Starting phenix.real_space_refine on Tue Feb 20 11:22:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs9_14927/02_2024/7zs9_14927_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs9_14927/02_2024/7zs9_14927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs9_14927/02_2024/7zs9_14927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs9_14927/02_2024/7zs9_14927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs9_14927/02_2024/7zs9_14927_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zs9_14927/02_2024/7zs9_14927_updated.pdb" } resolution = 3.1 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= 0.003 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 416 5.49 5 Mg 1 5.21 5 S 412 5.16 5 C 53329 2.51 5 N 15106 2.21 5 O 17072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 2": "OD1" <-> "OD2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 48": "OD1" <-> "OD2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "I TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I ASP 113": "OD1" <-> "OD2" Residue "J ASP 16": "OD1" <-> "OD2" Residue "J ASP 31": "OD1" <-> "OD2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 24": "OD1" <-> "OD2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "K ASP 53": "OD1" <-> "OD2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "O ASP 154": "OD1" <-> "OD2" Residue "O GLU 222": "OE1" <-> "OE2" Residue "Q TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 11": "OE1" <-> "OE2" Residue "U PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 264": "OD1" <-> "OD2" Residue "V ASP 109": "OD1" <-> "OD2" Residue "W PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 426": "OE1" <-> "OE2" Residue "2 TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 50": "OE1" <-> "OE2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 53": "OE1" <-> "OE2" Residue "c GLU 61": "OE1" <-> "OE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "d TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "d GLU 73": "OE1" <-> "OE2" Residue "d GLU 90": "OE1" <-> "OE2" Residue "d GLU 110": "OE1" <-> "OE2" Residue "e GLU 50": "OE1" <-> "OE2" Residue "e GLU 94": "OE1" <-> "OE2" Residue "e GLU 105": "OE1" <-> "OE2" Residue "f GLU 53": "OE1" <-> "OE2" Residue "f GLU 63": "OE1" <-> "OE2" Residue "f GLU 74": "OE1" <-> "OE2" Residue "g GLU 41": "OE1" <-> "OE2" Residue "g TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 91": "OE1" <-> "OE2" Residue "g GLU 92": "OE1" <-> "OE2" Residue "h TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "h TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 90": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 86357 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 11221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 11221 Classifications: {'peptide': 1426} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1359} Chain breaks: 3 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: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 977 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 4263 Classifications: {'DNA': 209} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 208} 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: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 4300 Classifications: {'DNA': 209} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 208} 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: "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: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "b" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "c" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "d" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "e" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "f" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "g" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "h" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 820 SG CYS A 107 96.210 110.130 115.454 1.00101.52 S ATOM 844 SG CYS A 110 95.330 111.284 118.839 1.00105.58 S ATOM 1149 SG CYS A 148 99.000 111.340 117.781 1.00129.21 S ATOM 1287 SG CYS A 167 97.317 108.072 118.531 1.00137.73 S ATOM 515 SG CYS A 67 55.656 128.359 100.414 1.00 88.25 S ATOM 537 SG CYS A 70 55.768 132.136 101.073 1.00 82.10 S ATOM 590 SG CYS A 77 57.894 130.669 98.274 1.00 68.59 S ATOM 20131 SG CYS B1163 68.149 135.056 111.215 1.00 67.98 S ATOM 20149 SG CYS B1166 69.942 132.213 109.731 1.00 73.27 S ATOM 20274 SG CYS B1182 66.058 131.984 110.660 1.00 78.64 S ATOM 20293 SG CYS B1185 68.825 131.801 113.213 1.00 92.39 S ATOM 21278 SG CYS C 86 34.449 162.486 45.716 1.00 68.17 S ATOM 21295 SG CYS C 88 34.488 158.909 47.035 1.00 77.31 S ATOM 21328 SG CYS C 92 32.998 159.813 43.614 1.00 55.58 S ATOM 21351 SG CYS C 95 36.793 159.785 44.271 1.00 53.78 S ATOM 29301 SG CYS I 7 132.784 87.846 60.796 1.00119.66 S ATOM 29326 SG CYS I 10 129.378 87.345 62.627 1.00119.38 S ATOM 29492 SG CYS I 29 132.111 88.914 64.516 1.00149.14 S ATOM 29516 SG CYS I 32 132.568 85.289 63.272 1.00151.16 S ATOM 29843 SG CYS I 75 130.837 119.967 31.399 1.00 77.37 S ATOM 29865 SG CYS I 78 130.616 118.367 27.837 1.00 84.02 S ATOM 30081 SG CYS I 103 127.570 118.589 29.995 1.00 70.73 S ATOM 30101 SG CYS I 106 130.471 116.242 30.876 1.00 74.03 S ATOM 30246 SG CYS J 7 65.354 153.569 33.112 1.00 36.64 S ATOM 30269 SG CYS J 10 64.209 157.015 31.962 1.00 39.85 S ATOM 30549 SG CYS J 45 68.014 155.965 31.975 1.00 27.36 S ATOM 30555 SG CYS J 46 65.347 154.831 29.443 1.00 27.09 S ATOM 31735 SG CYS L 31 46.005 115.656 44.078 1.00 66.13 S ATOM 31755 SG CYS L 34 43.981 115.323 40.950 1.00 67.24 S ATOM 31859 SG CYS L 48 42.926 113.345 43.947 1.00 67.33 S ATOM 31882 SG CYS L 51 46.332 112.566 42.217 1.00 71.90 S ATOM 32126 SG CYS M 24 39.522 145.240 88.454 1.00108.41 S ATOM 32148 SG CYS M 27 36.750 146.627 86.284 1.00115.18 S ATOM 32292 SG CYS M 45 39.331 144.248 84.744 1.00 93.98 S ATOM 32311 SG CYS M 48 40.322 147.802 85.953 1.00 88.82 S ATOM 51219 SG CYS W 124 42.877 123.965 109.569 1.00197.13 S ATOM 51240 SG CYS W 127 46.152 123.857 107.922 1.00198.84 S ATOM 51425 SG CYS W 149 44.555 127.279 108.890 1.00188.93 S ATOM 51445 SG CYS W 152 43.336 125.171 105.903 1.00190.14 S ATOM 55328 SG CYS 0 115 77.202 83.917 188.899 1.00143.10 S ATOM 55655 SG CYS 0 156 72.322 83.161 193.155 1.00146.76 S ATOM 55470 SG CYS 0 133 73.553 89.067 190.585 1.00144.65 S ATOM 55956 SG CYS 0 191 76.963 86.823 194.901 1.00141.59 S ATOM 68381 SG CYS 3 13 59.338 109.371 143.081 1.00201.73 S ATOM 68402 SG CYS 3 16 60.223 108.877 139.501 1.00204.49 S ATOM 68597 SG CYS 3 39 61.288 112.106 141.023 1.00201.26 S ATOM 68618 SG CYS 3 42 57.780 111.485 139.992 1.00200.13 S ATOM 68550 SG CYS 3 34 50.667 114.681 151.715 1.00181.89 S ATOM 68708 SG CYS 3 54 50.377 112.468 148.632 1.00183.72 S ATOM 68746 SG CYS 3 59 47.935 112.060 151.544 1.00182.80 S ATOM 71474 SG CYS 4 289 129.530 50.979 210.525 1.00133.23 S ATOM 71493 SG CYS 4 292 133.082 52.231 211.418 1.00137.51 S ATOM 71585 SG CYS 4 305 130.987 50.662 214.030 1.00143.41 S ATOM 71603 SG CYS 4 308 129.930 54.042 212.662 1.00145.87 S ATOM 74430 SG CYS 6 349 133.840 33.092 197.982 1.00137.09 S ATOM 74451 SG CYS 6 352 132.121 30.237 196.091 1.00140.23 S ATOM 74530 SG CYS 6 363 132.239 33.669 194.578 1.00143.65 S ATOM 74549 SG CYS 6 366 130.011 33.059 197.498 1.00145.88 S ATOM 74851 SG CYS 6 403 158.457 71.149 205.160 1.00161.55 S ATOM 74874 SG CYS 6 406 159.955 69.861 201.860 1.00151.33 S ATOM 75133 SG CYS 6 437 157.339 72.605 201.795 1.00168.83 S ATOM 75154 SG CYS 6 440 156.410 69.076 202.543 1.00163.00 S ATOM 75066 SG CYS 6 429 148.467 69.209 212.163 1.00169.58 S ATOM 75089 SG CYS 6 432 151.713 68.100 213.648 1.00164.22 S ATOM 75247 SG CYS 6 451 150.682 66.599 210.377 1.00147.33 S ATOM 75264 SG CYS 6 454 148.722 65.661 213.491 1.00147.46 S ATOM 74329 SG CYS 6 336 137.341 33.208 184.385 1.00160.73 S ATOM 74341 SG CYS 6 338 135.690 36.046 186.424 1.00159.87 S ATOM 74489 SG CYS 6 357 139.250 36.340 185.201 1.00143.85 S Time building chain proxies: 31.74, per 1000 atoms: 0.37 Number of scatterers: 86357 At special positions: 0 Unit cell: (303.45, 218.4, 242.55, 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 412 16.00 P 416 15.00 Mg 1 11.99 O 17072 8.00 N 15106 7.00 C 53329 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: 27.25 Conformation dependent library (CDL) restraints added in 10.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " 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 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " 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 34 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " 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 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " 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 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " 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 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " 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 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " 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 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " 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 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " 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 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " 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 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18454 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 377 helices and 71 sheets defined 40.3% alpha, 11.3% beta 207 base pairs and 342 stacking pairs defined. Time for finding SS restraints: 28.85 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 93 through 105 removed outlier: 3.727A pdb=" N ILE A 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.510A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.907A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix No H-bonds generated for 'chain 'A' and resid 473 through 478' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.765A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 660 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 810 through 844 Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 924 through 946 Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 5.118A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1098 through 1105 Processing helix chain 'A' and resid 1122 through 1124 No H-bonds generated for 'chain 'A' and resid 1122 through 1124' Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1167 through 1176 removed outlier: 3.922A pdb=" N LEU A1172 " --> pdb=" O GLU A1168 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1187 No H-bonds generated for 'chain 'A' and resid 1185 through 1187' Processing helix chain 'A' and resid 1201 through 1204 No H-bonds generated for 'chain 'A' and resid 1201 through 1204' Processing helix chain 'A' and resid 1209 through 1220 Processing helix chain 'A' and resid 1256 through 1269 removed outlier: 4.019A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 4.169A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1341 through 1356 Processing helix chain 'A' and resid 1365 through 1375 Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1396 through 1402 removed outlier: 3.506A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1405 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.576A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.617A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 66 removed outlier: 3.813A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 320 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.958A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 358 Processing helix chain 'B' and resid 371 through 389 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 437 Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 488 through 495 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 605 Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 700 Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 773 Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 808 through 810 No H-bonds generated for 'chain 'B' and resid 808 through 810' Processing helix chain 'B' and resid 843 through 847 Processing helix chain 'B' and resid 1014 through 1018 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1061 Processing helix chain 'B' and resid 1122 through 1124 No H-bonds generated for 'chain 'B' and resid 1122 through 1124' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.844A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 266 removed outlier: 3.718A pdb=" N VAL C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 removed outlier: 3.535A pdb=" N ARG D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.707A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 150 Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 174 through 182 removed outlier: 3.690A pdb=" N ALA D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 121 No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 25 through 31 Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 32 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'H' and resid 89 through 92 Processing helix chain 'H' and resid 129 through 132 No H-bonds generated for 'chain 'H' and resid 129 through 132' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.764A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.712A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.957A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 Processing helix chain 'M' and resid 104 through 115 removed outlier: 3.610A pdb=" N GLU M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 138 Processing helix chain 'M' and resid 144 through 156 Processing helix chain 'M' and resid 168 through 182 Processing helix chain 'M' and resid 189 through 195 Processing helix chain 'M' and resid 200 through 220 Processing helix chain 'M' and resid 236 through 246 Proline residue: M 240 - end of helix Processing helix chain 'M' and resid 250 through 264 removed outlier: 3.894A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 288 Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 306 through 316 Processing helix chain 'M' and resid 320 through 323 No H-bonds generated for 'chain 'M' and resid 320 through 323' Processing helix chain 'M' and resid 326 through 331 Processing helix chain 'M' and resid 336 through 338 No H-bonds generated for 'chain 'M' and resid 336 through 338' Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 235 removed outlier: 4.405A 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 25 through 34 Processing helix chain 'Q' and resid 153 through 167 Processing helix chain 'Q' and resid 337 through 345 Processing helix chain 'Q' and resid 370 through 372 No H-bonds generated for 'chain 'Q' and resid 370 through 372' Processing helix chain 'Q' and resid 407 through 413 removed outlier: 3.885A pdb=" N LYS Q 411 " --> pdb=" O ASP Q 407 " (cutoff:3.500A) Processing helix chain 'Q' and resid 424 through 431 removed outlier: 3.512A pdb=" N LEU Q 428 " --> pdb=" O LEU Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 437 through 449 removed outlier: 3.717A pdb=" N LYS Q 444 " --> pdb=" O ARG Q 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 52 Processing helix chain 'R' and resid 75 through 80 Processing helix chain 'R' and resid 233 through 243 Processing helix chain 'R' and resid 259 through 265 removed outlier: 4.630A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 284 Processing helix chain 'R' and resid 296 through 309 Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'R' and resid 326 through 336 removed outlier: 3.529A pdb=" N CYS R 332 " --> pdb=" O HIS R 328 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP R 334 " --> pdb=" O LYS R 330 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 353 through 356 No H-bonds generated for 'chain 'R' and resid 353 through 356' Processing helix chain 'U' and resid 4 through 28 removed outlier: 4.289A pdb=" N ARG U 22 " --> pdb=" O VAL U 18 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 49 removed outlier: 4.546A pdb=" N ASP U 37 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU U 48 " --> pdb=" O LYS U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 269 through 271 No H-bonds generated for 'chain 'U' and resid 269 through 271' Processing helix chain 'V' and resid 10 through 12 No H-bonds generated for 'chain 'V' and resid 10 through 12' Processing helix chain 'V' and resid 14 through 28 removed outlier: 3.771A pdb=" N ASP V 24 " --> pdb=" O VAL V 20 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR V 25 " --> pdb=" O ASP V 21 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU V 26 " --> pdb=" O ALA V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 51 Processing helix chain 'W' and resid 4 through 20 removed outlier: 3.540A pdb=" N VAL W 17 " --> pdb=" O LEU W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 34 Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 53 through 63 removed outlier: 4.341A pdb=" N LEU W 57 " --> pdb=" O GLU W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 91 through 117 Processing helix chain 'W' and resid 133 through 139 removed outlier: 3.803A pdb=" N VAL W 137 " --> pdb=" O GLN W 133 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 133 through 139' Processing helix chain 'W' and resid 165 through 176 Processing helix chain 'W' and resid 180 through 190 removed outlier: 4.081A pdb=" N LYS W 188 " --> pdb=" O ASP W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 204 removed outlier: 4.252A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) Processing helix chain 'W' and resid 269 through 287 Processing helix chain 'W' and resid 292 through 295 No H-bonds generated for 'chain 'W' and resid 292 through 295' Processing helix chain 'W' and resid 350 through 368 Processing helix chain 'X' and resid 107 through 115 removed outlier: 3.560A pdb=" N ALA X 111 " --> pdb=" O ILE X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 124 through 137 removed outlier: 3.624A pdb=" N LEU X 129 " --> pdb=" O SER X 125 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP X 130 " --> pdb=" O SER X 126 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA X 131 " --> pdb=" O LYS X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 150 Processing helix chain 'X' and resid 158 through 165 Processing helix chain 'X' and resid 189 through 197 Processing helix chain 'X' and resid 218 through 226 removed outlier: 3.622A pdb=" N GLU X 226 " --> pdb=" O ASN X 222 " (cutoff:3.500A) Processing helix chain 'X' and resid 257 through 265 removed outlier: 4.070A pdb=" N MET X 262 " --> pdb=" O GLU X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 274 through 280 removed outlier: 3.876A pdb=" N LEU X 278 " --> pdb=" O LEU X 274 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLN X 279 " --> pdb=" O PRO X 275 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP X 280 " --> pdb=" O ARG X 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 274 through 280' Processing helix chain 'X' and resid 315 through 317 No H-bonds generated for 'chain 'X' and resid 315 through 317' Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 48 through 62 Processing helix chain '0' and resid 76 through 97 Processing helix chain '0' and resid 112 through 114 No H-bonds generated for 'chain '0' and resid 112 through 114' Processing helix chain '0' and resid 126 through 136 Processing helix chain '0' and resid 140 through 147 Processing helix chain '0' and resid 157 through 164 removed outlier: 4.295A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 178 through 187 Processing helix chain '0' and resid 192 through 199 Processing helix chain '0' and resid 210 through 214 removed outlier: 3.906A pdb=" N LEU 0 214 " --> pdb=" O HIS 0 211 " (cutoff:3.500A) Processing helix chain '0' and resid 219 through 225 removed outlier: 3.787A pdb=" N ASN 0 224 " --> pdb=" O GLU 0 220 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU 0 225 " --> pdb=" O ARG 0 221 " (cutoff:3.500A) Processing helix chain '0' and resid 237 through 247 removed outlier: 5.381A pdb=" N ASP 0 241 " --> pdb=" O HIS 0 238 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 Processing helix chain '0' and resid 280 through 291 removed outlier: 4.366A pdb=" N GLU 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 313 through 315 No H-bonds generated for 'chain '0' and resid 313 through 315' Processing helix chain '0' and resid 328 through 346 Processing helix chain '0' and resid 356 through 367 Processing helix chain '0' and resid 371 through 375 Processing helix chain '0' and resid 377 through 388 Processing helix chain '0' and resid 394 through 411 removed outlier: 3.502A pdb=" N THR 0 397 " --> pdb=" O GLU 0 394 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA 0 398 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU 0 408 " --> pdb=" O PHE 0 405 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE 0 409 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER 0 410 " --> pdb=" O THR 0 407 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR 0 411 " --> pdb=" O LEU 0 408 " (cutoff:3.500A) Processing helix chain '0' and resid 443 through 452 Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 466 through 472 Proline residue: 0 470 - end of helix No H-bonds generated for 'chain '0' and resid 466 through 472' Processing helix chain '0' and resid 516 through 532 Processing helix chain '0' and resid 544 through 557 Processing helix chain '0' and resid 559 through 564 Processing helix chain '0' and resid 576 through 591 Processing helix chain '0' and resid 614 through 616 No H-bonds generated for 'chain '0' and resid 614 through 616' Processing helix chain '0' and resid 633 through 645 Processing helix chain '0' and resid 650 through 669 removed outlier: 4.507A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 689 removed outlier: 3.748A pdb=" N SER 0 687 " --> pdb=" O ARG 0 684 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) Processing helix chain '0' and resid 695 through 700 removed outlier: 3.670A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 703 through 705 No H-bonds generated for 'chain '0' and resid 703 through 705' Processing helix chain '0' and resid 710 through 724 Processing helix chain '0' and resid 741 through 751 Processing helix chain '1' and resid 94 through 120 Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 Processing helix chain '1' and resid 190 through 196 removed outlier: 3.869A pdb=" N VAL 1 194 " --> pdb=" O VAL 1 190 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 211 Processing helix chain '1' and resid 214 through 225 removed outlier: 3.938A pdb=" N THR 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 233 through 236 No H-bonds generated for 'chain '1' and resid 233 through 236' Processing helix chain '1' and resid 253 through 262 Processing helix chain '1' and resid 264 through 271 Processing helix chain '1' and resid 280 through 288 Processing helix chain '1' and resid 291 through 296 Processing helix chain '1' and resid 309 through 329 removed outlier: 3.855A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR 1 314 " --> pdb=" O ILE 1 310 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU 1 315 " --> pdb=" O ILE 1 311 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR 1 316 " --> pdb=" O ASP 1 312 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU 1 317 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 339 through 343 removed outlier: 3.764A pdb=" N ILE 1 343 " --> pdb=" O LEU 1 339 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 339 through 343' Processing helix chain '1' and resid 356 through 358 No H-bonds generated for 'chain '1' and resid 356 through 358' Processing helix chain '1' and resid 371 through 389 removed outlier: 3.832A pdb=" N LEU 1 375 " --> pdb=" O THR 1 371 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU 1 389 " --> pdb=" O MET 1 385 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 419 Processing helix chain '1' and resid 466 through 482 Processing helix chain '1' and resid 486 through 489 Processing helix chain '1' and resid 495 through 513 Processing helix chain '1' and resid 544 through 570 Processing helix chain '1' and resid 573 through 604 removed outlier: 4.915A pdb=" N SER 1 577 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN 1 602 " --> pdb=" O ASP 1 599 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY 1 603 " --> pdb=" O VAL 1 600 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP 1 604 " --> pdb=" O LEU 1 601 " (cutoff:3.500A) Processing helix chain '1' and resid 609 through 615 Processing helix chain '1' and resid 617 through 638 Processing helix chain '2' and resid 7 through 16 Processing helix chain '2' and resid 19 through 26 removed outlier: 3.514A pdb=" N TYR 2 26 " --> pdb=" O GLN 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 38 removed outlier: 3.736A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 51 Processing helix chain '2' and resid 59 through 65 Processing helix chain '2' and resid 71 through 83 Processing helix chain '2' and resid 102 through 113 Processing helix chain '2' and resid 135 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 191 Processing helix chain '2' and resid 196 through 210 Processing helix chain '2' and resid 218 through 230 Processing helix chain '2' and resid 244 through 256 Processing helix chain '2' and resid 273 through 277 Processing helix chain '2' and resid 354 through 362 removed outlier: 3.688A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 389 Processing helix chain '2' and resid 393 through 402 Processing helix chain '2' and resid 406 through 420 Processing helix chain '2' and resid 435 through 448 Processing helix chain '2' and resid 465 through 477 Processing helix chain '2' and resid 498 through 506 Processing helix chain '3' and resid 40 through 46 Processing helix chain '3' and resid 76 through 89 Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 126 through 138 removed outlier: 3.558A pdb=" N GLU 3 138 " --> pdb=" O ARG 3 134 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 43 Processing helix chain '4' and resid 49 through 67 Processing helix chain '4' and resid 91 through 96 Processing helix chain '4' and resid 116 through 138 removed outlier: 3.767A pdb=" N VAL 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 190 through 205 removed outlier: 4.355A pdb=" N ILE 4 194 " --> pdb=" O PHE 4 191 " (cutoff:3.500A) Proline residue: 4 195 - end of helix Processing helix chain '4' and resid 222 through 230 Processing helix chain '4' and resid 244 through 251 removed outlier: 3.635A pdb=" N THR 4 250 " --> pdb=" O GLN 4 246 " (cutoff:3.500A) Processing helix chain '4' and resid 256 through 258 No H-bonds generated for 'chain '4' and resid 256 through 258' Processing helix chain '4' and resid 301 through 303 No H-bonds generated for 'chain '4' and resid 301 through 303' Processing helix chain '4' and resid 314 through 320 removed outlier: 3.685A pdb=" N LYS 4 319 " --> pdb=" O HIS 4 315 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 26 removed outlier: 3.566A pdb=" N LEU 5 21 " --> pdb=" O LYS 5 17 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN 5 22 " --> pdb=" O ALA 5 18 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE 5 23 " --> pdb=" O LEU 5 19 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 61 removed outlier: 4.289A pdb=" N ARG 5 56 " --> pdb=" O HIS 5 52 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASN 5 61 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) Processing helix chain '6' and resid 83 through 86 No H-bonds generated for 'chain '6' and resid 83 through 86' Processing helix chain '6' and resid 97 through 112 removed outlier: 3.965A pdb=" N GLU 6 104 " --> pdb=" O ALA 6 100 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 137 No H-bonds generated for 'chain '6' and resid 135 through 137' Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 201 removed outlier: 3.765A pdb=" N LYS 6 201 " --> pdb=" O LYS 6 197 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 221 Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 280 Processing helix chain '6' and resid 285 through 287 No H-bonds generated for 'chain '6' and resid 285 through 287' Processing helix chain '6' and resid 294 through 303 Processing helix chain '6' and resid 373 through 383 removed outlier: 4.240A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU 6 383 " --> pdb=" O SER 6 379 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 444 Processing helix chain '6' and resid 452 through 456 Processing helix chain '7' and resid 108 through 110 No H-bonds generated for 'chain '7' and resid 108 through 110' Processing helix chain '7' and resid 127 through 129 No H-bonds generated for 'chain '7' and resid 127 through 129' Processing helix chain '7' and resid 151 through 160 removed outlier: 4.406A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 177 through 185 Processing helix chain '7' and resid 190 through 199 Processing helix chain '7' and resid 207 through 217 Processing helix chain '7' and resid 240 through 244 Processing helix chain '7' and resid 323 through 332 Processing helix chain '7' and resid 364 through 373 Processing helix chain '7' and resid 392 through 403 Processing helix chain '7' and resid 414 through 427 Processing helix chain '7' and resid 432 through 434 No H-bonds generated for 'chain '7' and resid 432 through 434' Processing helix chain '7' and resid 457 through 460 No H-bonds generated for 'chain '7' and resid 457 through 460' Processing helix chain '7' and resid 468 through 479 Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 498 through 504 removed outlier: 3.640A pdb=" N VAL 7 501 " --> pdb=" O PHE 7 498 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL 7 502 " --> pdb=" O ARG 7 499 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR 7 504 " --> pdb=" O VAL 7 501 " (cutoff:3.500A) Processing helix chain '7' and resid 522 through 530 removed outlier: 3.746A pdb=" N LEU 7 527 " --> pdb=" O ILE 7 524 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASN 7 528 " --> pdb=" O GLY 7 525 " (cutoff:3.500A) Processing helix chain '7' and resid 540 through 545 Processing helix chain '7' and resid 563 through 570 removed outlier: 3.638A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 582 removed outlier: 3.662A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE 7 582 " --> pdb=" O MET 7 578 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 Processing helix chain '7' and resid 612 through 622 Processing helix chain '7' and resid 633 through 645 Processing helix chain '7' and resid 656 through 659 No H-bonds generated for 'chain '7' and resid 656 through 659' Processing helix chain '7' and resid 680 through 689 Processing helix chain '7' and resid 694 through 697 removed outlier: 4.072A pdb=" N ASN 7 697 " --> pdb=" O LYS 7 694 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 694 through 697' Processing helix chain '7' and resid 714 through 729 removed outlier: 4.320A pdb=" N PHE 7 725 " --> pdb=" O LYS 7 721 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU 7 726 " --> pdb=" O ARG 7 722 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP 7 728 " --> pdb=" O ALA 7 724 " (cutoff:3.500A) Processing helix chain '7' and resid 753 through 766 Processing helix chain '7' and resid 833 through 835 No H-bonds generated for 'chain '7' and resid 833 through 835' Processing helix chain 'a' and resid 45 through 56 Processing helix chain 'a' and resid 64 through 77 removed outlier: 4.092A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) Processing helix chain 'a' and resid 86 through 113 Processing helix chain 'a' and resid 121 through 131 Processing helix chain 'b' and resid 26 through 28 No H-bonds generated for 'chain 'b' and resid 26 through 28' Processing helix chain 'b' and resid 31 through 40 Processing helix chain 'b' and resid 50 through 76 removed outlier: 3.550A pdb=" N HIS b 75 " --> pdb=" O THR b 71 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA b 76 " --> pdb=" O TYR b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 92 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 27 through 36 Processing helix chain 'c' and resid 45 through 72 removed outlier: 4.322A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 89 Processing helix chain 'c' and resid 91 through 96 Processing helix chain 'd' and resid 35 through 45 Processing helix chain 'd' and resid 53 through 80 Processing helix chain 'd' and resid 88 through 98 Processing helix chain 'd' and resid 101 through 120 Processing helix chain 'e' and resid 45 through 56 removed outlier: 3.502A pdb=" N ARG e 49 " --> pdb=" O THR e 45 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS e 56 " --> pdb=" O ARG e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 77 removed outlier: 3.916A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 113 Processing helix chain 'e' and resid 121 through 130 Processing helix chain 'f' and resid 31 through 41 Processing helix chain 'f' and resid 50 through 75 removed outlier: 4.322A pdb=" N THR f 71 " --> pdb=" O ARG f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 92 Processing helix chain 'g' and resid 17 through 21 Processing helix chain 'g' and resid 27 through 36 Processing helix chain 'g' and resid 45 through 72 removed outlier: 4.351A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 89 Processing helix chain 'g' and resid 91 through 94 No H-bonds generated for 'chain 'g' and resid 91 through 94' Processing helix chain 'h' and resid 35 through 45 Processing helix chain 'h' and resid 53 through 80 Processing helix chain 'h' and resid 88 through 98 Processing helix chain 'h' and resid 101 through 120 removed outlier: 4.093A pdb=" N SER h 109 " --> pdb=" O LYS h 105 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= C, first strand: chain 'A' and resid 173 through 176 removed outlier: 4.677A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 198 " --> pdb=" O TRP A 185 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.763A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.042A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.561A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.530A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= I, first strand: chain 'A' and resid 1115 through 1119 removed outlier: 3.889A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.713A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 68 through 73 Processing sheet with id= L, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.908A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= N, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= O, first strand: chain 'B' and resid 404 through 407 Processing sheet with id= P, first strand: chain 'B' and resid 223 through 227 removed outlier: 6.853A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.622A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 634 through 638 Processing sheet with id= S, first strand: chain 'B' and resid 792 through 796 removed outlier: 6.057A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 990 through 994 removed outlier: 7.057A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 872 through 874 Processing sheet with id= V, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= W, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= X, first strand: chain 'C' and resid 176 through 180 removed outlier: 6.431A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 96 through 104 removed outlier: 5.995A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AA, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AB, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.768A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AD, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.235A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 142 through 147 removed outlier: 6.744A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N ILE G 157 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N PHE G 109 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA G 159 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR G 111 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLY G 161 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.574A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.317A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 14 through 18 removed outlier: 3.933A pdb=" N LEU I 26 " --> pdb=" O ARG I 17 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 69 through 71 removed outlier: 3.621A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AL, first strand: chain 'L' and resid 37 through 40 Processing sheet with id= AM, first strand: chain 'M' and resid 34 through 37 removed outlier: 3.666A pdb=" N SER M 53 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N CYS M 45 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL M 51 " --> pdb=" O CYS M 45 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 155 through 157 Processing sheet with id= AO, first strand: chain 'O' and resid 193 through 196 removed outlier: 5.839A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Q' and resid 103 through 105 removed outlier: 6.089A pdb=" N PHE Q 384 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 118 through 122 removed outlier: 4.826A pdb=" N ALA Q 397 " --> pdb=" O GLN Q 122 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL Q 392 " --> pdb=" O GLU Q 366 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'R' and resid 93 through 98 removed outlier: 4.396A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS R 219 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU R 70 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU R 221 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG R 72 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN R 223 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'R' and resid 337 through 339 Processing sheet with id= AT, first strand: chain 'R' and resid 133 through 138 removed outlier: 3.555A pdb=" N GLY R 216 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR R 136 " --> pdb=" O ILE R 214 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE R 214 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLN R 138 " --> pdb=" O THR R 212 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR R 212 " --> pdb=" O GLN R 138 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'U' and resid 278 through 282 removed outlier: 3.948A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'V' and resid 60 through 63 Processing sheet with id= AW, first strand: chain 'V' and resid 110 through 116 removed outlier: 6.005A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'W' and resid 68 through 70 Processing sheet with id= AY, first strand: chain 'W' and resid 122 through 124 removed outlier: 3.690A pdb=" N THR W 129 " --> pdb=" O CYS W 124 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'X' and resid 169 through 172 removed outlier: 3.738A pdb=" N THR X 177 " --> pdb=" O ASP X 172 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'X' and resid 230 through 234 removed outlier: 3.761A pdb=" N TYR X 243 " --> pdb=" O LEU X 233 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '0' and resid 2 through 5 Processing sheet with id= BC, first strand: chain '0' and resid 480 through 482 removed outlier: 6.862A pdb=" N ILE 0 39 " --> pdb=" O LYS 0 481 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 205 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY 0 174 " --> pdb=" O GLY 0 105 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N GLY 0 107 " --> pdb=" O GLY 0 174 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N PHE 0 176 " --> pdb=" O GLY 0 107 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '0' and resid 250 through 253 removed outlier: 3.574A pdb=" N LEU 0 417 " --> pdb=" O THR 0 438 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '0' and resid 492 through 497 removed outlier: 7.444A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N MET 0 495 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE 0 497 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU 0 681 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG 0 618 " --> pdb=" O VAL 0 678 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL 0 680 " --> pdb=" O ARG 0 618 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL 0 620 " --> pdb=" O VAL 0 680 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA 0 682 " --> pdb=" O VAL 0 620 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N MET 0 622 " --> pdb=" O ALA 0 682 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLY 0 536 " --> pdb=" O THR 0 619 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N LEU 0 621 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL 0 538 " --> pdb=" O LEU 0 621 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE 0 623 " --> pdb=" O VAL 0 538 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE 0 540 " --> pdb=" O ILE 0 623 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA 0 596 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL 0 539 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain '1' and resid 4 through 9 removed outlier: 3.770A pdb=" N LEU 1 27 " --> pdb=" O VAL 1 40 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain '1' and resid 86 through 91 removed outlier: 4.408A pdb=" N MET 1 58 " --> pdb=" O PHE 1 91 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain '2' and resid 87 through 92 Processing sheet with id= BI, first strand: chain '2' and resid 236 through 238 Processing sheet with id= BJ, first strand: chain '2' and resid 338 through 341 removed outlier: 3.665A pdb=" N SER 2 338 " --> pdb=" O TYR 2 350 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER 2 349 " --> pdb=" O VAL 2 374 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain '2' and resid 456 through 459 removed outlier: 3.970A pdb=" N TRP 2 483 " --> pdb=" O PHE 2 492 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain '4' and resid 82 through 87 removed outlier: 3.519A pdb=" N GLY 4 82 " --> pdb=" O TYR 4 79 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL 4 178 " --> pdb=" O PRO 4 209 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP 4 211 " --> pdb=" O VAL 4 178 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR 4 180 " --> pdb=" O ASP 4 211 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL 4 213 " --> pdb=" O THR 4 180 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain '5' and resid 8 through 11 Processing sheet with id= BN, first strand: chain '6' and resid 178 through 183 removed outlier: 6.567A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain '6' and resid 326 through 328 removed outlier: 3.862A pdb=" N THR 6 326 " --> pdb=" O PHE 6 348 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY 6 346 " --> pdb=" O ILE 6 328 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain '7' and resid 132 through 134 removed outlier: 5.937A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain '7' and resid 223 through 227 removed outlier: 3.832A pdb=" N HIS 7 314 " --> pdb=" O THR 7 236 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain '7' and resid 435 through 438 removed outlier: 6.513A pdb=" N LEU 7 452 " --> pdb=" O ALA 7 436 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N PHE 7 438 " --> pdb=" O LEU 7 452 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL 7 454 " --> pdb=" O PHE 7 438 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA 7 509 " --> pdb=" O ILE 7 485 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU 7 487 " --> pdb=" O ALA 7 509 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU 7 511 " --> pdb=" O LEU 7 487 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR 7 514 " --> pdb=" O GLY 7 382 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE 7 384 " --> pdb=" O THR 7 514 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N VAL 7 385 " --> pdb=" O PRO 7 533 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU 7 535 " --> pdb=" O VAL 7 385 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain '7' and resid 734 through 736 removed outlier: 7.072A pdb=" N ALA 7 703 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA 7 555 " --> pdb=" O ALA 7 703 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE 7 705 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL 7 557 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N SER 7 707 " --> pdb=" O VAL 7 557 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N CYS 7 559 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL 7 709 " --> pdb=" O CYS 7 559 " (cutoff:3.500A) 2924 hydrogen bonds defined for protein. 8310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 514 hydrogen bonds 1028 hydrogen bond angles 0 basepair planarities 207 basepair parallelities 342 stacking parallelities Total time for adding SS restraints: 45.95 Time building geometry restraints manager: 29.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 37254 1.43 - 1.64: 50837 1.64 - 1.85: 650 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 88753 Sorted by residual: bond pdb=" N VAL 4 168 " pdb=" CA VAL 4 168 " ideal model delta sigma weight residual 1.461 1.491 -0.031 1.19e-02 7.06e+03 6.69e+00 bond pdb=" CA SER 4 164 " pdb=" CB SER 4 164 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.63e-02 3.76e+03 5.17e+00 bond pdb=" N LYS 4 173 " pdb=" CA LYS 4 173 " ideal model delta sigma weight residual 1.452 1.484 -0.032 1.41e-02 5.03e+03 5.15e+00 bond pdb=" N LEU 4 172 " pdb=" CA LEU 4 172 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.23e-02 6.61e+03 5.08e+00 bond pdb=" N THR 4 169 " pdb=" CA THR 4 169 " ideal model delta sigma weight residual 1.456 1.484 -0.027 1.21e-02 6.83e+03 5.07e+00 ... (remaining 88748 not shown) Histogram of bond angle deviations from ideal: 73.65 - 85.76: 12 85.76 - 97.86: 8 97.86 - 109.97: 16839 109.97 - 122.08: 87691 122.08 - 134.18: 17042 Bond angle restraints: 121592 Sorted by residual: angle pdb=" CA PRO 0 516 " pdb=" N PRO 0 516 " pdb=" CD PRO 0 516 " ideal model delta sigma weight residual 112.00 101.04 10.96 1.40e+00 5.10e-01 6.13e+01 angle pdb=" N VAL 4 168 " pdb=" CA VAL 4 168 " pdb=" C VAL 4 168 " ideal model delta sigma weight residual 110.62 105.98 4.64 1.02e+00 9.61e-01 2.07e+01 angle pdb=" CB MET 1 477 " pdb=" CG MET 1 477 " pdb=" SD MET 1 477 " ideal model delta sigma weight residual 112.70 125.60 -12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N LYS I 77 " pdb=" CA LYS I 77 " pdb=" C LYS I 77 " ideal model delta sigma weight residual 114.62 109.77 4.85 1.14e+00 7.69e-01 1.81e+01 angle pdb=" CB MET a 90 " pdb=" CG MET a 90 " pdb=" SD MET a 90 " ideal model delta sigma weight residual 112.70 125.45 -12.75 3.00e+00 1.11e-01 1.81e+01 ... (remaining 121587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.80: 50833 34.80 - 69.61: 2437 69.61 - 104.41: 73 104.41 - 139.22: 0 139.22 - 174.02: 2 Dihedral angle restraints: 53345 sinusoidal: 24917 harmonic: 28428 Sorted by residual: dihedral pdb=" CA PRO h 100 " pdb=" C PRO h 100 " pdb=" N GLY h 101 " pdb=" CA GLY h 101 " ideal model delta harmonic sigma weight residual -180.00 -150.43 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA PRO d 100 " pdb=" C PRO d 100 " pdb=" N GLY d 101 " pdb=" CA GLY d 101 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+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 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 53342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 12029 0.069 - 0.138: 1626 0.138 - 0.207: 83 0.207 - 0.276: 4 0.276 - 0.346: 3 Chirality restraints: 13745 Sorted by residual: 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 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB ILE 7 408 " pdb=" CA ILE 7 408 " pdb=" CG1 ILE 7 408 " pdb=" CG2 ILE 7 408 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CB THR I 3 " pdb=" CA THR I 3 " pdb=" OG1 THR I 3 " pdb=" CG2 THR I 3 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 13742 not shown) Planarity restraints: 14130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP 0 515 " -0.109 5.00e-02 4.00e+02 1.57e-01 3.92e+01 pdb=" N PRO 0 516 " 0.271 5.00e-02 4.00e+02 pdb=" CA PRO 0 516 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO 0 516 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 88 " 0.029 2.00e-02 2.50e+03 3.42e-02 2.34e+01 pdb=" CG TYR b 88 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR b 88 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYR b 88 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR b 88 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR b 88 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR b 88 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR b 88 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 127 " -0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO E 128 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " -0.052 5.00e-02 4.00e+02 ... (remaining 14127 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1850 2.67 - 3.23: 79225 3.23 - 3.79: 148552 3.79 - 4.34: 198754 4.34 - 4.90: 309712 Nonbonded interactions: 738093 Sorted by model distance: nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.117 2.170 nonbonded pdb=" OD1 ASP A 485 " pdb="MG MG A1803 " model vdw 2.171 2.170 nonbonded pdb=" OG SER a 57 " pdb=" OE1 GLU a 59 " model vdw 2.207 2.440 nonbonded pdb=" OE1 GLN 5 11 " pdb=" OG1 THR 5 38 " model vdw 2.212 2.440 nonbonded pdb=" O HIS A 451 " pdb=" OG SER A 454 " model vdw 2.220 2.440 ... (remaining 738088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'e' and resid 38 through 134) } ncs_group { reference = (chain 'b' and resid 23 through 102) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 13 through 118) selection = chain 'g' } ncs_group { reference = (chain 'd' and resid 28 through 122) selection = chain 'h' } 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 15.760 Check model and map are aligned: 0.950 Set scattering table: 0.580 Process input model: 226.450 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.380 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:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 251.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 0.110 88753 Z= 0.244 Angle : 0.686 13.319 121592 Z= 0.370 Chirality : 0.046 0.346 13745 Planarity : 0.005 0.157 14130 Dihedral : 16.830 174.022 34891 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: -0.69 (0.08), residues: 9581 helix: -0.27 (0.07), residues: 4134 sheet: -0.41 (0.14), residues: 1273 loop : -0.48 (0.09), residues: 4174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 561 HIS 0.008 0.001 HIS 2 223 PHE 0.057 0.002 PHE A 444 TYR 0.080 0.002 TYR b 88 ARG 0.017 0.001 ARG E 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1898 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1898 time to evaluate : 6.997 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: A 88 LYS cc_start: 0.8453 (mmtp) cc_final: 0.8114 (mmtp) REVERT: A 181 LEU cc_start: 0.7680 (mt) cc_final: 0.7399 (mt) REVERT: A 260 ASP cc_start: 0.7710 (t0) cc_final: 0.7216 (t70) REVERT: A 487 MET cc_start: 0.7956 (mtp) cc_final: 0.7721 (mtm) REVERT: A 873 MET cc_start: 0.8036 (mmt) cc_final: 0.7794 (mmp) REVERT: A 1128 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 1193 LEU cc_start: 0.8516 (tp) cc_final: 0.8108 (tt) REVERT: A 1239 ARG cc_start: 0.8168 (mtp-110) cc_final: 0.7775 (mtp180) REVERT: A 1259 MET cc_start: 0.7137 (mmp) cc_final: 0.6696 (ttm) REVERT: A 1285 MET cc_start: 0.7365 (mmp) cc_final: 0.7152 (mmm) REVERT: B 89 GLU cc_start: 0.8067 (tt0) cc_final: 0.7652 (tt0) REVERT: B 234 ILE cc_start: 0.8012 (mt) cc_final: 0.7725 (mt) REVERT: B 729 ILE cc_start: 0.7813 (mt) cc_final: 0.7566 (mm) REVERT: B 770 GLN cc_start: 0.8120 (tp40) cc_final: 0.7904 (tp40) REVERT: B 1022 THR cc_start: 0.8469 (m) cc_final: 0.8200 (p) REVERT: B 1028 GLU cc_start: 0.7663 (tt0) cc_final: 0.7444 (tm-30) REVERT: B 1098 MET cc_start: 0.8028 (mpp) cc_final: 0.7659 (mmt) REVERT: B 1149 GLU cc_start: 0.6749 (tt0) cc_final: 0.6544 (tt0) REVERT: D 58 VAL cc_start: 0.8092 (t) cc_final: 0.7516 (p) REVERT: E 52 ARG cc_start: 0.8003 (mmp80) cc_final: 0.7773 (ppt170) REVERT: E 91 LYS cc_start: 0.8263 (mmtt) cc_final: 0.8060 (mttp) REVERT: G 44 TYR cc_start: 0.7862 (m-80) cc_final: 0.7643 (m-80) REVERT: G 88 ASP cc_start: 0.4773 (m-30) cc_final: 0.3619 (m-30) REVERT: H 4 THR cc_start: 0.7938 (m) cc_final: 0.7425 (p) REVERT: I 20 LYS cc_start: 0.7783 (mmpt) cc_final: 0.7304 (mtmm) REVERT: I 47 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7016 (mt-10) REVERT: I 94 ASP cc_start: 0.7949 (p0) cc_final: 0.7038 (p0) REVERT: M 106 PHE cc_start: 0.7835 (m-80) cc_final: 0.6889 (m-80) REVERT: M 119 MET cc_start: 0.6409 (ppp) cc_final: 0.5533 (tpp) REVERT: M 196 ILE cc_start: 0.7782 (mp) cc_final: 0.7567 (mp) REVERT: M 234 GLN cc_start: 0.7210 (mm110) cc_final: 0.6956 (mm-40) REVERT: M 250 MET cc_start: 0.5906 (tmm) cc_final: 0.5187 (tmm) REVERT: Q 34 MET cc_start: 0.4363 (mmm) cc_final: 0.2536 (ttp) REVERT: Q 107 PRO cc_start: 0.3117 (Cg_exo) cc_final: 0.2383 (Cg_endo) REVERT: Q 131 THR cc_start: 0.6113 (p) cc_final: 0.5845 (p) REVERT: Q 340 LYS cc_start: 0.6753 (tmmt) cc_final: 0.6261 (tptt) REVERT: Q 350 TRP cc_start: 0.7656 (m100) cc_final: 0.6474 (m100) REVERT: Q 383 SER cc_start: 0.4842 (m) cc_final: 0.4411 (p) REVERT: Q 399 ASN cc_start: 0.7460 (t0) cc_final: 0.7095 (t0) REVERT: Q 410 GLU cc_start: 0.6693 (tt0) cc_final: 0.6308 (mt-10) REVERT: R 65 ASN cc_start: 0.8218 (m-40) cc_final: 0.7519 (p0) REVERT: R 138 GLN cc_start: 0.7696 (tp40) cc_final: 0.7176 (mp10) REVERT: R 228 MET cc_start: 0.7276 (mmp) cc_final: 0.6946 (ttp) REVERT: R 249 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7720 (mmtp) REVERT: R 273 ASP cc_start: 0.6119 (p0) cc_final: 0.5574 (p0) REVERT: R 294 MET cc_start: 0.1622 (tmm) cc_final: 0.0037 (ttt) REVERT: V 38 MET cc_start: 0.3986 (pmm) cc_final: 0.3351 (tpp) REVERT: W 20 PHE cc_start: 0.5013 (m-80) cc_final: 0.4719 (m-10) REVERT: W 104 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7335 (mm-40) REVERT: W 111 ASP cc_start: 0.8570 (m-30) cc_final: 0.8333 (m-30) REVERT: W 279 ARG cc_start: 0.8473 (tpt170) cc_final: 0.8032 (tpp-160) REVERT: X 216 GLN cc_start: 0.3575 (pp30) cc_final: 0.3195 (pt0) REVERT: X 240 THR cc_start: 0.5203 (p) cc_final: 0.4688 (p) REVERT: X 262 MET cc_start: 0.4750 (mtt) cc_final: 0.4469 (mtt) REVERT: 0 42 MET cc_start: 0.7758 (tpt) cc_final: 0.7525 (tpp) REVERT: 0 130 ASP cc_start: 0.8492 (m-30) cc_final: 0.8042 (t0) REVERT: 0 136 MET cc_start: 0.7680 (mtp) cc_final: 0.6857 (ttm) REVERT: 0 199 MET cc_start: 0.7425 (mtp) cc_final: 0.6985 (mtp) REVERT: 0 432 ASN cc_start: 0.7719 (t0) cc_final: 0.7341 (p0) REVERT: 0 516 PRO cc_start: 0.8533 (Cg_exo) cc_final: 0.8131 (Cg_endo) REVERT: 0 537 MET cc_start: 0.7423 (ttp) cc_final: 0.7006 (ttp) REVERT: 0 622 MET cc_start: 0.7475 (mmt) cc_final: 0.7176 (mmt) REVERT: 0 642 MET cc_start: 0.8388 (mtp) cc_final: 0.8144 (mtm) REVERT: 1 284 TRP cc_start: 0.8407 (m100) cc_final: 0.7920 (m100) REVERT: 3 20 ARG cc_start: 0.8204 (tpt90) cc_final: 0.7897 (mmt90) REVERT: 3 95 THR cc_start: 0.8908 (p) cc_final: 0.8355 (p) REVERT: 3 106 TYR cc_start: 0.8351 (t80) cc_final: 0.8104 (t80) REVERT: 4 197 MET cc_start: 0.8785 (mmp) cc_final: 0.8506 (mmp) REVERT: 4 234 VAL cc_start: 0.9141 (t) cc_final: 0.8881 (m) REVERT: 5 36 ASP cc_start: 0.5406 (m-30) cc_final: 0.5194 (t70) REVERT: 5 54 LEU cc_start: 0.8973 (tp) cc_final: 0.8762 (mt) REVERT: 6 84 TRP cc_start: 0.5484 (p90) cc_final: 0.4925 (p90) REVERT: 6 130 LEU cc_start: 0.8987 (mt) cc_final: 0.8677 (mt) REVERT: 6 148 MET cc_start: 0.7988 (ttt) cc_final: 0.7471 (ttt) REVERT: 6 216 MET cc_start: 0.7873 (ttm) cc_final: 0.7657 (ttt) REVERT: 6 243 ASP cc_start: 0.7853 (m-30) cc_final: 0.7419 (m-30) REVERT: 6 322 MET cc_start: 0.7754 (pmm) cc_final: 0.7312 (pmm) REVERT: 6 365 CYS cc_start: 0.8368 (m) cc_final: 0.7865 (m) REVERT: 7 463 THR cc_start: 0.6883 (p) cc_final: 0.6536 (t) REVERT: a 60 LEU cc_start: 0.8515 (mt) cc_final: 0.8303 (mt) REVERT: a 73 GLU cc_start: 0.7993 (tt0) cc_final: 0.7478 (tt0) REVERT: b 35 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7938 (ttp-170) REVERT: c 24 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7920 (mm110) REVERT: c 36 LYS cc_start: 0.8562 (mmtm) cc_final: 0.8310 (tmtt) REVERT: c 72 ASP cc_start: 0.8359 (m-30) cc_final: 0.8076 (m-30) REVERT: c 76 THR cc_start: 0.8340 (p) cc_final: 0.7963 (t) REVERT: e 50 GLU cc_start: 0.8322 (tt0) cc_final: 0.8115 (tt0) REVERT: e 118 THR cc_start: 0.9012 (m) cc_final: 0.8665 (p) REVERT: f 66 ILE cc_start: 0.8584 (mm) cc_final: 0.8290 (mm) REVERT: f 84 MET cc_start: 0.8108 (tpp) cc_final: 0.7364 (tpt) REVERT: g 76 THR cc_start: 0.8766 (m) cc_final: 0.8557 (p) REVERT: h 48 ASP cc_start: 0.7287 (p0) cc_final: 0.7047 (t0) outliers start: 0 outliers final: 0 residues processed: 1898 average time/residue: 0.8183 time to fit residues: 2616.8808 Evaluate side-chains 1044 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1044 time to evaluate : 6.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 841 optimal weight: 8.9990 chunk 755 optimal weight: 30.0000 chunk 419 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 509 optimal weight: 6.9990 chunk 403 optimal weight: 8.9990 chunk 781 optimal weight: 30.0000 chunk 302 optimal weight: 10.0000 chunk 475 optimal weight: 20.0000 chunk 581 optimal weight: 30.0000 chunk 905 optimal weight: 30.0000 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN A 736 ASN A 745 GLN A 851 HIS ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 GLN ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 215 GLN B 538 ASN B 572 HIS B 587 HIS ** B 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN E 5 ASN E 101 GLN E 114 ASN F 12 ASN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN M 193 GLN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 ASN ** Q 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 ASN R 328 HIS U 40 ASN V 82 ASN W 358 ASN X 136 GLN ** X 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 270 GLN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 224 ASN ** 0 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 707 ASN 1 201 ASN 1 331 HIS 1 365 ASN 1 468 GLN 1 575 GLN 1 584 ASN 2 431 GLN ** 3 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 39 HIS 5 64 ASN 6 202 GLN 6 269 GLN 6 351 ASN a 39 HIS a 68 GLN a 93 GLN ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 ASN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.176 88753 Z= 0.741 Angle : 0.827 16.350 121592 Z= 0.440 Chirality : 0.051 0.270 13745 Planarity : 0.007 0.110 14130 Dihedral : 19.766 169.096 15186 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.52 % Allowed : 9.49 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: -0.30 (0.08), residues: 9581 helix: 0.33 (0.08), residues: 4151 sheet: -0.58 (0.14), residues: 1286 loop : -0.47 (0.09), residues: 4144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 79 HIS 0.024 0.002 HIS W 261 PHE 0.049 0.003 PHE A 444 TYR 0.062 0.003 TYR b 88 ARG 0.016 0.001 ARG X 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1229 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1011 time to evaluate : 8.275 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: A 74 MET cc_start: 0.8254 (tpt) cc_final: 0.7565 (tpt) REVERT: A 146 MET cc_start: 0.8165 (mmp) cc_final: 0.7855 (mmm) REVERT: A 175 ARG cc_start: 0.8097 (ppt170) cc_final: 0.7844 (ppt170) REVERT: A 234 MET cc_start: 0.7797 (mtm) cc_final: 0.7541 (mtm) REVERT: A 304 MET cc_start: 0.8266 (mtt) cc_final: 0.7895 (mtm) REVERT: A 521 MET cc_start: 0.8727 (mtm) cc_final: 0.8455 (mtt) REVERT: A 618 GLU cc_start: 0.6140 (mt-10) cc_final: 0.5891 (mt-10) REVERT: A 672 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7415 (p0) REVERT: A 873 MET cc_start: 0.8551 (mmt) cc_final: 0.8091 (mmp) REVERT: A 903 ASN cc_start: 0.8086 (m110) cc_final: 0.7844 (t0) REVERT: A 988 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7928 (mm) REVERT: A 1199 ARG cc_start: 0.8253 (tpp80) cc_final: 0.8041 (tpp80) REVERT: A 1259 MET cc_start: 0.7116 (mmp) cc_final: 0.6696 (ttt) REVERT: B 234 ILE cc_start: 0.8725 (mt) cc_final: 0.8401 (mt) REVERT: B 312 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8284 (tm-30) REVERT: B 427 ASP cc_start: 0.8024 (m-30) cc_final: 0.7791 (t0) REVERT: B 446 LEU cc_start: 0.8966 (tp) cc_final: 0.8723 (tp) REVERT: B 770 GLN cc_start: 0.8504 (tp40) cc_final: 0.8293 (tp40) REVERT: B 1049 ASP cc_start: 0.7795 (p0) cc_final: 0.7586 (p0) REVERT: B 1116 ARG cc_start: 0.8737 (ttm170) cc_final: 0.8429 (mtt180) REVERT: B 1181 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7065 (tm-30) REVERT: C 60 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: D 58 VAL cc_start: 0.8122 (t) cc_final: 0.7912 (p) REVERT: D 173 HIS cc_start: 0.7882 (t-90) cc_final: 0.7645 (t-90) REVERT: E 52 ARG cc_start: 0.8098 (mmp80) cc_final: 0.7813 (ptt90) REVERT: F 12 ASN cc_start: 0.2285 (OUTLIER) cc_final: 0.1018 (t0) REVERT: G 44 TYR cc_start: 0.8333 (m-80) cc_final: 0.8113 (m-80) REVERT: H 136 LYS cc_start: 0.7890 (pttt) cc_final: 0.7621 (pttp) REVERT: M 106 PHE cc_start: 0.7062 (m-80) cc_final: 0.6795 (m-80) REVERT: M 119 MET cc_start: 0.6317 (ppp) cc_final: 0.5665 (tpp) REVERT: M 155 LYS cc_start: 0.8311 (tttm) cc_final: 0.8097 (tppt) REVERT: M 196 ILE cc_start: 0.8360 (mp) cc_final: 0.7983 (mp) REVERT: M 234 GLN cc_start: 0.7399 (mm110) cc_final: 0.6958 (mm-40) REVERT: Q 31 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6550 (t80) REVERT: Q 34 MET cc_start: 0.3980 (mmm) cc_final: 0.2306 (ttp) REVERT: Q 101 PHE cc_start: 0.7236 (m-10) cc_final: 0.6983 (m-80) REVERT: Q 114 MET cc_start: 0.5537 (ptp) cc_final: 0.4819 (ttm) REVERT: Q 350 TRP cc_start: 0.7859 (m100) cc_final: 0.6845 (m100) REVERT: Q 399 ASN cc_start: 0.7387 (t0) cc_final: 0.6818 (t0) REVERT: R 75 MET cc_start: 0.7412 (pmm) cc_final: 0.7161 (pmm) REVERT: R 228 MET cc_start: 0.7369 (mmp) cc_final: 0.7031 (ttp) REVERT: R 273 ASP cc_start: 0.6025 (p0) cc_final: 0.5308 (p0) REVERT: R 294 MET cc_start: 0.2026 (tmm) cc_final: 0.1081 (ttp) REVERT: U 273 ASP cc_start: 0.4922 (m-30) cc_final: 0.4605 (p0) REVERT: V 38 MET cc_start: 0.3742 (pmm) cc_final: 0.3187 (mmm) REVERT: W 111 ASP cc_start: 0.8594 (m-30) cc_final: 0.8355 (m-30) REVERT: X 136 GLN cc_start: 0.3572 (mt0) cc_final: 0.2651 (tp40) REVERT: X 168 ARG cc_start: 0.5423 (mmm160) cc_final: 0.5173 (mmm160) REVERT: X 216 GLN cc_start: 0.3826 (pp30) cc_final: 0.3228 (pt0) REVERT: 0 130 ASP cc_start: 0.8672 (m-30) cc_final: 0.8135 (t0) REVERT: 0 199 MET cc_start: 0.7694 (mtp) cc_final: 0.7111 (mtp) REVERT: 0 432 ASN cc_start: 0.7907 (t0) cc_final: 0.7243 (p0) REVERT: 0 468 MET cc_start: 0.8068 (tpp) cc_final: 0.7773 (tpp) REVERT: 0 495 MET cc_start: 0.8184 (ptp) cc_final: 0.7396 (mpp) REVERT: 0 531 LYS cc_start: 0.9154 (mtmt) cc_final: 0.8954 (mtmt) REVERT: 0 537 MET cc_start: 0.7336 (ttp) cc_final: 0.6845 (ttp) REVERT: 0 642 MET cc_start: 0.8567 (mtp) cc_final: 0.8024 (mtp) REVERT: 1 284 TRP cc_start: 0.8538 (m100) cc_final: 0.7931 (m100) REVERT: 1 469 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7825 (ptp) REVERT: 2 50 MET cc_start: 0.8527 (tpp) cc_final: 0.8301 (tpp) REVERT: 2 81 MET cc_start: 0.8033 (mmm) cc_final: 0.7825 (mpp) REVERT: 2 227 MET cc_start: 0.8818 (ptp) cc_final: 0.8290 (ppp) REVERT: 3 95 THR cc_start: 0.8696 (p) cc_final: 0.8323 (p) REVERT: 3 106 TYR cc_start: 0.8681 (t80) cc_final: 0.8111 (t80) REVERT: 4 26 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8614 (tp) REVERT: 4 81 GLN cc_start: 0.8536 (tt0) cc_final: 0.8285 (mt0) REVERT: 4 197 MET cc_start: 0.8997 (mmp) cc_final: 0.8752 (mmm) REVERT: 6 148 MET cc_start: 0.8144 (ttt) cc_final: 0.7766 (ttt) REVERT: 6 216 MET cc_start: 0.8070 (ttm) cc_final: 0.7858 (ttp) REVERT: 6 322 MET cc_start: 0.7360 (pmm) cc_final: 0.7101 (pmm) REVERT: a 73 GLU cc_start: 0.8357 (tt0) cc_final: 0.7938 (tt0) REVERT: c 24 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8184 (mm110) REVERT: c 36 LYS cc_start: 0.8828 (mmtm) cc_final: 0.8568 (ttpt) REVERT: c 72 ASP cc_start: 0.8526 (m-30) cc_final: 0.8310 (m-30) REVERT: c 76 THR cc_start: 0.8763 (p) cc_final: 0.8404 (t) REVERT: c 90 ASP cc_start: 0.7643 (t0) cc_final: 0.7243 (t0) REVERT: d 77 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8834 (mp) REVERT: f 27 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8227 (mm-40) REVERT: f 79 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.6811 (pttt) REVERT: g 92 GLU cc_start: 0.8336 (tp30) cc_final: 0.8049 (tp30) REVERT: h 48 ASP cc_start: 0.7673 (p0) cc_final: 0.7245 (t0) REVERT: h 90 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7934 (mp0) outliers start: 218 outliers final: 145 residues processed: 1152 average time/residue: 0.7745 time to fit residues: 1542.5732 Evaluate side-chains 1014 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 860 time to evaluate : 6.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1194 ARG Chi-restraints excluded: chain A residue 1270 ASN Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 38 CYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 24 CYS Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 31 PHE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 351 VAL Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain V residue 15 ILE Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 245 TRP Chi-restraints excluded: chain X residue 313 THR Chi-restraints excluded: chain X residue 315 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 127 THR Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 474 ASN Chi-restraints excluded: chain 0 residue 517 SER Chi-restraints excluded: chain 0 residue 535 ASP Chi-restraints excluded: chain 0 residue 571 VAL Chi-restraints excluded: chain 0 residue 600 SER Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 469 MET Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 3 residue 90 ASN Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 206 MET Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 367 ASP Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain 7 residue 836 MET Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 13 LYS Chi-restraints excluded: chain c residue 27 VAL Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain d residue 60 ASN Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 85 THR Chi-restraints excluded: chain h residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 503 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 753 optimal weight: 5.9990 chunk 616 optimal weight: 10.0000 chunk 249 optimal weight: 0.9990 chunk 907 optimal weight: 20.0000 chunk 979 optimal weight: 3.9990 chunk 807 optimal weight: 10.0000 chunk 899 optimal weight: 40.0000 chunk 309 optimal weight: 3.9990 chunk 727 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1278 ASN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 433 GLN B 794 ASN B 951 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN F 12 ASN G 53 ASN I 12 ASN K 2 ASN K 29 ASN K 89 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 239 GLN ** X 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 224 ASN ** 0 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 372 ASN ** 3 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN d 60 ASN d 92 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 88753 Z= 0.330 Angle : 0.587 10.884 121592 Z= 0.316 Chirality : 0.042 0.223 13745 Planarity : 0.004 0.067 14130 Dihedral : 19.696 171.191 15186 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.16 % Allowed : 12.09 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: 0.08 (0.08), residues: 9581 helix: 0.81 (0.08), residues: 4150 sheet: -0.51 (0.14), residues: 1265 loop : -0.42 (0.09), residues: 4166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP X 263 HIS 0.009 0.001 HIS A 659 PHE 0.029 0.002 PHE A 219 TYR 0.038 0.002 TYR b 88 ARG 0.013 0.001 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 951 time to evaluate : 7.049 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: A 74 MET cc_start: 0.8062 (tpt) cc_final: 0.7705 (tpp) REVERT: A 108 MET cc_start: 0.7737 (mmt) cc_final: 0.7223 (mmt) REVERT: A 234 MET cc_start: 0.7828 (mtm) cc_final: 0.7571 (mtm) REVERT: A 304 MET cc_start: 0.8193 (mtt) cc_final: 0.7914 (mtm) REVERT: A 618 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5889 (mt-10) REVERT: A 746 MET cc_start: 0.8618 (mtm) cc_final: 0.8371 (mtm) REVERT: A 873 MET cc_start: 0.8400 (mmt) cc_final: 0.7973 (mmp) REVERT: A 1036 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7746 (mtp85) REVERT: A 1194 ARG cc_start: 0.7459 (OUTLIER) cc_final: 0.7112 (mtp180) REVERT: A 1259 MET cc_start: 0.7084 (mmp) cc_final: 0.6592 (ttm) REVERT: B 427 ASP cc_start: 0.7923 (m-30) cc_final: 0.7721 (t0) REVERT: B 770 GLN cc_start: 0.8379 (tp40) cc_final: 0.8120 (tp40) REVERT: B 1049 ASP cc_start: 0.7839 (p0) cc_final: 0.7580 (p0) REVERT: B 1116 ARG cc_start: 0.8656 (ttm170) cc_final: 0.8328 (mtt180) REVERT: B 1181 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6813 (tm-30) REVERT: C 249 ASP cc_start: 0.6443 (m-30) cc_final: 0.6241 (m-30) REVERT: D 58 VAL cc_start: 0.8134 (t) cc_final: 0.7928 (p) REVERT: D 195 ILE cc_start: 0.8431 (mt) cc_final: 0.8187 (mt) REVERT: E 54 GLN cc_start: 0.7205 (pm20) cc_final: 0.6469 (pp30) REVERT: F 12 ASN cc_start: 0.2939 (OUTLIER) cc_final: 0.2477 (m-40) REVERT: F 104 ASN cc_start: 0.8745 (t0) cc_final: 0.8309 (t0) REVERT: G 44 TYR cc_start: 0.8288 (m-80) cc_final: 0.7963 (m-80) REVERT: G 144 ARG cc_start: 0.6433 (mtp-110) cc_final: 0.5416 (mtt90) REVERT: H 52 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7715 (mm-40) REVERT: H 136 LYS cc_start: 0.7638 (pttt) cc_final: 0.7419 (pttp) REVERT: I 8 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7810 (ttp80) REVERT: J 27 GLU cc_start: 0.7153 (pt0) cc_final: 0.6948 (pt0) REVERT: M 56 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8877 (pp) REVERT: M 81 GLU cc_start: 0.5117 (tp30) cc_final: 0.4410 (tt0) REVERT: M 106 PHE cc_start: 0.7046 (m-80) cc_final: 0.6773 (m-80) REVERT: M 119 MET cc_start: 0.6385 (ppp) cc_final: 0.5622 (tpp) REVERT: M 196 ILE cc_start: 0.8233 (mp) cc_final: 0.7874 (mp) REVERT: M 234 GLN cc_start: 0.7408 (mm110) cc_final: 0.6922 (mm-40) REVERT: Q 31 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.6597 (t80) REVERT: Q 34 MET cc_start: 0.3864 (mmm) cc_final: 0.2156 (ttp) REVERT: Q 114 MET cc_start: 0.5299 (ptp) cc_final: 0.4924 (ttm) REVERT: Q 384 PHE cc_start: 0.5261 (m-80) cc_final: 0.4964 (m-10) REVERT: Q 399 ASN cc_start: 0.7387 (t0) cc_final: 0.6943 (t0) REVERT: R 228 MET cc_start: 0.7347 (mmp) cc_final: 0.7024 (ttp) REVERT: R 273 ASP cc_start: 0.5995 (p0) cc_final: 0.5143 (p0) REVERT: R 294 MET cc_start: 0.1623 (tmm) cc_final: 0.0651 (ttp) REVERT: V 38 MET cc_start: 0.3786 (pmm) cc_final: 0.3166 (tpp) REVERT: W 111 ASP cc_start: 0.8586 (m-30) cc_final: 0.8366 (m-30) REVERT: X 136 GLN cc_start: 0.3791 (mt0) cc_final: 0.2906 (tp40) REVERT: X 216 GLN cc_start: 0.4120 (pp30) cc_final: 0.3510 (pt0) REVERT: 0 42 MET cc_start: 0.7962 (tpt) cc_final: 0.7645 (tpp) REVERT: 0 136 MET cc_start: 0.7839 (mtp) cc_final: 0.7578 (mtp) REVERT: 0 199 MET cc_start: 0.7690 (mtp) cc_final: 0.7147 (mtp) REVERT: 0 432 ASN cc_start: 0.7887 (t0) cc_final: 0.7249 (p0) REVERT: 0 468 MET cc_start: 0.8160 (tpp) cc_final: 0.7892 (tpp) REVERT: 0 495 MET cc_start: 0.8525 (ptp) cc_final: 0.7633 (mpp) REVERT: 0 528 GLU cc_start: 0.7655 (tp30) cc_final: 0.7405 (tp30) REVERT: 0 642 MET cc_start: 0.8559 (mtp) cc_final: 0.8039 (mtp) REVERT: 1 210 TRP cc_start: 0.8421 (m100) cc_final: 0.7889 (m100) REVERT: 1 284 TRP cc_start: 0.8584 (m100) cc_final: 0.7906 (m100) REVERT: 1 469 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7871 (ptp) REVERT: 2 50 MET cc_start: 0.8514 (tpp) cc_final: 0.8174 (tpp) REVERT: 2 227 MET cc_start: 0.8791 (ptp) cc_final: 0.8254 (tmm) REVERT: 3 106 TYR cc_start: 0.8598 (t80) cc_final: 0.8347 (t80) REVERT: 3 107 ASN cc_start: 0.8115 (m110) cc_final: 0.7731 (m-40) REVERT: 4 26 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8597 (tp) REVERT: 4 197 MET cc_start: 0.8872 (mmp) cc_final: 0.8656 (mmm) REVERT: 5 19 LEU cc_start: 0.8073 (tt) cc_final: 0.7829 (tp) REVERT: 6 95 MET cc_start: 0.2506 (mtm) cc_final: 0.1092 (tpp) REVERT: 6 136 MET cc_start: 0.7911 (mmm) cc_final: 0.7045 (mmm) REVERT: 6 148 MET cc_start: 0.8187 (ttt) cc_final: 0.7812 (ttt) REVERT: a 73 GLU cc_start: 0.8346 (tt0) cc_final: 0.7898 (tt0) REVERT: c 24 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8163 (mm110) REVERT: c 72 ASP cc_start: 0.8489 (m-30) cc_final: 0.8237 (m-30) REVERT: c 76 THR cc_start: 0.8636 (p) cc_final: 0.8262 (t) REVERT: c 90 ASP cc_start: 0.7359 (t0) cc_final: 0.6575 (t0) REVERT: d 77 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8774 (mp) REVERT: f 27 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8213 (mm-40) REVERT: f 63 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7565 (mt-10) REVERT: f 79 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7381 (ptpt) REVERT: f 92 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8170 (ttp-170) REVERT: g 95 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8289 (tptt) REVERT: h 48 ASP cc_start: 0.7539 (p0) cc_final: 0.7139 (t0) REVERT: h 90 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7917 (mp0) outliers start: 187 outliers final: 132 residues processed: 1064 average time/residue: 0.7714 time to fit residues: 1424.2976 Evaluate side-chains 1008 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 866 time to evaluate : 7.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1194 ARG Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 27 MET Chi-restraints excluded: chain Q residue 31 PHE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 148 GLN Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 313 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 517 SER Chi-restraints excluded: chain 0 residue 524 SER Chi-restraints excluded: chain 0 residue 535 ASP Chi-restraints excluded: chain 0 residue 560 LEU Chi-restraints excluded: chain 0 residue 571 VAL Chi-restraints excluded: chain 0 residue 600 SER Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 469 MET Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 206 MET Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 6 residue 149 ILE Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 367 ASP Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain 7 residue 836 MET Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 13 LYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 60 ASN Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain f residue 85 ASP Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 95 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 896 optimal weight: 8.9990 chunk 681 optimal weight: 50.0000 chunk 470 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 432 optimal weight: 20.0000 chunk 609 optimal weight: 9.9990 chunk 910 optimal weight: 40.0000 chunk 963 optimal weight: 2.9990 chunk 475 optimal weight: 0.2980 chunk 862 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1432 GLN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 HIS I 12 ASN K 29 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 272 ASN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 60 GLN ** 0 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 88753 Z= 0.375 Angle : 0.598 10.543 121592 Z= 0.321 Chirality : 0.043 0.214 13745 Planarity : 0.004 0.086 14130 Dihedral : 19.688 170.003 15186 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.81 % Allowed : 12.80 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: 0.19 (0.08), residues: 9581 helix: 0.95 (0.08), residues: 4146 sheet: -0.51 (0.14), residues: 1272 loop : -0.40 (0.09), residues: 4163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP X 263 HIS 0.009 0.001 HIS A 659 PHE 0.036 0.002 PHE 0 720 TYR 0.033 0.002 TYR V 10 ARG 0.015 0.001 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 899 time to evaluate : 7.177 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: A 74 MET cc_start: 0.8022 (tpt) cc_final: 0.7652 (tpp) REVERT: A 234 MET cc_start: 0.7813 (mtm) cc_final: 0.7562 (mtm) REVERT: A 304 MET cc_start: 0.8299 (mtt) cc_final: 0.8037 (mtm) REVERT: A 1036 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7790 (mtp85) REVERT: A 1128 GLN cc_start: 0.8306 (tm-30) cc_final: 0.8095 (tm-30) REVERT: A 1194 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6961 (mtp85) REVERT: A 1199 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7893 (tpp80) REVERT: A 1259 MET cc_start: 0.7044 (mmp) cc_final: 0.6554 (ttm) REVERT: A 1453 TYR cc_start: 0.6051 (m-80) cc_final: 0.5752 (m-80) REVERT: B 101 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8353 (ptt) REVERT: B 312 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8367 (tm-30) REVERT: B 358 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7399 (ttmt) REVERT: B 427 ASP cc_start: 0.7958 (m-30) cc_final: 0.7714 (t0) REVERT: B 770 GLN cc_start: 0.8402 (tp40) cc_final: 0.8138 (tp40) REVERT: B 1049 ASP cc_start: 0.7808 (p0) cc_final: 0.7528 (p0) REVERT: B 1116 ARG cc_start: 0.8693 (ttm170) cc_final: 0.8282 (mtt180) REVERT: B 1181 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6883 (tm-30) REVERT: C 60 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: C 82 TYR cc_start: 0.7966 (m-80) cc_final: 0.7760 (m-80) REVERT: C 249 ASP cc_start: 0.6516 (m-30) cc_final: 0.6267 (m-30) REVERT: D 58 VAL cc_start: 0.8181 (t) cc_final: 0.7961 (p) REVERT: D 195 ILE cc_start: 0.8410 (mt) cc_final: 0.8165 (mt) REVERT: E 3 GLN cc_start: 0.8305 (pp30) cc_final: 0.8075 (pm20) REVERT: F 12 ASN cc_start: 0.4053 (OUTLIER) cc_final: 0.3092 (m-40) REVERT: F 70 LYS cc_start: 0.6876 (tppt) cc_final: 0.6443 (tppt) REVERT: G 44 TYR cc_start: 0.8391 (m-80) cc_final: 0.8012 (m-80) REVERT: H 64 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7512 (p0) REVERT: K 113 THR cc_start: 0.6983 (p) cc_final: 0.6709 (t) REVERT: M 56 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8920 (pp) REVERT: M 106 PHE cc_start: 0.7142 (m-80) cc_final: 0.6837 (m-80) REVERT: M 119 MET cc_start: 0.6313 (ppp) cc_final: 0.5532 (tpp) REVERT: M 196 ILE cc_start: 0.8161 (mp) cc_final: 0.7796 (mp) REVERT: M 234 GLN cc_start: 0.7527 (mm110) cc_final: 0.7043 (mm-40) REVERT: M 267 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6221 (tttt) REVERT: Q 31 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6533 (t80) REVERT: Q 34 MET cc_start: 0.3959 (mmm) cc_final: 0.2244 (ttp) REVERT: Q 114 MET cc_start: 0.5547 (ptp) cc_final: 0.5259 (ttm) REVERT: Q 384 PHE cc_start: 0.5378 (m-80) cc_final: 0.5032 (m-10) REVERT: R 228 MET cc_start: 0.7356 (mmp) cc_final: 0.6954 (ttp) REVERT: R 273 ASP cc_start: 0.5576 (p0) cc_final: 0.4591 (p0) REVERT: R 294 MET cc_start: 0.1455 (tmm) cc_final: -0.0100 (ttp) REVERT: V 38 MET cc_start: 0.3114 (OUTLIER) cc_final: 0.2717 (tpp) REVERT: W 111 ASP cc_start: 0.8600 (m-30) cc_final: 0.8379 (m-30) REVERT: X 216 GLN cc_start: 0.4220 (pp30) cc_final: 0.3605 (pt0) REVERT: X 234 ARG cc_start: 0.4210 (mtm180) cc_final: 0.3994 (mpp80) REVERT: 0 42 MET cc_start: 0.7996 (tpt) cc_final: 0.7684 (tpp) REVERT: 0 90 MET cc_start: 0.8386 (mmp) cc_final: 0.7973 (mmp) REVERT: 0 199 MET cc_start: 0.7755 (mtp) cc_final: 0.7092 (mtp) REVERT: 0 468 MET cc_start: 0.8175 (tpp) cc_final: 0.7887 (tpp) REVERT: 0 528 GLU cc_start: 0.7797 (tp30) cc_final: 0.7374 (tp30) REVERT: 0 642 MET cc_start: 0.8567 (mtp) cc_final: 0.8039 (mtp) REVERT: 1 210 TRP cc_start: 0.8491 (m100) cc_final: 0.7910 (m100) REVERT: 1 284 TRP cc_start: 0.8633 (m100) cc_final: 0.7938 (m100) REVERT: 1 469 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8123 (ptp) REVERT: 2 50 MET cc_start: 0.8563 (tpp) cc_final: 0.8216 (tpp) REVERT: 2 150 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7898 (tmm) REVERT: 2 210 MET cc_start: 0.8443 (tmm) cc_final: 0.8141 (ppp) REVERT: 2 227 MET cc_start: 0.8717 (ptp) cc_final: 0.8251 (tmm) REVERT: 2 253 MET cc_start: 0.8938 (mmm) cc_final: 0.8628 (mmt) REVERT: 3 12 MET cc_start: 0.5724 (tpp) cc_final: 0.5394 (tpp) REVERT: 3 53 GLN cc_start: 0.7585 (pp30) cc_final: 0.7313 (pp30) REVERT: 3 99 PHE cc_start: 0.7177 (m-10) cc_final: 0.6945 (m-10) REVERT: 3 106 TYR cc_start: 0.8538 (t80) cc_final: 0.8288 (t80) REVERT: 3 107 ASN cc_start: 0.8202 (m110) cc_final: 0.7830 (m-40) REVERT: 4 197 MET cc_start: 0.8860 (mmp) cc_final: 0.8632 (mmm) REVERT: a 39 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.6695 (t-170) REVERT: a 73 GLU cc_start: 0.8333 (tt0) cc_final: 0.7802 (tt0) REVERT: c 24 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8234 (mm110) REVERT: c 72 ASP cc_start: 0.8598 (m-30) cc_final: 0.8308 (m-30) REVERT: c 76 THR cc_start: 0.8632 (p) cc_final: 0.8253 (t) REVERT: f 79 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7475 (ptpt) REVERT: g 95 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8453 (tptt) REVERT: h 48 ASP cc_start: 0.7493 (p0) cc_final: 0.7067 (t0) REVERT: h 90 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7922 (mp0) outliers start: 243 outliers final: 176 residues processed: 1054 average time/residue: 0.7630 time to fit residues: 1397.6074 Evaluate side-chains 1020 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 829 time to evaluate : 7.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1194 ARG Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1187 ASN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 27 MET Chi-restraints excluded: chain Q residue 31 PHE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain V residue 38 MET Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 313 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 517 SER Chi-restraints excluded: chain 0 residue 524 SER Chi-restraints excluded: chain 0 residue 535 ASP Chi-restraints excluded: chain 0 residue 571 VAL Chi-restraints excluded: chain 0 residue 600 SER Chi-restraints excluded: chain 0 residue 712 MET Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 469 MET Chi-restraints excluded: chain 1 residue 612 CYS Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 245 THR Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 206 MET Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 149 ILE Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 367 ASP Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 607 VAL Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain 7 residue 836 MET Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 13 LYS Chi-restraints excluded: chain c residue 27 VAL Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain g residue 95 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 802 optimal weight: 20.0000 chunk 547 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 717 optimal weight: 30.0000 chunk 397 optimal weight: 10.0000 chunk 822 optimal weight: 40.0000 chunk 666 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 492 optimal weight: 3.9990 chunk 864 optimal weight: 9.9990 chunk 243 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN B 484 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 GLN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN E 114 ASN I 89 GLN K 29 ASN ** M 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 3 ASN ** X 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 38 HIS 1 196 GLN ** 2 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 GLN 5 64 ASN 6 184 GLN ** d 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 GLN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.123 88753 Z= 0.540 Angle : 0.689 14.241 121592 Z= 0.368 Chirality : 0.046 0.230 13745 Planarity : 0.005 0.063 14130 Dihedral : 19.857 169.364 15186 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.36 % Allowed : 13.83 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: -0.04 (0.08), residues: 9581 helix: 0.80 (0.08), residues: 4147 sheet: -0.66 (0.14), residues: 1272 loop : -0.56 (0.09), residues: 4162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP X 263 HIS 0.019 0.002 HIS 1 38 PHE 0.037 0.002 PHE A 219 TYR 0.022 0.002 TYR b 88 ARG 0.011 0.001 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 897 time to evaluate : 8.420 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: A 74 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7527 (tpp) REVERT: A 234 MET cc_start: 0.7918 (mtm) cc_final: 0.7654 (mtm) REVERT: A 260 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7626 (m-30) REVERT: A 304 MET cc_start: 0.8216 (mtt) cc_final: 0.7896 (mtm) REVERT: A 1013 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.5640 (m-30) REVERT: A 1036 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7789 (mtp85) REVERT: A 1144 LYS cc_start: 0.8708 (mttp) cc_final: 0.7880 (mttm) REVERT: A 1199 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7734 (tpp-160) REVERT: A 1259 MET cc_start: 0.7031 (mmp) cc_final: 0.6667 (tpp) REVERT: A 1403 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7214 (mm-30) REVERT: A 1453 TYR cc_start: 0.6290 (m-80) cc_final: 0.5834 (m-80) REVERT: B 241 ARG cc_start: 0.7813 (mpt-90) cc_final: 0.7401 (mmt90) REVERT: B 358 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7548 (ttmt) REVERT: B 770 GLN cc_start: 0.8437 (tp40) cc_final: 0.8166 (tp40) REVERT: B 1116 ARG cc_start: 0.8751 (ttm170) cc_final: 0.8320 (mtt180) REVERT: B 1181 GLU cc_start: 0.7326 (tm-30) cc_final: 0.6956 (tm-30) REVERT: C 60 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: D 58 VAL cc_start: 0.8312 (t) cc_final: 0.8064 (p) REVERT: D 195 ILE cc_start: 0.8501 (mt) cc_final: 0.8255 (mt) REVERT: E 46 TYR cc_start: 0.8147 (m-80) cc_final: 0.7768 (m-80) REVERT: E 91 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8066 (mmtm) REVERT: E 92 THR cc_start: 0.8505 (p) cc_final: 0.8084 (t) REVERT: F 70 LYS cc_start: 0.6726 (tppt) cc_final: 0.6490 (tppt) REVERT: H 64 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7558 (p0) REVERT: I 8 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7917 (tmm-80) REVERT: K 113 THR cc_start: 0.7041 (p) cc_final: 0.6770 (t) REVERT: M 56 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9062 (pp) REVERT: M 81 GLU cc_start: 0.4832 (tp30) cc_final: 0.4007 (tm-30) REVERT: M 106 PHE cc_start: 0.7211 (m-80) cc_final: 0.6911 (m-80) REVERT: M 119 MET cc_start: 0.6469 (ppp) cc_final: 0.5846 (tpp) REVERT: M 196 ILE cc_start: 0.8314 (mp) cc_final: 0.7898 (mp) REVERT: M 234 GLN cc_start: 0.7437 (mm110) cc_final: 0.7031 (mm-40) REVERT: M 267 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6320 (tttt) REVERT: Q 31 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6425 (t80) REVERT: Q 34 MET cc_start: 0.4252 (mmm) cc_final: 0.2595 (ttp) REVERT: Q 148 GLN cc_start: 0.5639 (OUTLIER) cc_final: 0.5326 (mm110) REVERT: Q 384 PHE cc_start: 0.5640 (m-80) cc_final: 0.5249 (m-10) REVERT: R 138 GLN cc_start: 0.6635 (tp-100) cc_final: 0.6274 (tp-100) REVERT: R 228 MET cc_start: 0.7510 (mmp) cc_final: 0.7175 (ttp) REVERT: U 231 ILE cc_start: 0.2733 (tp) cc_final: 0.2413 (tt) REVERT: V 38 MET cc_start: 0.3044 (OUTLIER) cc_final: 0.2772 (mmm) REVERT: W 111 ASP cc_start: 0.8668 (m-30) cc_final: 0.8465 (m-30) REVERT: X 136 GLN cc_start: 0.3731 (mt0) cc_final: 0.2818 (tp40) REVERT: X 234 ARG cc_start: 0.4287 (mtm180) cc_final: 0.4065 (mpp80) REVERT: 0 42 MET cc_start: 0.8105 (tpt) cc_final: 0.7810 (tpp) REVERT: 0 90 MET cc_start: 0.8483 (mmp) cc_final: 0.8110 (mmp) REVERT: 0 199 MET cc_start: 0.7885 (mtp) cc_final: 0.7389 (mtp) REVERT: 0 468 MET cc_start: 0.8220 (tpp) cc_final: 0.7767 (tpp) REVERT: 0 528 GLU cc_start: 0.7989 (tp30) cc_final: 0.7525 (tp30) REVERT: 0 642 MET cc_start: 0.8603 (mtp) cc_final: 0.7997 (mtp) REVERT: 1 210 TRP cc_start: 0.8542 (m100) cc_final: 0.7946 (m100) REVERT: 1 284 TRP cc_start: 0.8714 (m100) cc_final: 0.8061 (m100) REVERT: 1 469 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.8051 (ptp) REVERT: 2 50 MET cc_start: 0.8611 (tpp) cc_final: 0.8383 (tpp) REVERT: 2 97 MET cc_start: 0.6972 (tpp) cc_final: 0.6527 (tpp) REVERT: 2 150 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7856 (tmm) REVERT: 2 210 MET cc_start: 0.8512 (tmm) cc_final: 0.8187 (ppp) REVERT: 2 227 MET cc_start: 0.8692 (ptp) cc_final: 0.8291 (tmm) REVERT: 2 277 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8296 (mmm) REVERT: 3 12 MET cc_start: 0.5859 (tpp) cc_final: 0.5580 (tpp) REVERT: 3 20 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6667 (mmt90) REVERT: 3 53 GLN cc_start: 0.7543 (pp30) cc_final: 0.7291 (pp30) REVERT: 3 106 TYR cc_start: 0.8597 (t80) cc_final: 0.8303 (t80) REVERT: 3 107 ASN cc_start: 0.8134 (m110) cc_final: 0.7823 (m-40) REVERT: 4 193 TYR cc_start: 0.8678 (t80) cc_final: 0.8425 (t80) REVERT: 4 197 MET cc_start: 0.8877 (mmp) cc_final: 0.8585 (mmm) REVERT: 6 148 MET cc_start: 0.8191 (ttt) cc_final: 0.7899 (ttm) REVERT: 7 716 MET cc_start: 0.7068 (mtp) cc_final: 0.6842 (mtt) REVERT: a 39 HIS cc_start: 0.6700 (OUTLIER) cc_final: 0.6478 (t-170) REVERT: a 73 GLU cc_start: 0.8308 (tt0) cc_final: 0.7913 (tt0) REVERT: c 24 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8179 (mm110) REVERT: c 72 ASP cc_start: 0.8712 (m-30) cc_final: 0.8448 (m-30) REVERT: c 76 THR cc_start: 0.8772 (p) cc_final: 0.8382 (t) REVERT: d 77 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8772 (mp) REVERT: f 27 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8234 (mm-40) REVERT: f 79 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7911 (ptpt) REVERT: f 84 MET cc_start: 0.8008 (tpp) cc_final: 0.7616 (mmm) REVERT: h 48 ASP cc_start: 0.7684 (p0) cc_final: 0.7201 (t0) REVERT: h 90 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7944 (mp0) outliers start: 290 outliers final: 207 residues processed: 1091 average time/residue: 0.7875 time to fit residues: 1495.4411 Evaluate side-chains 1054 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 828 time to evaluate : 7.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1242 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1403 GLU Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 683 SER Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1187 ASN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 132 SER Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 27 MET Chi-restraints excluded: chain Q residue 31 PHE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 148 GLN Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain V residue 38 MET Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 313 THR Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 127 THR Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 425 ILE Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 474 ASN Chi-restraints excluded: chain 0 residue 517 SER Chi-restraints excluded: chain 0 residue 524 SER Chi-restraints excluded: chain 0 residue 535 ASP Chi-restraints excluded: chain 0 residue 571 VAL Chi-restraints excluded: chain 0 residue 600 SER Chi-restraints excluded: chain 0 residue 712 MET Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 364 ILE Chi-restraints excluded: chain 1 residue 469 MET Chi-restraints excluded: chain 1 residue 612 CYS Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 245 THR Chi-restraints excluded: chain 2 residue 277 MET Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 20 ARG Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 149 ILE Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 182 VAL Chi-restraints excluded: chain 6 residue 222 LEU Chi-restraints excluded: chain 6 residue 300 LEU Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 367 ASP Chi-restraints excluded: chain 6 residue 388 THR Chi-restraints excluded: chain 7 residue 234 VAL Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 607 VAL Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 82 THR Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 13 LYS Chi-restraints excluded: chain c residue 27 VAL Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 60 ASN Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 324 optimal weight: 9.9990 chunk 867 optimal weight: 0.3980 chunk 190 optimal weight: 0.7980 chunk 565 optimal weight: 6.9990 chunk 237 optimal weight: 0.9990 chunk 964 optimal weight: 0.7980 chunk 800 optimal weight: 10.0000 chunk 446 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 319 optimal weight: 0.9980 chunk 506 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN A 802 ASN A 854 ASN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN B 776 GLN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN H 11 GLN K 29 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 HIS ** R 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 196 GLN ** 2 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN d 60 ASN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 88753 Z= 0.167 Angle : 0.534 10.333 121592 Z= 0.289 Chirality : 0.040 0.197 13745 Planarity : 0.004 0.059 14130 Dihedral : 19.662 169.452 15186 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.07 % Allowed : 15.56 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: 0.41 (0.09), residues: 9581 helix: 1.20 (0.08), residues: 4151 sheet: -0.46 (0.14), residues: 1266 loop : -0.34 (0.10), residues: 4164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP X 263 HIS 0.008 0.001 HIS W 103 PHE 0.030 0.001 PHE O 190 TYR 0.032 0.001 TYR b 51 ARG 0.012 0.000 ARG G 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 922 time to evaluate : 7.069 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: A 74 MET cc_start: 0.7891 (tpt) cc_final: 0.7636 (tpt) REVERT: A 122 MET cc_start: 0.7814 (tpt) cc_final: 0.7411 (tpt) REVERT: A 175 ARG cc_start: 0.7984 (ptm-80) cc_final: 0.7646 (ppt170) REVERT: A 234 MET cc_start: 0.7876 (mtm) cc_final: 0.7633 (mtm) REVERT: A 802 ASN cc_start: 0.7839 (m-40) cc_final: 0.7534 (m-40) REVERT: A 1036 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7747 (mtp85) REVERT: A 1199 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7860 (tpp-160) REVERT: A 1259 MET cc_start: 0.6974 (mmp) cc_final: 0.6611 (tpp) REVERT: A 1422 ARG cc_start: 0.7855 (mmt-90) cc_final: 0.7645 (mmt-90) REVERT: A 1453 TYR cc_start: 0.5961 (m-80) cc_final: 0.5640 (m-80) REVERT: B 358 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7365 (ttmt) REVERT: B 427 ASP cc_start: 0.7820 (m-30) cc_final: 0.7616 (t0) REVERT: B 770 GLN cc_start: 0.8253 (tp40) cc_final: 0.7949 (tp40) REVERT: B 1049 ASP cc_start: 0.7742 (p0) cc_final: 0.7475 (p0) REVERT: B 1116 ARG cc_start: 0.8628 (ttm170) cc_final: 0.8153 (mtt-85) REVERT: D 58 VAL cc_start: 0.8337 (t) cc_final: 0.8082 (p) REVERT: D 186 ASP cc_start: 0.5152 (m-30) cc_final: 0.4921 (p0) REVERT: E 91 LYS cc_start: 0.8425 (mmtp) cc_final: 0.7982 (mmtm) REVERT: F 104 ASN cc_start: 0.8681 (t0) cc_final: 0.8358 (t0) REVERT: G 88 ASP cc_start: 0.5485 (m-30) cc_final: 0.4806 (m-30) REVERT: G 144 ARG cc_start: 0.6010 (mtp-110) cc_final: 0.5141 (mtt90) REVERT: K 113 THR cc_start: 0.6900 (p) cc_final: 0.6640 (t) REVERT: M 81 GLU cc_start: 0.4676 (tp30) cc_final: 0.4063 (tm-30) REVERT: M 106 PHE cc_start: 0.7085 (m-80) cc_final: 0.6787 (m-80) REVERT: M 119 MET cc_start: 0.6457 (ppp) cc_final: 0.5849 (tpp) REVERT: M 234 GLN cc_start: 0.7490 (mm110) cc_final: 0.6979 (mm-40) REVERT: M 267 LYS cc_start: 0.6646 (OUTLIER) cc_final: 0.6155 (tttt) REVERT: Q 31 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6433 (t80) REVERT: Q 34 MET cc_start: 0.4458 (mmm) cc_final: 0.2737 (ttp) REVERT: Q 148 GLN cc_start: 0.5709 (OUTLIER) cc_final: 0.5392 (mm110) REVERT: Q 384 PHE cc_start: 0.5604 (m-80) cc_final: 0.5323 (m-10) REVERT: R 65 ASN cc_start: 0.8422 (m-40) cc_final: 0.7787 (p0) REVERT: R 138 GLN cc_start: 0.7007 (tp-100) cc_final: 0.6507 (tp-100) REVERT: R 225 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6974 (mmt) REVERT: R 228 MET cc_start: 0.7378 (mmp) cc_final: 0.7039 (ttp) REVERT: R 268 MET cc_start: 0.7382 (mmp) cc_final: 0.7139 (mmp) REVERT: R 294 MET cc_start: 0.2248 (tmm) cc_final: 0.0312 (ttt) REVERT: V 38 MET cc_start: 0.3170 (OUTLIER) cc_final: 0.2963 (mmm) REVERT: X 136 GLN cc_start: 0.3853 (mt0) cc_final: 0.3036 (tp40) REVERT: X 216 GLN cc_start: 0.4306 (pp30) cc_final: 0.3812 (pt0) REVERT: 0 42 MET cc_start: 0.7929 (tpt) cc_final: 0.7654 (tpp) REVERT: 0 136 MET cc_start: 0.8024 (mtp) cc_final: 0.7745 (mtp) REVERT: 0 468 MET cc_start: 0.8117 (tpp) cc_final: 0.7824 (tpp) REVERT: 0 495 MET cc_start: 0.8570 (ptp) cc_final: 0.7926 (mpp) REVERT: 0 528 GLU cc_start: 0.7973 (tp30) cc_final: 0.7523 (tp30) REVERT: 0 642 MET cc_start: 0.8563 (mtp) cc_final: 0.8003 (mtp) REVERT: 1 16 ILE cc_start: -0.0614 (OUTLIER) cc_final: -0.1287 (tt) REVERT: 1 210 TRP cc_start: 0.8551 (m100) cc_final: 0.7913 (m100) REVERT: 1 284 TRP cc_start: 0.8715 (m100) cc_final: 0.8061 (m100) REVERT: 1 469 MET cc_start: 0.8342 (ptm) cc_final: 0.8058 (ptp) REVERT: 2 50 MET cc_start: 0.8527 (tpp) cc_final: 0.7908 (mmm) REVERT: 2 97 MET cc_start: 0.7201 (tpp) cc_final: 0.6850 (tpp) REVERT: 2 150 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7688 (tmm) REVERT: 2 210 MET cc_start: 0.8457 (tmm) cc_final: 0.8216 (ppp) REVERT: 2 227 MET cc_start: 0.8716 (ptp) cc_final: 0.8290 (tmm) REVERT: 2 253 MET cc_start: 0.8872 (mmm) cc_final: 0.8625 (mmt) REVERT: 3 12 MET cc_start: 0.5671 (tpp) cc_final: 0.5394 (tpp) REVERT: 3 45 ARG cc_start: 0.7216 (ttp80) cc_final: 0.6630 (ttm-80) REVERT: 3 53 GLN cc_start: 0.7532 (pp30) cc_final: 0.7330 (pp30) REVERT: 3 89 PHE cc_start: 0.8720 (m-10) cc_final: 0.8191 (m-80) REVERT: 3 106 TYR cc_start: 0.8578 (t80) cc_final: 0.8215 (t80) REVERT: 3 107 ASN cc_start: 0.8236 (m110) cc_final: 0.7946 (m-40) REVERT: 4 26 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8639 (tp) REVERT: 6 84 TRP cc_start: 0.5827 (p90) cc_final: 0.4903 (p90) REVERT: 6 95 MET cc_start: 0.3106 (ptt) cc_final: 0.2539 (ptm) REVERT: 6 136 MET cc_start: 0.7707 (mmm) cc_final: 0.7008 (mmm) REVERT: 7 716 MET cc_start: 0.6951 (mtp) cc_final: 0.6744 (mtt) REVERT: a 39 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6747 (t-170) REVERT: a 73 GLU cc_start: 0.8233 (tt0) cc_final: 0.7869 (tt0) REVERT: c 24 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8123 (mm-40) REVERT: c 72 ASP cc_start: 0.8499 (m-30) cc_final: 0.8265 (m-30) REVERT: c 76 THR cc_start: 0.8678 (p) cc_final: 0.8225 (t) REVERT: e 120 MET cc_start: 0.8590 (mtp) cc_final: 0.8201 (mtp) REVERT: f 43 VAL cc_start: 0.8893 (t) cc_final: 0.8660 (p) REVERT: f 79 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7809 (ptpt) REVERT: f 84 MET cc_start: 0.7976 (tpp) cc_final: 0.7554 (mmm) REVERT: h 48 ASP cc_start: 0.7484 (p0) cc_final: 0.7041 (t0) REVERT: h 90 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7894 (mp0) outliers start: 179 outliers final: 110 residues processed: 1035 average time/residue: 0.7733 time to fit residues: 1391.9402 Evaluate side-chains 982 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 861 time to evaluate : 6.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 31 PHE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 148 GLN Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain U residue 254 THR Chi-restraints excluded: chain V residue 38 MET Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 425 ILE Chi-restraints excluded: chain 0 residue 502 ASP Chi-restraints excluded: chain 0 residue 535 ASP Chi-restraints excluded: chain 0 residue 571 VAL Chi-restraints excluded: chain 0 residue 606 VAL Chi-restraints excluded: chain 1 residue 16 ILE Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 149 ILE Chi-restraints excluded: chain 6 residue 300 LEU Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 367 ASP Chi-restraints excluded: chain 7 residue 234 VAL Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 125 GLN Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 13 LYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 60 ASN Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 930 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 549 optimal weight: 9.9990 chunk 704 optimal weight: 40.0000 chunk 545 optimal weight: 9.9990 chunk 812 optimal weight: 9.9990 chunk 538 optimal weight: 5.9990 chunk 960 optimal weight: 7.9990 chunk 601 optimal weight: 4.9990 chunk 585 optimal weight: 0.0020 chunk 443 optimal weight: 5.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN K 29 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 265 ASN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN d 60 ASN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 88753 Z= 0.405 Angle : 0.611 11.354 121592 Z= 0.327 Chirality : 0.043 0.205 13745 Planarity : 0.004 0.086 14130 Dihedral : 19.689 168.590 15186 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.71 % Allowed : 15.58 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: 0.31 (0.09), residues: 9581 helix: 1.14 (0.08), residues: 4159 sheet: -0.54 (0.14), residues: 1276 loop : -0.41 (0.10), residues: 4146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP U 258 HIS 0.011 0.001 HIS A 659 PHE 0.033 0.002 PHE O 190 TYR 0.029 0.002 TYR B 486 ARG 0.017 0.001 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 863 time to evaluate : 7.179 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: A 43 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: A 74 MET cc_start: 0.7980 (tpt) cc_final: 0.7570 (tpp) REVERT: A 88 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8188 (mmmt) REVERT: A 122 MET cc_start: 0.7594 (tpt) cc_final: 0.7290 (tpp) REVERT: A 175 ARG cc_start: 0.8058 (ptm-80) cc_final: 0.7798 (ppt170) REVERT: A 212 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8166 (mttp) REVERT: A 234 MET cc_start: 0.7837 (mtm) cc_final: 0.7586 (mtm) REVERT: A 290 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7402 (tm-30) REVERT: A 470 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8640 (pt) REVERT: A 501 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8431 (mp) REVERT: A 658 LEU cc_start: 0.8622 (tp) cc_final: 0.8403 (tp) REVERT: A 802 ASN cc_start: 0.7980 (m-40) cc_final: 0.7731 (m110) REVERT: A 1036 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.7756 (mtp85) REVERT: A 1259 MET cc_start: 0.6991 (mmp) cc_final: 0.6619 (tpp) REVERT: A 1422 ARG cc_start: 0.8013 (mmt-90) cc_final: 0.7678 (mmt-90) REVERT: A 1453 TYR cc_start: 0.6120 (m-80) cc_final: 0.5601 (m-80) REVERT: B 226 PHE cc_start: 0.8187 (m-10) cc_final: 0.7851 (m-10) REVERT: B 770 GLN cc_start: 0.8367 (tp40) cc_final: 0.8076 (tp40) REVERT: B 1116 ARG cc_start: 0.8688 (ttm170) cc_final: 0.8211 (mtt-85) REVERT: D 58 VAL cc_start: 0.8355 (t) cc_final: 0.8092 (p) REVERT: D 186 ASP cc_start: 0.4908 (m-30) cc_final: 0.4659 (p0) REVERT: E 91 LYS cc_start: 0.8459 (mmtp) cc_final: 0.8031 (mmtm) REVERT: G 144 ARG cc_start: 0.6332 (mtp-110) cc_final: 0.5330 (mtt90) REVERT: H 64 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7499 (p0) REVERT: K 113 THR cc_start: 0.6950 (p) cc_final: 0.6704 (t) REVERT: M 56 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8946 (pp) REVERT: M 81 GLU cc_start: 0.4664 (tp30) cc_final: 0.4197 (tm-30) REVERT: M 106 PHE cc_start: 0.7208 (m-80) cc_final: 0.6897 (m-80) REVERT: M 119 MET cc_start: 0.6574 (ppp) cc_final: 0.5969 (tpp) REVERT: M 234 GLN cc_start: 0.7514 (mm110) cc_final: 0.7073 (mm-40) REVERT: M 267 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.6200 (tttt) REVERT: Q 31 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6475 (t80) REVERT: Q 34 MET cc_start: 0.4465 (mmm) cc_final: 0.2784 (ttp) REVERT: Q 148 GLN cc_start: 0.5565 (OUTLIER) cc_final: 0.5214 (mm110) REVERT: Q 384 PHE cc_start: 0.5667 (m-80) cc_final: 0.5266 (m-10) REVERT: Q 425 MET cc_start: 0.6415 (mmt) cc_final: 0.6151 (mmt) REVERT: R 138 GLN cc_start: 0.6900 (tp-100) cc_final: 0.6304 (tp-100) REVERT: R 225 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7015 (mmt) REVERT: R 228 MET cc_start: 0.7398 (mmp) cc_final: 0.7020 (ttp) REVERT: R 268 MET cc_start: 0.7397 (mmp) cc_final: 0.7103 (mmp) REVERT: R 294 MET cc_start: 0.2269 (tmm) cc_final: 0.0292 (ttt) REVERT: R 302 TYR cc_start: 0.3102 (OUTLIER) cc_final: 0.2637 (m-80) REVERT: U 231 ILE cc_start: 0.2544 (tp) cc_final: 0.2126 (tt) REVERT: V 38 MET cc_start: 0.3042 (OUTLIER) cc_final: 0.2831 (mmm) REVERT: X 136 GLN cc_start: 0.3700 (mt0) cc_final: 0.2837 (tp40) REVERT: X 234 ARG cc_start: 0.4142 (mpp80) cc_final: 0.3860 (mpp80) REVERT: 0 42 MET cc_start: 0.8047 (tpt) cc_final: 0.7766 (tpp) REVERT: 0 136 MET cc_start: 0.8129 (mtp) cc_final: 0.7828 (mtp) REVERT: 0 468 MET cc_start: 0.8198 (tpp) cc_final: 0.7886 (tpp) REVERT: 0 495 MET cc_start: 0.8573 (ptp) cc_final: 0.7899 (mpp) REVERT: 0 528 GLU cc_start: 0.8036 (tp30) cc_final: 0.7599 (tp30) REVERT: 0 642 MET cc_start: 0.8580 (mtp) cc_final: 0.7979 (mtp) REVERT: 0 679 MET cc_start: 0.7076 (mpp) cc_final: 0.6579 (mtt) REVERT: 1 16 ILE cc_start: -0.0711 (OUTLIER) cc_final: -0.1379 (tt) REVERT: 1 210 TRP cc_start: 0.8570 (m100) cc_final: 0.7932 (m100) REVERT: 1 284 TRP cc_start: 0.8744 (m100) cc_final: 0.8069 (m100) REVERT: 1 469 MET cc_start: 0.8358 (ptm) cc_final: 0.8095 (ptp) REVERT: 2 48 MET cc_start: 0.9293 (tpp) cc_final: 0.8975 (tpp) REVERT: 2 50 MET cc_start: 0.8566 (tpp) cc_final: 0.7925 (mmm) REVERT: 2 150 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7883 (tmm) REVERT: 2 210 MET cc_start: 0.8499 (tmm) cc_final: 0.8223 (ppp) REVERT: 2 227 MET cc_start: 0.8721 (ptp) cc_final: 0.8338 (tmm) REVERT: 2 253 MET cc_start: 0.8892 (mmm) cc_final: 0.8582 (mmt) REVERT: 3 12 MET cc_start: 0.5787 (tpp) cc_final: 0.5511 (tpp) REVERT: 3 45 ARG cc_start: 0.7206 (ttp80) cc_final: 0.6619 (ttm-80) REVERT: 3 53 GLN cc_start: 0.7566 (pp30) cc_final: 0.7352 (pp30) REVERT: 3 106 TYR cc_start: 0.8588 (t80) cc_final: 0.8331 (t80) REVERT: 4 26 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8658 (tp) REVERT: 4 197 MET cc_start: 0.8664 (mmm) cc_final: 0.8451 (mmm) REVERT: 6 95 MET cc_start: 0.3063 (ptt) cc_final: 0.2506 (ptm) REVERT: 6 136 MET cc_start: 0.7786 (mmm) cc_final: 0.7332 (mmm) REVERT: 6 142 ARG cc_start: 0.7347 (pmt-80) cc_final: 0.7049 (pmt-80) REVERT: 6 148 MET cc_start: 0.8256 (ttt) cc_final: 0.7730 (ttm) REVERT: 7 716 MET cc_start: 0.7010 (mtp) cc_final: 0.6802 (mtt) REVERT: a 73 GLU cc_start: 0.8315 (tt0) cc_final: 0.7969 (tt0) REVERT: c 24 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8183 (mm110) REVERT: c 72 ASP cc_start: 0.8625 (m-30) cc_final: 0.8386 (m-30) REVERT: c 76 THR cc_start: 0.8674 (p) cc_final: 0.8256 (t) REVERT: c 95 LYS cc_start: 0.9045 (tppp) cc_final: 0.8744 (tptp) REVERT: f 79 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7816 (ptpt) REVERT: f 84 MET cc_start: 0.8075 (tpp) cc_final: 0.7609 (mmm) REVERT: g 99 ARG cc_start: 0.7796 (mmt90) cc_final: 0.7520 (mmt-90) REVERT: h 48 ASP cc_start: 0.7590 (p0) cc_final: 0.7040 (t0) REVERT: h 90 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7939 (mp0) outliers start: 234 outliers final: 174 residues processed: 1005 average time/residue: 0.7809 time to fit residues: 1362.5379 Evaluate side-chains 1025 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 835 time to evaluate : 7.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1103 GLU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 27 MET Chi-restraints excluded: chain Q residue 31 PHE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 148 GLN Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 273 ASP Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain U residue 254 THR Chi-restraints excluded: chain V residue 38 MET Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 425 ILE Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 535 ASP Chi-restraints excluded: chain 0 residue 571 VAL Chi-restraints excluded: chain 0 residue 600 SER Chi-restraints excluded: chain 0 residue 606 VAL Chi-restraints excluded: chain 0 residue 712 MET Chi-restraints excluded: chain 1 residue 16 ILE Chi-restraints excluded: chain 1 residue 33 ASP Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 2 residue 277 MET Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 206 MET Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 149 ILE Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 300 LEU Chi-restraints excluded: chain 6 residue 320 VAL Chi-restraints excluded: chain 6 residue 388 THR Chi-restraints excluded: chain 7 residue 234 VAL Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 13 LYS Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 594 optimal weight: 0.0000 chunk 383 optimal weight: 2.9990 chunk 573 optimal weight: 9.9990 chunk 289 optimal weight: 20.0000 chunk 188 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 610 optimal weight: 10.0000 chunk 654 optimal weight: 9.9990 chunk 475 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 755 optimal weight: 20.0000 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1312 ASN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 248 ASN ** 2 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 31 ASN ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN d 60 ASN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 88753 Z= 0.207 Angle : 0.543 15.774 121592 Z= 0.292 Chirality : 0.040 0.266 13745 Planarity : 0.004 0.058 14130 Dihedral : 19.621 168.849 15186 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.21 % Allowed : 16.31 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: 0.47 (0.09), residues: 9581 helix: 1.28 (0.08), residues: 4159 sheet: -0.46 (0.15), residues: 1257 loop : -0.33 (0.10), residues: 4165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 263 HIS 0.007 0.001 HIS A 451 PHE 0.034 0.001 PHE O 190 TYR 0.026 0.001 TYR B 486 ARG 0.012 0.000 ARG B1096 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 901 time to evaluate : 7.417 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: A 74 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7574 (tpp) REVERT: A 88 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8358 (mmtt) REVERT: A 175 ARG cc_start: 0.8055 (ptm-80) cc_final: 0.7757 (ppt170) REVERT: A 212 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8134 (mttp) REVERT: A 234 MET cc_start: 0.7797 (mtm) cc_final: 0.7576 (mtm) REVERT: A 250 ILE cc_start: 0.8583 (tp) cc_final: 0.7915 (tt) REVERT: A 290 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7303 (tm-30) REVERT: A 470 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8542 (pt) REVERT: A 501 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 658 LEU cc_start: 0.8599 (tp) cc_final: 0.8375 (tp) REVERT: A 802 ASN cc_start: 0.7871 (m-40) cc_final: 0.7575 (m110) REVERT: A 1199 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7744 (tpp80) REVERT: A 1259 MET cc_start: 0.6927 (mmp) cc_final: 0.6548 (tpp) REVERT: A 1453 TYR cc_start: 0.6004 (m-80) cc_final: 0.5568 (m-80) REVERT: B 226 PHE cc_start: 0.8198 (m-10) cc_final: 0.7806 (m-10) REVERT: B 358 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7248 (ttmt) REVERT: B 770 GLN cc_start: 0.8264 (tp40) cc_final: 0.7953 (tp40) REVERT: B 778 MET cc_start: 0.7922 (mtm) cc_final: 0.7630 (mtm) REVERT: B 885 MET cc_start: 0.7872 (mmm) cc_final: 0.7641 (mmm) REVERT: B 1049 ASP cc_start: 0.7699 (p0) cc_final: 0.7406 (p0) REVERT: B 1116 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8189 (mtt-85) REVERT: B 1220 ARG cc_start: 0.7936 (mmt90) cc_final: 0.7537 (tpp80) REVERT: C 60 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7507 (m-30) REVERT: D 58 VAL cc_start: 0.8379 (t) cc_final: 0.8038 (p) REVERT: D 186 ASP cc_start: 0.5062 (m-30) cc_final: 0.4775 (p0) REVERT: E 91 LYS cc_start: 0.8424 (mmtp) cc_final: 0.7996 (mmtm) REVERT: G 144 ARG cc_start: 0.6337 (mtp-110) cc_final: 0.5259 (mtt90) REVERT: I 8 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7980 (tmm-80) REVERT: K 113 THR cc_start: 0.6696 (p) cc_final: 0.6494 (t) REVERT: M 81 GLU cc_start: 0.4662 (tp30) cc_final: 0.4146 (tm-30) REVERT: M 106 PHE cc_start: 0.7219 (m-80) cc_final: 0.6912 (m-80) REVERT: M 119 MET cc_start: 0.6577 (ppp) cc_final: 0.5996 (tpp) REVERT: M 234 GLN cc_start: 0.7459 (mm110) cc_final: 0.6991 (mm-40) REVERT: M 250 MET cc_start: 0.6261 (tmm) cc_final: 0.5952 (tmm) REVERT: M 267 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.6054 (tttt) REVERT: Q 31 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6417 (t80) REVERT: Q 34 MET cc_start: 0.4440 (mmm) cc_final: 0.2826 (ttp) REVERT: Q 148 GLN cc_start: 0.5519 (OUTLIER) cc_final: 0.5165 (mm110) REVERT: Q 384 PHE cc_start: 0.5616 (m-80) cc_final: 0.5179 (m-10) REVERT: R 65 ASN cc_start: 0.8390 (m-40) cc_final: 0.7735 (p0) REVERT: R 138 GLN cc_start: 0.7000 (tp-100) cc_final: 0.6454 (tp-100) REVERT: R 228 MET cc_start: 0.7362 (mmp) cc_final: 0.6972 (ttp) REVERT: R 268 MET cc_start: 0.7351 (mmp) cc_final: 0.7062 (mmp) REVERT: R 294 MET cc_start: 0.2034 (tmm) cc_final: 0.0075 (ttt) REVERT: R 302 TYR cc_start: 0.3064 (OUTLIER) cc_final: 0.2607 (m-80) REVERT: R 304 PHE cc_start: 0.5928 (m-80) cc_final: 0.5437 (m-80) REVERT: U 244 MET cc_start: 0.0489 (tmm) cc_final: -0.1171 (ptp) REVERT: V 81 LYS cc_start: 0.4899 (OUTLIER) cc_final: 0.4332 (mmmt) REVERT: X 136 GLN cc_start: 0.3822 (mt0) cc_final: 0.3049 (tp40) REVERT: 0 42 MET cc_start: 0.7958 (tpt) cc_final: 0.7693 (tpp) REVERT: 0 136 MET cc_start: 0.8073 (mtp) cc_final: 0.7801 (mtp) REVERT: 0 199 MET cc_start: 0.7890 (mtm) cc_final: 0.7312 (mtp) REVERT: 0 468 MET cc_start: 0.8139 (tpp) cc_final: 0.7849 (tpp) REVERT: 0 495 MET cc_start: 0.8603 (ptp) cc_final: 0.7891 (mpp) REVERT: 0 528 GLU cc_start: 0.8027 (tp30) cc_final: 0.7590 (tp30) REVERT: 0 642 MET cc_start: 0.8575 (mtp) cc_final: 0.7995 (mtp) REVERT: 0 679 MET cc_start: 0.7067 (mpp) cc_final: 0.6539 (mtt) REVERT: 1 16 ILE cc_start: -0.0869 (OUTLIER) cc_final: -0.1589 (tt) REVERT: 1 284 TRP cc_start: 0.8745 (m100) cc_final: 0.8055 (m100) REVERT: 1 469 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8075 (ptp) REVERT: 2 50 MET cc_start: 0.8560 (tpp) cc_final: 0.7924 (mmm) REVERT: 2 97 MET cc_start: 0.6636 (tpp) cc_final: 0.6346 (tpp) REVERT: 2 150 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7900 (tmm) REVERT: 2 210 MET cc_start: 0.8456 (tmm) cc_final: 0.8212 (ppp) REVERT: 2 227 MET cc_start: 0.8712 (ptp) cc_final: 0.8298 (tmm) REVERT: 2 253 MET cc_start: 0.8832 (mmm) cc_final: 0.8537 (mmt) REVERT: 3 12 MET cc_start: 0.5733 (tpp) cc_final: 0.5459 (tpp) REVERT: 4 26 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8646 (tp) REVERT: 4 193 TYR cc_start: 0.8768 (t80) cc_final: 0.8337 (t80) REVERT: 5 54 LEU cc_start: 0.8604 (tt) cc_final: 0.8398 (mt) REVERT: 6 95 MET cc_start: 0.3080 (ptt) cc_final: 0.2601 (ptm) REVERT: 6 136 MET cc_start: 0.7722 (mmm) cc_final: 0.7287 (mmm) REVERT: 6 142 ARG cc_start: 0.7276 (pmt-80) cc_final: 0.6881 (pmt-80) REVERT: 6 148 MET cc_start: 0.8265 (ttt) cc_final: 0.7595 (ttm) REVERT: 7 622 MET cc_start: 0.7219 (tpp) cc_final: 0.7005 (tpp) REVERT: a 73 GLU cc_start: 0.8277 (tt0) cc_final: 0.7878 (tt0) REVERT: a 125 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: c 24 GLN cc_start: 0.8508 (mm-40) cc_final: 0.8128 (mm110) REVERT: c 72 ASP cc_start: 0.8501 (m-30) cc_final: 0.8278 (m-30) REVERT: c 76 THR cc_start: 0.8630 (p) cc_final: 0.8211 (t) REVERT: c 95 LYS cc_start: 0.9013 (tppp) cc_final: 0.8726 (tptp) REVERT: e 120 MET cc_start: 0.8558 (mtp) cc_final: 0.8124 (mtp) REVERT: f 43 VAL cc_start: 0.8865 (t) cc_final: 0.8557 (p) REVERT: f 79 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7826 (ptpt) REVERT: h 48 ASP cc_start: 0.7503 (p0) cc_final: 0.7000 (t0) REVERT: h 90 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7907 (mp0) outliers start: 191 outliers final: 138 residues processed: 1019 average time/residue: 0.7898 time to fit residues: 1393.2437 Evaluate side-chains 1010 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 855 time to evaluate : 7.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1103 GLU Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1425 SER Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 31 PHE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 148 GLN Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 273 ASP Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain U residue 254 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 81 LYS Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 425 ILE Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 502 ASP Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 0 residue 535 ASP Chi-restraints excluded: chain 0 residue 571 VAL Chi-restraints excluded: chain 0 residue 600 SER Chi-restraints excluded: chain 0 residue 606 VAL Chi-restraints excluded: chain 1 residue 16 ILE Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 469 MET Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 206 MET Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 5 residue 20 ILE Chi-restraints excluded: chain 5 residue 27 MET Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 149 ILE Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 300 LEU Chi-restraints excluded: chain 6 residue 388 THR Chi-restraints excluded: chain 7 residue 234 VAL Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 125 GLN Chi-restraints excluded: chain c residue 13 LYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 60 ASN Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 874 optimal weight: 50.0000 chunk 920 optimal weight: 9.9990 chunk 839 optimal weight: 8.9990 chunk 895 optimal weight: 30.0000 chunk 538 optimal weight: 0.6980 chunk 390 optimal weight: 0.0570 chunk 703 optimal weight: 20.0000 chunk 274 optimal weight: 0.5980 chunk 809 optimal weight: 20.0000 chunk 846 optimal weight: 8.9990 chunk 892 optimal weight: 0.0770 overall best weight: 2.0858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 484 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 11 GLN M 290 GLN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 192 GLN 5 64 ASN ** 7 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 88753 Z= 0.268 Angle : 0.565 15.172 121592 Z= 0.303 Chirality : 0.041 0.234 13745 Planarity : 0.004 0.083 14130 Dihedral : 19.592 168.555 15186 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.34 % Allowed : 16.23 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: 0.48 (0.09), residues: 9581 helix: 1.29 (0.08), residues: 4147 sheet: -0.48 (0.14), residues: 1257 loop : -0.31 (0.10), residues: 4177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP X 263 HIS 0.007 0.001 HIS B 440 PHE 0.030 0.002 PHE O 190 TYR 0.029 0.001 TYR B 486 ARG 0.009 0.000 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 873 time to evaluate : 7.271 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: A 74 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7620 (tpp) REVERT: A 88 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8375 (mmtt) REVERT: A 175 ARG cc_start: 0.8027 (ptm-80) cc_final: 0.7783 (ppt170) REVERT: A 212 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8141 (mttp) REVERT: A 234 MET cc_start: 0.7817 (mtm) cc_final: 0.7599 (mtm) REVERT: A 250 ILE cc_start: 0.8639 (tp) cc_final: 0.8008 (tt) REVERT: A 290 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7380 (tm-30) REVERT: A 501 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8443 (mp) REVERT: A 658 LEU cc_start: 0.8611 (tp) cc_final: 0.8384 (tp) REVERT: A 802 ASN cc_start: 0.7903 (m-40) cc_final: 0.7637 (m110) REVERT: A 1259 MET cc_start: 0.6948 (mmp) cc_final: 0.6582 (tpp) REVERT: A 1453 TYR cc_start: 0.6039 (m-80) cc_final: 0.5552 (m-80) REVERT: B 106 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8492 (p0) REVERT: B 226 PHE cc_start: 0.8186 (m-10) cc_final: 0.7762 (m-10) REVERT: B 358 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7193 (ttmt) REVERT: B 770 GLN cc_start: 0.8353 (tp40) cc_final: 0.8072 (tp40) REVERT: B 885 MET cc_start: 0.7875 (mmm) cc_final: 0.7641 (mmm) REVERT: B 1116 ARG cc_start: 0.8696 (ttm170) cc_final: 0.8225 (mtt-85) REVERT: B 1220 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7588 (tpp80) REVERT: C 60 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: D 58 VAL cc_start: 0.8345 (t) cc_final: 0.8062 (p) REVERT: D 152 SER cc_start: 0.7767 (t) cc_final: 0.7434 (p) REVERT: E 91 LYS cc_start: 0.8430 (mmtp) cc_final: 0.7978 (mmtm) REVERT: E 121 MET cc_start: 0.8846 (mmt) cc_final: 0.7949 (mmt) REVERT: G 144 ARG cc_start: 0.6424 (mtp-110) cc_final: 0.5352 (mtt90) REVERT: M 56 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8889 (pp) REVERT: M 81 GLU cc_start: 0.4682 (tp30) cc_final: 0.4171 (tm-30) REVERT: M 106 PHE cc_start: 0.7254 (m-80) cc_final: 0.6972 (m-80) REVERT: M 135 MET cc_start: 0.8294 (tmm) cc_final: 0.7993 (tmm) REVERT: M 234 GLN cc_start: 0.7484 (mm110) cc_final: 0.7034 (mm-40) REVERT: M 267 LYS cc_start: 0.6615 (OUTLIER) cc_final: 0.6063 (tttt) REVERT: Q 31 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.6471 (t80) REVERT: Q 34 MET cc_start: 0.4453 (mmm) cc_final: 0.2878 (ttp) REVERT: Q 148 GLN cc_start: 0.5473 (OUTLIER) cc_final: 0.5131 (mm110) REVERT: Q 384 PHE cc_start: 0.5618 (m-80) cc_final: 0.5189 (m-10) REVERT: R 65 ASN cc_start: 0.8397 (m-40) cc_final: 0.7742 (p0) REVERT: R 138 GLN cc_start: 0.7022 (tp-100) cc_final: 0.6418 (tp-100) REVERT: R 228 MET cc_start: 0.7324 (mmp) cc_final: 0.6911 (ttp) REVERT: R 268 MET cc_start: 0.7352 (mmp) cc_final: 0.7021 (mmp) REVERT: R 294 MET cc_start: 0.2083 (tmm) cc_final: 0.0091 (ttt) REVERT: R 302 TYR cc_start: 0.3117 (OUTLIER) cc_final: 0.2629 (m-80) REVERT: U 244 MET cc_start: 0.0457 (tmm) cc_final: -0.0997 (ptp) REVERT: V 81 LYS cc_start: 0.4905 (OUTLIER) cc_final: 0.4312 (mmmt) REVERT: X 136 GLN cc_start: 0.3813 (mt0) cc_final: 0.3034 (tp40) REVERT: 0 42 MET cc_start: 0.8005 (tpt) cc_final: 0.7733 (tpp) REVERT: 0 136 MET cc_start: 0.8105 (mtp) cc_final: 0.7824 (mtp) REVERT: 0 199 MET cc_start: 0.7870 (mtm) cc_final: 0.7309 (mtp) REVERT: 0 468 MET cc_start: 0.8153 (tpp) cc_final: 0.7863 (tpp) REVERT: 0 495 MET cc_start: 0.8589 (ptp) cc_final: 0.7859 (mpp) REVERT: 0 528 GLU cc_start: 0.8047 (tp30) cc_final: 0.7614 (tp30) REVERT: 0 642 MET cc_start: 0.8575 (mtp) cc_final: 0.7986 (mtp) REVERT: 0 679 MET cc_start: 0.7056 (mpp) cc_final: 0.6526 (mtt) REVERT: 1 16 ILE cc_start: -0.0937 (OUTLIER) cc_final: -0.1587 (tt) REVERT: 1 59 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.3840 (tmm) REVERT: 1 284 TRP cc_start: 0.8750 (m100) cc_final: 0.8063 (m100) REVERT: 1 469 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8156 (ptp) REVERT: 2 50 MET cc_start: 0.8575 (tpp) cc_final: 0.7913 (mmm) REVERT: 2 97 MET cc_start: 0.6896 (tpp) cc_final: 0.6572 (tpp) REVERT: 2 150 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7917 (tmm) REVERT: 2 210 MET cc_start: 0.8466 (tmm) cc_final: 0.8205 (ppp) REVERT: 2 227 MET cc_start: 0.8716 (ptp) cc_final: 0.8326 (tmm) REVERT: 2 253 MET cc_start: 0.8835 (mmm) cc_final: 0.8632 (mmm) REVERT: 3 12 MET cc_start: 0.5863 (tpp) cc_final: 0.5545 (tpp) REVERT: 3 45 ARG cc_start: 0.7133 (ttp80) cc_final: 0.6609 (ttm-80) REVERT: 4 26 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8653 (tp) REVERT: 5 54 LEU cc_start: 0.8626 (tt) cc_final: 0.8408 (mt) REVERT: 6 95 MET cc_start: 0.2975 (ptt) cc_final: 0.2637 (ptm) REVERT: 6 136 MET cc_start: 0.7752 (mmm) cc_final: 0.7421 (mmm) REVERT: 6 148 MET cc_start: 0.8253 (ttt) cc_final: 0.8025 (ttm) REVERT: 6 216 MET cc_start: 0.8856 (tpp) cc_final: 0.8260 (mmm) REVERT: 7 561 MET cc_start: 0.5954 (tpp) cc_final: 0.5372 (tpp) REVERT: a 73 GLU cc_start: 0.8320 (tt0) cc_final: 0.7797 (tt0) REVERT: c 24 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8165 (mm110) REVERT: c 76 THR cc_start: 0.8626 (p) cc_final: 0.8204 (t) REVERT: c 95 LYS cc_start: 0.9013 (tppp) cc_final: 0.8725 (tptp) REVERT: f 79 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7873 (ptpt) REVERT: h 48 ASP cc_start: 0.7498 (p0) cc_final: 0.6954 (t0) REVERT: h 90 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7935 (mp0) outliers start: 202 outliers final: 159 residues processed: 1001 average time/residue: 0.7868 time to fit residues: 1367.5935 Evaluate side-chains 1022 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 845 time to evaluate : 7.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1103 GLU Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1187 ASN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain E residue 33 GLU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 31 PHE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 148 GLN Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain R residue 273 ASP Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain U residue 254 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 81 LYS Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 85 VAL Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 425 ILE Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 502 ASP Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 0 residue 535 ASP Chi-restraints excluded: chain 0 residue 600 SER Chi-restraints excluded: chain 0 residue 606 VAL Chi-restraints excluded: chain 0 residue 712 MET Chi-restraints excluded: chain 1 residue 16 ILE Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 469 MET Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 206 MET Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 149 ILE Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 300 LEU Chi-restraints excluded: chain 6 residue 388 THR Chi-restraints excluded: chain 7 residue 234 VAL Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 60 ASN Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain h residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 588 optimal weight: 5.9990 chunk 946 optimal weight: 0.9980 chunk 577 optimal weight: 40.0000 chunk 449 optimal weight: 9.9990 chunk 658 optimal weight: 0.8980 chunk 993 optimal weight: 0.0970 chunk 914 optimal weight: 20.0000 chunk 790 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 610 optimal weight: 8.9990 chunk 484 optimal weight: 20.0000 overall best weight: 2.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 314 ASN ** 0 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 7 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 88753 Z= 0.275 Angle : 0.571 12.383 121592 Z= 0.305 Chirality : 0.041 0.222 13745 Planarity : 0.004 0.059 14130 Dihedral : 19.587 168.571 15186 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.19 % Allowed : 16.56 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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: 0.48 (0.09), residues: 9581 helix: 1.28 (0.08), residues: 4157 sheet: -0.48 (0.14), residues: 1246 loop : -0.31 (0.10), residues: 4178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP X 263 HIS 0.007 0.001 HIS B 440 PHE 0.034 0.002 PHE O 190 TYR 0.042 0.001 TYR 3 106 ARG 0.008 0.000 ARG I 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19162 Ramachandran restraints generated. 9581 Oldfield, 0 Emsley, 9581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 860 time to evaluate : 7.068 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: A 74 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7612 (tpp) REVERT: A 88 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8354 (mttm) REVERT: A 175 ARG cc_start: 0.8051 (ptm-80) cc_final: 0.7812 (ppt170) REVERT: A 212 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8137 (mttp) REVERT: A 234 MET cc_start: 0.7825 (mtm) cc_final: 0.7604 (mtm) REVERT: A 250 ILE cc_start: 0.8679 (tp) cc_final: 0.8057 (tt) REVERT: A 290 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7356 (tm-30) REVERT: A 501 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8447 (mp) REVERT: A 658 LEU cc_start: 0.8642 (tp) cc_final: 0.8390 (tp) REVERT: A 802 ASN cc_start: 0.7892 (m-40) cc_final: 0.7637 (m110) REVERT: A 1259 MET cc_start: 0.7015 (mmp) cc_final: 0.6656 (tpp) REVERT: A 1453 TYR cc_start: 0.6052 (m-80) cc_final: 0.5580 (m-80) REVERT: B 106 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8490 (p0) REVERT: B 226 PHE cc_start: 0.8196 (m-10) cc_final: 0.7828 (m-10) REVERT: B 358 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.7053 (ttmt) REVERT: B 770 GLN cc_start: 0.8361 (tp40) cc_final: 0.8076 (tp40) REVERT: B 885 MET cc_start: 0.7821 (mmm) cc_final: 0.7588 (mmm) REVERT: B 1116 ARG cc_start: 0.8668 (ttm170) cc_final: 0.8170 (mtt180) REVERT: C 60 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: D 58 VAL cc_start: 0.8348 (t) cc_final: 0.8062 (p) REVERT: D 152 SER cc_start: 0.7731 (t) cc_final: 0.7413 (p) REVERT: E 91 LYS cc_start: 0.8435 (mmtp) cc_final: 0.7981 (mmtm) REVERT: E 121 MET cc_start: 0.8850 (mmt) cc_final: 0.8386 (mmm) REVERT: G 144 ARG cc_start: 0.6397 (mtp-110) cc_final: 0.5212 (mtt90) REVERT: M 56 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8892 (pp) REVERT: M 81 GLU cc_start: 0.4969 (tp30) cc_final: 0.4568 (tm-30) REVERT: M 106 PHE cc_start: 0.7379 (m-80) cc_final: 0.7110 (m-80) REVERT: M 135 MET cc_start: 0.8305 (tmm) cc_final: 0.7990 (tmm) REVERT: M 234 GLN cc_start: 0.7460 (mm110) cc_final: 0.7048 (mm-40) REVERT: M 250 MET cc_start: 0.6304 (tmm) cc_final: 0.5993 (tmm) REVERT: M 267 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.6048 (tttt) REVERT: O 99 PHE cc_start: 0.5073 (t80) cc_final: 0.4775 (t80) REVERT: Q 31 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6539 (t80) REVERT: Q 34 MET cc_start: 0.4325 (mmm) cc_final: 0.2766 (ttp) REVERT: Q 120 LYS cc_start: 0.7926 (mtpt) cc_final: 0.7600 (mmmm) REVERT: Q 148 GLN cc_start: 0.5441 (OUTLIER) cc_final: 0.5091 (mm110) REVERT: Q 384 PHE cc_start: 0.5659 (m-80) cc_final: 0.4562 (m-10) REVERT: R 65 ASN cc_start: 0.8369 (m-40) cc_final: 0.7716 (p0) REVERT: R 69 TRP cc_start: 0.7332 (m-10) cc_final: 0.6817 (m-10) REVERT: R 138 GLN cc_start: 0.6956 (tp-100) cc_final: 0.6330 (tp-100) REVERT: R 228 MET cc_start: 0.7318 (mmp) cc_final: 0.6920 (ttp) REVERT: R 294 MET cc_start: 0.2057 (tmm) cc_final: 0.0075 (ttt) REVERT: U 244 MET cc_start: 0.0446 (tmm) cc_final: -0.1008 (ptp) REVERT: X 136 GLN cc_start: 0.3669 (mt0) cc_final: 0.2877 (tp40) REVERT: 0 42 MET cc_start: 0.7998 (tpt) cc_final: 0.7731 (tpp) REVERT: 0 136 MET cc_start: 0.8110 (mtp) cc_final: 0.7819 (mtp) REVERT: 0 199 MET cc_start: 0.7902 (mtm) cc_final: 0.7358 (mtp) REVERT: 0 468 MET cc_start: 0.8153 (tpp) cc_final: 0.7869 (tpp) REVERT: 0 495 MET cc_start: 0.8574 (ptp) cc_final: 0.7847 (mpp) REVERT: 0 528 GLU cc_start: 0.8050 (tp30) cc_final: 0.7616 (tp30) REVERT: 0 642 MET cc_start: 0.8580 (mtp) cc_final: 0.7987 (mtp) REVERT: 1 16 ILE cc_start: -0.1067 (OUTLIER) cc_final: -0.1727 (tt) REVERT: 1 59 MET cc_start: 0.5535 (tmm) cc_final: 0.3829 (tmm) REVERT: 1 284 TRP cc_start: 0.8762 (m100) cc_final: 0.8055 (m100) REVERT: 1 469 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8144 (ptp) REVERT: 2 50 MET cc_start: 0.8610 (tpp) cc_final: 0.7991 (mmm) REVERT: 2 97 MET cc_start: 0.7160 (tpp) cc_final: 0.6857 (tpp) REVERT: 2 150 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7925 (tmm) REVERT: 2 210 MET cc_start: 0.8475 (tmm) cc_final: 0.8256 (ppp) REVERT: 2 227 MET cc_start: 0.8712 (ptp) cc_final: 0.8320 (tmm) REVERT: 2 253 MET cc_start: 0.8826 (mmm) cc_final: 0.8521 (mmt) REVERT: 3 12 MET cc_start: 0.5889 (tpp) cc_final: 0.5571 (tpp) REVERT: 3 45 ARG cc_start: 0.7159 (ttp80) cc_final: 0.6635 (ttm-80) REVERT: 4 26 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8662 (tp) REVERT: 5 54 LEU cc_start: 0.8688 (tt) cc_final: 0.8482 (mt) REVERT: 6 136 MET cc_start: 0.7819 (mmm) cc_final: 0.7499 (mmm) REVERT: 6 148 MET cc_start: 0.8247 (ttt) cc_final: 0.8018 (ttm) REVERT: 6 216 MET cc_start: 0.8914 (tpp) cc_final: 0.8712 (mmm) REVERT: a 73 GLU cc_start: 0.8304 (tt0) cc_final: 0.7899 (tt0) REVERT: a 125 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: c 24 GLN cc_start: 0.8525 (mm-40) cc_final: 0.8152 (mm110) REVERT: c 76 THR cc_start: 0.8667 (p) cc_final: 0.8290 (t) REVERT: c 95 LYS cc_start: 0.9011 (tppp) cc_final: 0.8728 (tptp) REVERT: e 39 HIS cc_start: 0.6886 (t70) cc_final: 0.6559 (t70) REVERT: e 50 GLU cc_start: 0.8347 (tt0) cc_final: 0.8117 (tt0) REVERT: f 79 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7862 (ptpt) REVERT: f 84 MET cc_start: 0.7957 (mmm) cc_final: 0.7433 (mmm) REVERT: h 48 ASP cc_start: 0.7482 (p0) cc_final: 0.6933 (t0) REVERT: h 90 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7929 (mp0) outliers start: 189 outliers final: 165 residues processed: 976 average time/residue: 0.7999 time to fit residues: 1356.0016 Evaluate side-chains 1020 residues out of total 8644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 839 time to evaluate : 7.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 796 SER Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 976 THR Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1013 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1045 VAL Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain A residue 1103 GLU Chi-restraints excluded: chain A residue 1106 ASN Chi-restraints excluded: chain A residue 1112 LYS Chi-restraints excluded: chain A residue 1133 LEU Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1317 MET Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1176 ASN Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 32 LYS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 64 ASN Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 22 ASN Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain L residue 47 ARG Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 171 ILE Chi-restraints excluded: chain M residue 172 MET Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 LYS Chi-restraints excluded: chain M residue 309 ILE Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 161 VAL Chi-restraints excluded: chain O residue 214 LEU Chi-restraints excluded: chain O residue 233 VAL Chi-restraints excluded: chain O residue 235 SER Chi-restraints excluded: chain Q residue 31 PHE Chi-restraints excluded: chain Q residue 99 ASN Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 111 LEU Chi-restraints excluded: chain Q residue 113 ASN Chi-restraints excluded: chain Q residue 148 GLN Chi-restraints excluded: chain Q residue 387 ILE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 97 ILE Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 244 VAL Chi-restraints excluded: chain U residue 254 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 82 ASN Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 142 VAL Chi-restraints excluded: chain 0 residue 110 SER Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 287 GLU Chi-restraints excluded: chain 0 residue 349 LEU Chi-restraints excluded: chain 0 residue 425 ILE Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 485 MET Chi-restraints excluded: chain 0 residue 502 ASP Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 0 residue 535 ASP Chi-restraints excluded: chain 0 residue 600 SER Chi-restraints excluded: chain 0 residue 606 VAL Chi-restraints excluded: chain 0 residue 712 MET Chi-restraints excluded: chain 1 residue 16 ILE Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 301 ILE Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 414 ASP Chi-restraints excluded: chain 1 residue 469 MET Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 150 MET Chi-restraints excluded: chain 2 residue 194 GLN Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 126 VAL Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 26 LEU Chi-restraints excluded: chain 4 residue 51 ILE Chi-restraints excluded: chain 4 residue 125 LEU Chi-restraints excluded: chain 4 residue 206 MET Chi-restraints excluded: chain 4 residue 316 VAL Chi-restraints excluded: chain 5 residue 27 MET Chi-restraints excluded: chain 6 residue 137 LEU Chi-restraints excluded: chain 6 residue 149 ILE Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 6 residue 300 LEU Chi-restraints excluded: chain 6 residue 388 THR Chi-restraints excluded: chain 7 residue 234 VAL Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 660 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 80 THR Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 97 GLU Chi-restraints excluded: chain a residue 125 GLN Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 81 ARG Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 29 THR Chi-restraints excluded: chain d residue 44 GLN Chi-restraints excluded: chain d residue 60 ASN Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain f residue 73 THR Chi-restraints excluded: chain f residue 79 LYS Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain h residue 60 ASN Chi-restraints excluded: chain h residue 75 SER Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain h residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 997 random chunks: chunk 628 optimal weight: 10.0000 chunk 842 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 729 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 792 optimal weight: 6.9990 chunk 331 optimal weight: 2.9990 chunk 813 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 ASN ** A1218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 106 GLN ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 64 ASN ** 7 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN ** h 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.161841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.101029 restraints weight = 187034.542| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.40 r_work: 0.3172 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 88753 Z= 0.230 Angle : 0.551 16.835 121592 Z= 0.295 Chirality : 0.040 0.245 13745 Planarity : 0.004 0.058 14130 Dihedral : 19.535 168.729 15186 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.16 % Allowed : 16.71 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.32 % 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 (0.09), residues: 9581 helix: 1.36 (0.08), residues: 4157 sheet: -0.42 (0.14), residues: 1253 loop : -0.25 (0.10), residues: 4171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP X 263 HIS 0.007 0.001 HIS W 103 PHE 0.036 0.001 PHE O 190 TYR 0.026 0.001 TYR B 486 ARG 0.009 0.000 ARG B1135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25122.27 seconds wall clock time: 440 minutes 31.86 seconds (26431.86 seconds total)