1386 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7739 (ptp90) REVERT: B 545 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8850 (mp) REVERT: B 763 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7752 (tt0) REVERT: C 179 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: C 265 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7040 (ptm) REVERT: L 34 CYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8351 (p) REVERT: W 368 GLN cc_start: -0.1882 (OUTLIER) cc_final: -0.2264 (mt0) REVERT: X 317 MET cc_start: -0.2684 (ptt) cc_final: -0.2993 (ptt) REVERT: a 281 ASP cc_start: 0.4076 (OUTLIER) cc_final: 0.3727 (p0) REVERT: c 1 MET cc_start: 0.2802 (tmt) cc_final: 0.2369 (tmm) REVERT: d 411 MET cc_start: 0.4205 (OUTLIER) cc_final: 0.3889 (tpp) REVERT: f 86 ASP cc_start: 0.5740 (OUTLIER) cc_final: 0.5529 (p0) REVERT: i 95 MET cc_start: -0.1154 (mtp) cc_final: -0.1582 (mtt) REVERT: k 114 LYS cc_start: 0.1385 (OUTLIER) cc_final: 0.0757 (tmmt) REVERT: l 190 MET cc_start: -0.0762 (mmt) cc_final: -0.1979 (mtt) REVERT: l 510 MET cc_start: -0.0367 (ppp) cc_final: -0.0724 (pp-130) REVERT: l 676 MET cc_start: 0.4204 (pp-130) cc_final: 0.3956 (ppp) REVERT: m 25 TYR cc_start: -0.0170 (OUTLIER) cc_final: -0.0772 (t80) REVERT: m 60 LEU cc_start: -0.3286 (OUTLIER) cc_final: -0.4582 (tt) REVERT: p 14 MET cc_start: 0.3339 (tmm) cc_final: 0.2596 (tpp) REVERT: p 256 MET cc_start: 0.2644 (OUTLIER) cc_final: 0.2190 (tpt) outliers start: 192 outliers final: 105 residues processed: 822 average time/residue: 1.7844 time to fit residues: 2033.1478 Evaluate side-chains 778 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 653 time to evaluate : 9.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 724 MET Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 3 residue 96 ILE Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 45 GLN Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 406 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain V residue 50 GLU Chi-restraints excluded: chain V residue 111 LEU Chi-restraints excluded: chain V residue 119 LYS Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 157 VAL Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain a residue 281 ASP Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain d residue 411 MET Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 170 ASP Chi-restraints excluded: chain e residue 217 THR Chi-restraints excluded: chain e residue 273 THR Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 86 ASP Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 187 ASP Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain h residue 90 TYR Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 186 ASP Chi-restraints excluded: chain h residue 193 LEU Chi-restraints excluded: chain j residue 10 GLN Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain m residue 14 TYR Chi-restraints excluded: chain m residue 15 TYR Chi-restraints excluded: chain m residue 25 TYR Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain n residue 83 VAL Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain n residue 110 GLU Chi-restraints excluded: chain n residue 121 HIS Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 256 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 1077 optimal weight: 20.0000 chunk 1134 optimal weight: 0.0670 chunk 1035 optimal weight: 0.8980 chunk 1103 optimal weight: 50.0000 chunk 664 optimal weight: 3.9990 chunk 480 optimal weight: 0.6980 chunk 866 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 997 optimal weight: 9.9990 chunk 1044 optimal weight: 20.0000 chunk 1100 optimal weight: 40.0000 overall best weight: 3.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN A 209 ASN A 650 GLN A1106 ASN ** A1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN K 29 ASN M 114 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 270 GLN ** b 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 371 HIS d 502 ASN f 65 HIS f 141 ASN i 160 HIS ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 74 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5413 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 104070 Z= 0.368 Angle : 0.665 14.080 141152 Z= 0.338 Chirality : 0.044 0.392 16015 Planarity : 0.005 0.116 17567 Dihedral : 11.577 175.821 14931 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.11 % Favored : 96.88 % Rotamer: Outliers : 1.60 % Allowed : 16.09 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.08), residues: 12095 helix: 1.36 (0.07), residues: 5438 sheet: -0.14 (0.13), residues: 1622 loop : -0.43 (0.09), residues: 5035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP o 125 HIS 0.012 0.001 HIS A 659 PHE 0.060 0.002 PHE n 19 TYR 0.036 0.001 TYR 3 136 ARG 0.015 0.001 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 671 time to evaluate : 9.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: -0.1081 (mmm) cc_final: -0.2131 (mmt) REVERT: 0 42 MET cc_start: -0.0436 (OUTLIER) cc_final: -0.1619 (ttt) REVERT: 0 61 MET cc_start: 0.0639 (mpt) cc_final: -0.0189 (mpt) REVERT: 0 90 MET cc_start: -0.1689 (mmt) cc_final: -0.2852 (mpt) REVERT: 0 136 MET cc_start: 0.0274 (OUTLIER) cc_final: -0.0593 (ppp) REVERT: 0 468 MET cc_start: -0.0794 (ttt) cc_final: -0.1522 (tmm) REVERT: 0 472 MET cc_start: 0.0371 (ttt) cc_final: -0.0759 (tmm) REVERT: 0 485 MET cc_start: -0.1128 (ptm) cc_final: -0.1371 (ptm) REVERT: 0 642 MET cc_start: 0.0287 (mmt) cc_final: -0.0339 (mmp) REVERT: 0 724 MET cc_start: -0.1169 (OUTLIER) cc_final: -0.2038 (ptt) REVERT: 1 1 MET cc_start: -0.0559 (tpt) cc_final: -0.0888 (tpt) REVERT: 1 58 MET cc_start: -0.1353 (mtm) cc_final: -0.1597 (mtp) REVERT: 1 469 MET cc_start: -0.2502 (tpt) cc_final: -0.3005 (tpt) REVERT: 1 608 MET cc_start: -0.1003 (tmm) cc_final: -0.1301 (tpt) REVERT: 2 50 MET cc_start: 0.0726 (tmt) cc_final: -0.0006 (tmt) REVERT: 2 81 MET cc_start: -0.3131 (mtm) cc_final: -0.3526 (mmm) REVERT: 2 173 MET cc_start: -0.1424 (mmt) cc_final: -0.1993 (mmt) REVERT: 2 194 GLN cc_start: -0.1618 (OUTLIER) cc_final: -0.2252 (pp30) REVERT: 2 210 MET cc_start: 0.0874 (ptm) cc_final: 0.0175 (ptp) REVERT: 2 227 MET cc_start: -0.1500 (ttp) cc_final: -0.5303 (mtt) REVERT: 2 253 MET cc_start: -0.2340 (mmt) cc_final: -0.4648 (mtm) REVERT: 4 114 MET cc_start: -0.0973 (OUTLIER) cc_final: -0.1629 (tpt) REVERT: 4 252 MET cc_start: 0.0045 (OUTLIER) cc_final: -0.0372 (tpt) REVERT: 5 27 MET cc_start: -0.3316 (ptt) cc_final: -0.3891 (pp-130) REVERT: 6 95 MET cc_start: 0.0049 (ppp) cc_final: -0.2001 (tmt) REVERT: 6 106 ARG cc_start: -0.0455 (mmp-170) cc_final: -0.1372 (mmt180) REVERT: 6 322 MET cc_start: 0.0382 (pp-130) cc_final: 0.0146 (tmt) REVERT: 7 112 MET cc_start: -0.1647 (ppp) cc_final: -0.1911 (ppp) REVERT: 7 561 MET cc_start: -0.0211 (mmt) cc_final: -0.0874 (mmt) REVERT: 7 622 MET cc_start: -0.2542 (mtt) cc_final: -0.3251 (mtt) REVERT: A 22 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: A 63 ARG cc_start: 0.8171 (ttp-110) cc_final: 0.7921 (mtm110) REVERT: A 1062 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: A 1386 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7689 (ptp90) REVERT: B 468 GLU cc_start: 0.5209 (OUTLIER) cc_final: 0.5009 (tt0) REVERT: B 545 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8953 (mt) REVERT: B 763 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: B 1133 MET cc_start: 0.8614 (mtp) cc_final: 0.8411 (mtp) REVERT: C 179 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6918 (tm-30) REVERT: C 265 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7181 (ptm) REVERT: L 34 CYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8410 (p) REVERT: W 368 GLN cc_start: -0.1953 (OUTLIER) cc_final: -0.2335 (mt0) REVERT: X 317 MET cc_start: -0.2602 (ptt) cc_final: -0.2910 (ptt) REVERT: a 281 ASP cc_start: 0.4122 (OUTLIER) cc_final: 0.3762 (p0) REVERT: c 1 MET cc_start: 0.2969 (tmt) cc_final: 0.2698 (tmm) REVERT: d 411 MET cc_start: 0.4141 (mmp) cc_final: 0.3906 (tpp) REVERT: i 95 MET cc_start: -0.1297 (mtp) cc_final: -0.1722 (mtt) REVERT: k 114 LYS cc_start: 0.1301 (OUTLIER) cc_final: 0.0698 (tmmt) REVERT: l 190 MET cc_start: -0.0679 (mmt) cc_final: -0.2110 (mpp) REVERT: l 510 MET cc_start: -0.0451 (ppp) cc_final: -0.0817 (pp-130) REVERT: l 676 MET cc_start: 0.4280 (pp-130) cc_final: 0.3916 (ppp) REVERT: m 25 TYR cc_start: -0.0039 (OUTLIER) cc_final: -0.0662 (t80) REVERT: m 60 LEU cc_start: -0.3276 (OUTLIER) cc_final: -0.4574 (tt) REVERT: p 14 MET cc_start: 0.3250 (tmm) cc_final: 0.2565 (tpp) REVERT: p 256 MET cc_start: 0.2492 (OUTLIER) cc_final: 0.2231 (tpt) outliers start: 178 outliers final: 115 residues processed: 802 average time/residue: 1.8006 time to fit residues: 1998.9062 Evaluate side-chains 782 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 646 time to evaluate : 8.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 724 MET Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 364 ILE Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 96 ILE Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1048 ASN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 GLN Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 885 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 971 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 139 LYS Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain M residue 236 LEU Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 335 LEU Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain Q residue 406 ILE Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain V residue 50 GLU Chi-restraints excluded: chain V residue 111 LEU Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 157 VAL Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain a residue 281 ASP Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain d residue 313 MET Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 170 ASP Chi-restraints excluded: chain e residue 217 THR Chi-restraints excluded: chain e residue 273 THR Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 86 ASP Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain h residue 68 ASP Chi-restraints excluded: chain h residue 90 TYR Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 186 ASP Chi-restraints excluded: chain i residue 20 VAL Chi-restraints excluded: chain j residue 10 GLN Chi-restraints excluded: chain k residue 114 LYS Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain m residue 14 TYR Chi-restraints excluded: chain m residue 15 TYR Chi-restraints excluded: chain m residue 25 TYR Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain n residue 83 VAL Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain n residue 110 GLU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 256 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 724 optimal weight: 0.9980 chunk 1167 optimal weight: 1.9990 chunk 712 optimal weight: 0.9990 chunk 553 optimal weight: 0.9980 chunk 811 optimal weight: 30.0000 chunk 1224 optimal weight: 40.0000 chunk 1126 optimal weight: 30.0000 chunk 974 optimal weight: 30.0000 chunk 101 optimal weight: 8.9990 chunk 753 optimal weight: 5.9990 chunk 597 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 19 GLN 2 85 HIS 6 212 ASN A 209 ASN A1106 ASN ** A1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 GLN B 706 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN M 114 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 159 ASN ** b 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 371 HIS i 160 HIS ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 339 ASN n 74 ASN o 119 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 104070 Z= 0.206 Angle : 0.640 13.459 141152 Z= 0.324 Chirality : 0.042 0.401 16015 Planarity : 0.004 0.131 17567 Dihedral : 11.534 176.071 14931 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.91 % Favored : 97.08 % Rotamer: Outliers : 1.22 % Allowed : 16.64 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.08), residues: 12095 helix: 1.42 (0.07), residues: 5449 sheet: -0.10 (0.13), residues: 1623 loop : -0.39 (0.09), residues: 5023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP l 181 HIS 0.011 0.001 HIS i 200 PHE 0.031 0.001 PHE B 557 TYR 0.044 0.001 TYR 3 136 ARG 0.016 0.000 ARG A 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24190 Ramachandran restraints generated. 12095 Oldfield, 0 Emsley, 12095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 675 time to evaluate : 9.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 25 MET cc_start: -0.1086 (mmm) cc_final: -0.2141 (mmt) REVERT: 0 42 MET cc_start: -0.0491 (OUTLIER) cc_final: -0.1532 (ttt) REVERT: 0 61 MET cc_start: 0.0604 (mpt) cc_final: -0.0162 (mpt) REVERT: 0 90 MET cc_start: -0.1701 (mmt) cc_final: -0.2804 (mpt) REVERT: 0 136 MET cc_start: 0.0280 (OUTLIER) cc_final: -0.0635 (ppp) REVERT: 0 468 MET cc_start: -0.0338 (ttt) cc_final: -0.1074 (tmm) REVERT: 0 472 MET cc_start: 0.0348 (ttt) cc_final: -0.0615 (tmm) REVERT: 0 485 MET cc_start: -0.0997 (ptm) cc_final: -0.1255 (ptm) REVERT: 0 547 MET cc_start: 0.3243 (mpt) cc_final: 0.2665 (mmt) REVERT: 0 557 MET cc_start: 0.2388 (pmm) cc_final: 0.2095 (pmt) REVERT: 0 642 MET cc_start: 0.0281 (mmt) cc_final: -0.0384 (mmp) REVERT: 0 724 MET cc_start: -0.1200 (OUTLIER) cc_final: -0.2041 (ptt) REVERT: 1 1 MET cc_start: -0.0697 (tpt) cc_final: -0.1000 (tpt) REVERT: 1 58 MET cc_start: -0.1359 (mtm) cc_final: -0.2211 (mtm) REVERT: 1 469 MET cc_start: -0.2535 (tpt) cc_final: -0.3031 (tpt) REVERT: 1 608 MET cc_start: -0.0986 (tmm) cc_final: -0.1273 (tpt) REVERT: 2 50 MET cc_start: 0.0443 (tmt) cc_final: -0.0138 (tmt) REVERT: 2 81 MET cc_start: -0.3142 (mtm) cc_final: -0.3519 (mmm) REVERT: 2 173 MET cc_start: -0.1426 (mmt) cc_final: -0.1886 (mmt) REVERT: 2 194 GLN cc_start: -0.1625 (OUTLIER) cc_final: -0.2253 (pp30) REVERT: 2 227 MET cc_start: -0.1643 (ttp) cc_final: -0.5376 (mtt) REVERT: 2 253 MET cc_start: -0.2345 (mmt) cc_final: -0.4646 (mtt) REVERT: 4 114 MET cc_start: -0.1002 (OUTLIER) cc_final: -0.1660 (tpt) REVERT: 4 252 MET cc_start: 0.0127 (OUTLIER) cc_final: -0.0315 (tpt) REVERT: 5 27 MET cc_start: -0.3364 (ptt) cc_final: -0.3961 (pp-130) REVERT: 6 95 MET cc_start: 0.0094 (ppp) cc_final: -0.2363 (tmt) REVERT: 6 106 ARG cc_start: -0.0472 (mmp-170) cc_final: -0.1404 (mmt180) REVERT: 6 136 MET cc_start: -0.0504 (mpt) cc_final: -0.1025 (mpt) REVERT: 6 322 MET cc_start: 0.0651 (pp-130) cc_final: 0.0450 (tmt) REVERT: 7 112 MET cc_start: -0.1593 (ppp) cc_final: -0.2173 (ppp) REVERT: 7 561 MET cc_start: -0.0118 (mmt) cc_final: -0.0790 (mmt) REVERT: 7 622 MET cc_start: -0.2541 (mtt) cc_final: -0.3254 (mtt) REVERT: A 22 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: A 63 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7892 (mtm110) REVERT: A 1333 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8155 (mt) REVERT: A 1386 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7967 (ptp90) REVERT: B 545 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8820 (mp) REVERT: B 868 MET cc_start: 0.3973 (mmm) cc_final: 0.3511 (mmm) REVERT: C 179 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: G 32 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6773 (pp20) REVERT: G 33 GLU cc_start: 0.6651 (mm-30) cc_final: 0.5839 (mm-30) REVERT: L 34 CYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8312 (p) REVERT: W 368 GLN cc_start: -0.1705 (OUTLIER) cc_final: -0.2146 (mt0) REVERT: X 317 MET cc_start: -0.2589 (ptt) cc_final: -0.2948 (ptt) REVERT: a 281 ASP cc_start: 0.4071 (OUTLIER) cc_final: 0.3724 (p0) REVERT: h 192 MET cc_start: 0.2553 (pp-130) cc_final: 0.2328 (pp-130) REVERT: i 95 MET cc_start: -0.1315 (mtp) cc_final: -0.1741 (mtt) REVERT: l 190 MET cc_start: -0.0654 (mmt) cc_final: -0.2081 (mpp) REVERT: l 339 ASN cc_start: 0.3584 (OUTLIER) cc_final: 0.2774 (t0) REVERT: l 510 MET cc_start: -0.0378 (ppp) cc_final: -0.0719 (pp-130) REVERT: l 676 MET cc_start: 0.4249 (pp-130) cc_final: 0.3881 (ppp) REVERT: m 25 TYR cc_start: -0.0195 (OUTLIER) cc_final: -0.0774 (t80) REVERT: m 60 LEU cc_start: -0.3213 (OUTLIER) cc_final: -0.4600 (tt) REVERT: p 14 MET cc_start: 0.3281 (tmm) cc_final: 0.2718 (tpp) REVERT: p 256 MET cc_start: 0.2591 (OUTLIER) cc_final: 0.2336 (tpt) outliers start: 136 outliers final: 87 residues processed: 774 average time/residue: 1.9182 time to fit residues: 2091.5021 Evaluate side-chains 757 residues out of total 11141 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 651 time to evaluate : 8.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 MET Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 495 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 724 MET Chi-restraints excluded: chain 1 residue 192 MET Chi-restraints excluded: chain 1 residue 364 ILE Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 96 ILE Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 252 MET Chi-restraints excluded: chain 7 residue 453 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 1116 LEU Chi-restraints excluded: chain A residue 1144 LYS Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 423 LYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 531 GLN Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 165 GLN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain H residue 92 ASP Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 34 CYS Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain O residue 130 ASP Chi-restraints excluded: chain Q residue 144 THR Chi-restraints excluded: chain Q residue 364 SER Chi-restraints excluded: chain R residue 39 VAL Chi-restraints excluded: chain R residue 79 GLU Chi-restraints excluded: chain V residue 50 GLU Chi-restraints excluded: chain V residue 111 LEU Chi-restraints excluded: chain W residue 89 VAL Chi-restraints excluded: chain W residue 157 VAL Chi-restraints excluded: chain W residue 368 GLN Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain a residue 281 ASP Chi-restraints excluded: chain b residue 194 LYS Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 2 VAL Chi-restraints excluded: chain e residue 170 ASP Chi-restraints excluded: chain e residue 273 THR Chi-restraints excluded: chain f residue 13 THR Chi-restraints excluded: chain f residue 20 LEU Chi-restraints excluded: chain f residue 86 ASP Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain h residue 90 TYR Chi-restraints excluded: chain h residue 103 ASP Chi-restraints excluded: chain h residue 186 ASP Chi-restraints excluded: chain i residue 20 VAL Chi-restraints excluded: chain j residue 10 GLN Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 339 ASN Chi-restraints excluded: chain m residue 14 TYR Chi-restraints excluded: chain m residue 15 TYR Chi-restraints excluded: chain m residue 25 TYR Chi-restraints excluded: chain m residue 60 LEU Chi-restraints excluded: chain n residue 83 VAL Chi-restraints excluded: chain n residue 85 VAL Chi-restraints excluded: chain n residue 110 GLU Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 39 VAL Chi-restraints excluded: chain p residue 256 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1229 random chunks: chunk 774 optimal weight: 0.9980 chunk 1038 optimal weight: 2.9990 chunk 298 optimal weight: 9.9990 chunk 899 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 270 optimal weight: 50.0000 chunk 976 optimal weight: 9.9990 chunk 408 optimal weight: 0.8980 chunk 1002 optimal weight: 1.9990 chunk 123 optimal weight: 40.0000 chunk 179 optimal weight: 30.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: