Starting phenix.real_space_refine on Sun Feb 18 13:20:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o73_12744/02_2024/7o73_12744_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o73_12744/02_2024/7o73_12744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o73_12744/02_2024/7o73_12744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o73_12744/02_2024/7o73_12744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o73_12744/02_2024/7o73_12744_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o73_12744/02_2024/7o73_12744_updated.pdb" } resolution = 3.4 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: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 131 5.49 5 Mg 2 5.21 5 S 401 5.16 5 Be 1 3.05 5 C 46301 2.51 5 N 12748 2.21 5 O 14160 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 80": "OE1" <-> "OE2" Residue "0 TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 73768 Number of models: 1 Model: "" Number of chains: 43 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: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3597 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 4 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: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2274 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 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: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2794 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 334} 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: 11238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1428, 11238 Classifications: {'peptide': 1428} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1361} 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: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1307 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 2 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: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 697 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 79} 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: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2360 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Chain: "N" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1332 Classifications: {'DNA': 65} Link IDs: {'rna3p': 64} 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: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1330 Classifications: {'DNA': 65} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 64} 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: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2532 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 15, 'TRANS': 296} Chain breaks: 3 Chain: "X" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1661 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 938 SG CYS 0 115 74.443 89.777 188.325 1.00136.69 S ATOM 1265 SG CYS 0 156 69.247 89.337 192.269 1.00146.92 S ATOM 1080 SG CYS 0 133 71.577 95.090 190.072 1.00141.39 S ATOM 1566 SG CYS 0 191 74.406 92.178 194.573 1.00138.55 S ATOM 13941 SG CYS 3 13 59.975 120.198 142.404 1.00180.44 S ATOM 13962 SG CYS 3 16 61.024 119.762 138.775 1.00176.32 S ATOM 14157 SG CYS 3 39 62.349 122.713 140.782 1.00184.60 S ATOM 14178 SG CYS 3 42 58.785 122.665 139.651 1.00180.18 S ATOM 14110 SG CYS 3 34 52.460 126.219 150.935 1.00179.26 S ATOM 14268 SG CYS 3 54 51.703 124.885 147.396 1.00173.75 S ATOM 14306 SG CYS 3 59 48.938 124.783 150.087 1.00171.03 S ATOM 16970 SG CYS 4 289 123.281 50.459 209.607 1.00173.27 S ATOM 16989 SG CYS 4 292 126.831 51.111 210.792 1.00168.71 S ATOM 17081 SG CYS 4 305 124.405 49.201 213.026 1.00173.77 S ATOM 17099 SG CYS 4 308 123.871 52.871 212.484 1.00176.26 S ATOM 19766 SG CYS 6 349 127.684 33.156 195.703 1.00176.26 S ATOM 19787 SG CYS 6 352 125.504 30.747 193.724 1.00178.91 S ATOM 19866 SG CYS 6 363 126.358 34.124 192.271 1.00177.92 S ATOM 19885 SG CYS 6 366 123.965 33.911 195.199 1.00181.51 S ATOM 20187 SG CYS 6 403 154.462 68.499 207.043 1.00178.93 S ATOM 20210 SG CYS 6 406 156.524 67.561 203.974 1.00174.32 S ATOM 20404 SG CYS 6 437 153.879 70.328 203.746 1.00183.27 S ATOM 20425 SG CYS 6 440 152.867 66.720 204.077 1.00180.08 S ATOM 20337 SG CYS 6 429 144.381 66.638 213.569 1.00176.90 S ATOM 20360 SG CYS 6 432 147.564 65.237 215.139 1.00173.13 S ATOM 20518 SG CYS 6 451 146.542 64.126 211.673 1.00173.97 S ATOM 20535 SG CYS 6 454 144.506 63.011 214.688 1.00174.28 S ATOM 19665 SG CYS 6 336 131.336 33.966 181.662 1.00180.36 S ATOM 19677 SG CYS 6 338 130.152 37.163 183.411 1.00177.01 S ATOM 19825 SG CYS 6 357 133.848 36.173 183.460 1.00170.73 S ATOM 26347 SG CYS A 107 98.688 114.467 115.739 1.00 66.47 S ATOM 26371 SG CYS A 110 97.774 115.953 119.052 1.00 70.70 S ATOM 26676 SG CYS A 148 101.406 115.117 118.328 1.00 94.49 S ATOM 26814 SG CYS A 167 98.889 112.257 118.759 1.00102.67 S ATOM 26042 SG CYS A 67 60.867 139.687 100.662 1.00 63.89 S ATOM 26064 SG CYS A 70 61.382 143.331 101.731 1.00 55.27 S ATOM 26117 SG CYS A 77 63.565 141.814 98.957 1.00 43.86 S ATOM 45675 SG CYS B1163 73.680 144.385 112.886 1.00 41.07 S ATOM 45693 SG CYS B1166 75.121 141.517 110.685 1.00 43.57 S ATOM 45818 SG CYS B1182 71.418 141.708 111.491 1.00 44.16 S ATOM 45837 SG CYS B1185 74.072 140.830 114.163 1.00 54.93 S ATOM 46822 SG CYS C 86 46.141 179.729 46.601 1.00 68.45 S ATOM 46839 SG CYS C 88 45.412 176.330 48.185 1.00 84.81 S ATOM 46872 SG CYS C 92 44.001 177.302 44.730 1.00 53.74 S ATOM 46895 SG CYS C 95 47.720 176.574 45.203 1.00 48.32 S ATOM 54529 SG CYS I 7 131.713 88.590 59.663 1.00131.99 S ATOM 54554 SG CYS I 10 128.177 88.357 61.155 1.00127.70 S ATOM 54720 SG CYS I 29 130.846 89.888 63.222 1.00152.22 S ATOM 54744 SG CYS I 32 131.153 86.162 62.315 1.00150.28 S ATOM 55071 SG CYS I 75 135.621 121.931 31.426 1.00140.80 S ATOM 55093 SG CYS I 78 135.202 120.764 27.741 1.00147.46 S ATOM 55309 SG CYS I 103 132.159 121.399 29.761 1.00126.12 S ATOM 55329 SG CYS I 106 134.389 118.466 30.646 1.00135.93 S ATOM 55474 SG CYS J 7 75.512 165.927 33.868 1.00 21.18 S ATOM 55497 SG CYS J 10 75.078 169.613 32.899 1.00 20.84 S ATOM 55777 SG CYS J 45 78.541 167.978 32.740 1.00 23.60 S ATOM 55783 SG CYS J 46 75.766 167.210 30.254 1.00 22.77 S ATOM 56963 SG CYS L 31 49.948 130.976 43.057 1.00 78.62 S ATOM 56983 SG CYS L 34 47.646 130.787 40.049 1.00 85.58 S ATOM 57087 SG CYS L 48 46.480 129.477 43.406 1.00 89.14 S ATOM 57110 SG CYS L 51 49.148 127.580 41.516 1.00 91.25 S ATOM 57354 SG CYS M 24 47.793 160.068 89.694 1.00108.02 S ATOM 57376 SG CYS M 27 45.238 161.798 87.510 1.00122.99 S ATOM 57520 SG CYS M 45 47.515 159.215 85.933 1.00 87.22 S ATOM 57539 SG CYS M 48 49.023 162.499 87.250 1.00 86.50 S ATOM 70527 SG CYS W 124 47.128 137.205 109.778 1.00154.49 S ATOM 70548 SG CYS W 127 50.512 136.529 108.401 1.00148.96 S ATOM 70733 SG CYS W 149 49.519 140.103 109.431 1.00140.67 S ATOM 70753 SG CYS W 152 48.027 138.482 106.286 1.00138.09 S Time building chain proxies: 28.24, per 1000 atoms: 0.38 Number of scatterers: 73768 At special positions: 0 Unit cell: (213.15, 228.9, 243.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 401 16.00 P 131 15.00 Mg 2 11.99 F 3 9.00 O 14160 8.00 N 12748 7.00 C 46301 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.16 Conformation dependent library (CDL) restraints added in 9.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " 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 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " 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 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " 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 6 454 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " 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 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 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " 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 ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " 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 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 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 48 " 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 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 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " 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 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16878 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 344 helices and 72 sheets defined 39.6% alpha, 12.6% beta 63 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 25.78 Creating SS restraints... Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 49 through 62 Processing helix chain '0' and resid 76 through 97 Processing helix chain '0' and resid 111 through 113 No H-bonds generated for 'chain '0' and resid 111 through 113' Processing helix chain '0' and resid 126 through 137 Processing helix chain '0' and resid 140 through 147 Processing helix chain '0' and resid 157 through 164 removed outlier: 3.644A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 167 through 169 No H-bonds generated for 'chain '0' and resid 167 through 169' Processing helix chain '0' and resid 178 through 188 removed outlier: 3.503A pdb=" N LYS 0 188 " --> pdb=" O TYR 0 184 " (cutoff:3.500A) Processing helix chain '0' and resid 192 through 202 removed outlier: 5.435A pdb=" N SER 0 201 " --> pdb=" O ARG 0 197 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU 0 202 " --> pdb=" O ARG 0 198 " (cutoff:3.500A) Processing helix chain '0' and resid 210 through 214 removed outlier: 4.105A pdb=" N LEU 0 214 " --> pdb=" O HIS 0 211 " (cutoff:3.500A) Processing helix chain '0' and resid 216 through 223 removed outlier: 3.817A pdb=" N GLU 0 220 " --> pdb=" O PRO 0 216 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG 0 221 " --> pdb=" O LYS 0 217 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL 0 222 " --> pdb=" O ILE 0 218 " (cutoff:3.500A) Processing helix chain '0' and resid 240 through 248 removed outlier: 4.002A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 removed outlier: 3.734A pdb=" N ARG 0 262 " --> pdb=" O ARG 0 258 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL 0 277 " --> pdb=" O GLU 0 273 " (cutoff:3.500A) Processing helix chain '0' and resid 280 through 291 removed outlier: 3.927A pdb=" N GLN 0 291 " --> pdb=" O GLU 0 287 " (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 347 removed outlier: 4.147A pdb=" N LYS 0 347 " --> pdb=" O LYS 0 343 " (cutoff:3.500A) Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 388 removed outlier: 3.871A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS 0 377 " --> pdb=" O PRO 0 373 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU 0 383 " --> pdb=" O GLU 0 379 " (cutoff:3.500A) Processing helix chain '0' and resid 395 through 411 removed outlier: 4.004A pdb=" N ALA 0 398 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE 0 409 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER 0 410 " --> pdb=" O THR 0 407 " (cutoff:3.500A) Processing helix chain '0' and resid 444 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 510 through 512 No H-bonds generated for 'chain '0' and resid 510 through 512' Processing helix chain '0' and resid 516 through 532 removed outlier: 3.619A pdb=" N ILE 0 532 " --> pdb=" O GLU 0 528 " (cutoff:3.500A) Processing helix chain '0' and resid 544 through 557 Processing helix chain '0' and resid 559 through 566 removed outlier: 3.571A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 592 Processing helix chain '0' and resid 606 through 608 No H-bonds generated for 'chain '0' and resid 606 through 608' 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 668 removed outlier: 3.524A pdb=" N HIS 0 661 " --> pdb=" O ASP 0 657 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 688 removed outlier: 3.686A pdb=" N SER 0 687 " --> pdb=" O ARG 0 684 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 684 through 688' Processing helix chain '0' and resid 695 through 698 No H-bonds generated for 'chain '0' and resid 695 through 698' 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 725 Processing helix chain '0' and resid 730 through 733 Processing helix chain '0' and resid 741 through 751 Processing helix chain '1' and resid 42 through 44 No H-bonds generated for 'chain '1' and resid 42 through 44' Processing helix chain '1' and resid 94 through 120 removed outlier: 4.113A pdb=" N THR 1 103 " --> pdb=" O ASN 1 99 " (cutoff:3.500A) Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 removed outlier: 3.621A pdb=" N GLY 1 187 " --> pdb=" O SER 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 199 Processing helix chain '1' and resid 206 through 224 removed outlier: 4.189A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE 1 214 " --> pdb=" O TRP 1 210 " (cutoff:3.500A) Proline residue: 1 215 - end of helix removed outlier: 3.847A 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 289 Processing helix chain '1' and resid 291 through 296 Processing helix chain '1' and resid 309 through 329 removed outlier: 3.597A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TYR 1 314 " --> pdb=" O ILE 1 310 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU 1 315 " --> pdb=" O ILE 1 311 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N THR 1 316 " --> pdb=" O ASP 1 312 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU 1 317 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 335 through 337 No H-bonds generated for 'chain '1' and resid 335 through 337' Processing helix chain '1' and resid 339 through 344 removed outlier: 3.660A pdb=" N ILE 1 343 " --> pdb=" O LEU 1 339 " (cutoff:3.500A) 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 Processing helix chain '1' and resid 414 through 419 Processing helix chain '1' and resid 422 through 424 No H-bonds generated for 'chain '1' and resid 422 through 424' Processing helix chain '1' and resid 466 through 482 Processing helix chain '1' and resid 487 through 489 No H-bonds generated for 'chain '1' and resid 487 through 489' Processing helix chain '1' and resid 496 through 516 removed outlier: 4.228A pdb=" N HIS 1 516 " --> pdb=" O LYS 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 544 through 568 removed outlier: 3.506A pdb=" N SER 1 549 " --> pdb=" O ASP 1 545 " (cutoff:3.500A) Processing helix chain '1' and resid 573 through 604 removed outlier: 4.644A pdb=" N SER 1 577 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN 1 602 " --> pdb=" O ASP 1 599 " (cutoff:3.500A) removed outlier: 3.911A 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 6 through 16 Processing helix chain '2' and resid 19 through 26 removed outlier: 3.660A pdb=" N ARG 2 24 " --> pdb=" O GLN 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 38 Processing helix chain '2' and resid 41 through 51 Processing helix chain '2' and resid 59 through 65 Processing helix chain '2' and resid 69 through 83 removed outlier: 4.471A pdb=" N LEU 2 72 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE 2 78 " --> pdb=" O GLN 2 75 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER 2 80 " --> pdb=" O ALA 2 77 " (cutoff:3.500A) 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 192 Processing helix chain '2' and resid 196 through 210 removed outlier: 3.822A pdb=" N LEU 2 203 " --> pdb=" O GLN 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 230 Processing helix chain '2' and resid 245 through 256 removed outlier: 3.638A pdb=" N ASP 2 255 " --> pdb=" O GLN 2 251 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR 2 256 " --> pdb=" O ASP 2 252 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 279 removed outlier: 4.124A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 354 through 363 removed outlier: 3.560A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE 2 363 " --> pdb=" O VAL 2 359 " (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 422 Processing helix chain '2' and resid 435 through 450 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 47 Processing helix chain '3' and resid 65 through 67 No H-bonds generated for 'chain '3' and resid 65 through 67' Processing helix chain '3' and resid 76 through 89 Processing helix chain '3' and resid 96 through 99 Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 126 through 138 removed outlier: 3.845A pdb=" N GLU 3 138 " --> pdb=" O ARG 3 134 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 43 removed outlier: 3.538A pdb=" N THR 4 39 " --> pdb=" O LYS 4 35 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE 4 40 " --> pdb=" O LEU 4 36 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 67 Processing helix chain '4' and resid 116 through 138 removed outlier: 3.864A pdb=" N THR 4 124 " --> pdb=" O ASN 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 190 through 205 removed outlier: 4.306A pdb=" N ILE 4 194 " --> pdb=" O ILE 4 190 " (cutoff:3.500A) Proline residue: 4 195 - end of helix removed outlier: 3.542A pdb=" N PHE 4 201 " --> pdb=" O MET 4 197 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 231 removed outlier: 3.507A pdb=" N THR 4 227 " --> pdb=" O PHE 4 223 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR 4 228 " --> pdb=" O LEU 4 224 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 251 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 321 removed outlier: 3.866A pdb=" N LEU 4 320 " --> pdb=" O VAL 4 316 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 44 through 61 removed outlier: 4.523A pdb=" N GLU 5 48 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS 5 52 " --> pdb=" O GLU 5 48 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG 5 56 " --> pdb=" O HIS 5 52 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU 5 57 " --> pdb=" O GLU 5 53 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN 5 61 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 113 removed outlier: 3.985A pdb=" N ALA 6 111 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 199 Processing helix chain '6' and resid 210 through 220 Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 281 removed outlier: 3.737A pdb=" N ASN 6 281 " --> pdb=" O CYS 6 277 " (cutoff:3.500A) Processing helix chain '6' and resid 294 through 305 removed outlier: 3.988A pdb=" N LYS 6 298 " --> pdb=" O GLU 6 294 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU 6 299 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL 6 305 " --> pdb=" O PHE 6 301 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 380 removed outlier: 4.223A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 446 Processing helix chain '6' and resid 452 through 456 Processing helix chain '7' and resid 150 through 160 removed outlier: 3.747A pdb=" N ASP 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL 7 158 " --> pdb=" O GLN 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 177 through 183 Processing helix chain '7' and resid 190 through 199 Processing helix chain '7' and resid 207 through 217 removed outlier: 3.863A pdb=" N ALA 7 216 " --> pdb=" O PHE 7 212 " (cutoff:3.500A) Processing helix chain '7' and resid 239 through 245 removed outlier: 3.821A pdb=" N LEU 7 245 " --> pdb=" O LEU 7 242 " (cutoff:3.500A) Processing helix chain '7' and resid 321 through 332 removed outlier: 4.018A pdb=" N GLU 7 324 " --> pdb=" O GLU 7 321 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS 7 327 " --> pdb=" O GLU 7 324 " (cutoff:3.500A) Processing helix chain '7' and resid 364 through 373 Processing helix chain '7' and resid 392 through 403 Processing helix chain '7' and resid 415 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 461 removed outlier: 4.105A pdb=" N ALA 7 461 " --> pdb=" O SER 7 458 " (cutoff:3.500A) Processing helix chain '7' and resid 468 through 479 Processing helix chain '7' and resid 498 through 504 removed outlier: 3.610A pdb=" N THR 7 504 " --> pdb=" O VAL 7 501 " (cutoff:3.500A) Processing helix chain '7' and resid 522 through 530 Processing helix chain '7' and resid 541 through 545 Processing helix chain '7' and resid 563 through 571 removed outlier: 3.722A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 582 removed outlier: 3.662A pdb=" N MET 7 578 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU 7 580 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR 7 581 " --> pdb=" O ARG 7 577 " (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 658 No H-bonds generated for 'chain '7' and resid 656 through 658' Processing helix chain '7' and resid 680 through 690 removed outlier: 3.748A pdb=" N ALA 7 684 " --> pdb=" O ARG 7 680 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG 7 689 " --> pdb=" O GLN 7 685 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE 7 690 " --> pdb=" O ARG 7 686 " (cutoff:3.500A) Processing helix chain '7' and resid 715 through 722 Processing helix chain '7' and resid 724 through 729 Processing helix chain '7' and resid 753 through 766 Processing helix chain '7' and resid 832 through 836 removed outlier: 3.796A pdb=" N LYS 7 835 " --> pdb=" O LEU 7 832 " (cutoff:3.500A) 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: 3.855A pdb=" N ILE A 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.584A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 3.628A pdb=" N HIS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 247 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 335 through 339 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 472 through 478 removed outlier: 4.062A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix 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 removed outlier: 3.810A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.710A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 660 removed outlier: 3.631A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) 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 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 923 through 946 Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.866A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 3.584A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.624A 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 1078 Proline residue: A1075 - end of helix removed outlier: 3.912A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) 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 1129 through 1138 Processing helix chain 'A' and resid 1143 through 1146 Processing helix chain 'A' and resid 1165 through 1176 removed outlier: 3.701A pdb=" N GLU A1168 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A1169 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A1170 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS A1173 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE A1174 " --> pdb=" O GLN A1171 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A1175 " --> pdb=" O LEU A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 removed outlier: 3.622A pdb=" N ASP A1204 " --> pdb=" O ALA A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1256 through 1269 Processing helix chain 'A' and resid 1313 through 1317 Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1341 through 1358 Processing helix chain 'A' and resid 1365 through 1376 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 1401 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: 3.660A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.639A pdb=" N LYS B 41 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.517A pdb=" N LEU B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 320 removed outlier: 3.665A pdb=" N MET B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 314 " --> pdb=" O MET B 310 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.856A 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 438 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 451 through 462 Processing helix chain 'B' and resid 488 through 496 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 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 700 Processing helix chain 'B' and resid 745 through 748 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 776 removed outlier: 3.840A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) 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 848 Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 removed outlier: 3.691A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1151 Processing helix chain 'B' and resid 1175 through 1177 No H-bonds generated for 'chain 'B' and resid 1175 through 1177' 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 69 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' 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: 3.833A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 267 removed outlier: 3.575A pdb=" N VAL C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 157 through 169 removed outlier: 4.781A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 3.504A pdb=" N GLY D 181 " --> pdb=" O VAL D 177 " (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 216 Processing helix chain 'E' and resid 3 through 26 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 45 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'E' and resid 118 through 123 removed outlier: 4.518A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) 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 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 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 127 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 34 Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' 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 '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 removed outlier: 3.512A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.641A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 3.698A 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: 3.880A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.683A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 118 through 140 removed outlier: 4.174A pdb=" N LYS M 122 " --> pdb=" O VAL M 118 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU M 125 " --> pdb=" O LYS M 121 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 168 through 182 Processing helix chain 'M' and resid 189 through 195 removed outlier: 4.007A pdb=" N LEU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 220 Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 235 through 246 removed outlier: 3.631A pdb=" N ILE M 239 " --> pdb=" O ASN M 235 " (cutoff:3.500A) Proline residue: M 240 - end of helix Processing helix chain 'M' and resid 250 through 265 removed outlier: 3.785A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 270 No H-bonds generated for 'chain 'M' and resid 267 through 270' 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 323 removed outlier: 3.674A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU M 318 " --> pdb=" O LYS M 314 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS M 319 " --> pdb=" O ILE M 315 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LYS M 322 " --> pdb=" O GLU M 318 " (cutoff:3.500A) 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 237 Proline residue: O 232 - end of helix removed outlier: 3.830A pdb=" N PHE O 237 " --> pdb=" O VAL O 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 34 Processing helix chain 'Q' and resid 108 through 110 No H-bonds generated for 'chain 'Q' and resid 108 through 110' Processing helix chain 'Q' and resid 153 through 167 Processing helix chain 'Q' and resid 337 through 345 Processing helix chain 'Q' and resid 406 through 413 Processing helix chain 'Q' and resid 424 through 431 Processing helix chain 'Q' and resid 437 through 449 removed outlier: 3.515A pdb=" N LYS Q 444 " --> pdb=" O ARG Q 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 52 removed outlier: 3.652A pdb=" N LYS R 51 " --> pdb=" O ASN R 48 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL R 52 " --> pdb=" O GLU R 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 48 through 52' Processing helix chain 'R' and resid 75 through 81 removed outlier: 3.993A pdb=" N LYS R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing helix chain 'R' and resid 235 through 245 removed outlier: 4.037A pdb=" N VAL R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 265 removed outlier: 4.760A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 296 through 309 removed outlier: 5.412A pdb=" N ASP R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR R 302 " --> pdb=" O GLU R 298 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE R 304 " --> pdb=" O LEU R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'R' and resid 326 through 336 removed outlier: 3.795A pdb=" N GLU R 331 " --> pdb=" O ALA R 327 " (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: 3.564A pdb=" N ARG U 22 " --> pdb=" O VAL U 18 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 49 removed outlier: 3.649A pdb=" N ILE U 41 " --> pdb=" O LEU U 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP U 42 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR U 47 " --> pdb=" O LYS U 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 12 Processing helix chain 'V' and resid 14 through 29 Processing helix chain 'V' and resid 34 through 54 removed outlier: 3.671A pdb=" N LYS V 46 " --> pdb=" O GLU V 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 20 Processing helix chain 'W' and resid 23 through 34 removed outlier: 3.547A pdb=" N LEU W 27 " --> pdb=" O GLY W 23 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 51 through 63 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 91 through 117 Processing helix chain 'W' and resid 133 through 138 removed outlier: 4.296A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) Processing helix chain 'W' and resid 163 through 191 removed outlier: 4.043A pdb=" N LYS W 166 " --> pdb=" O LYS W 163 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS W 168 " --> pdb=" O ASN W 165 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET W 176 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Proline residue: W 181 - end of helix Processing helix chain 'W' and resid 199 through 205 removed outlier: 3.569A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ARG W 205 " --> pdb=" O ILE W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 288 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 Processing helix chain 'X' and resid 124 through 136 removed outlier: 3.561A pdb=" N TRP X 130 " --> pdb=" O SER X 126 " (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 207 through 211 Processing helix chain 'X' and resid 218 through 227 Processing helix chain 'X' and resid 257 through 265 removed outlier: 3.799A pdb=" N MET X 262 " --> pdb=" O GLU X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 271 through 281 Proline residue: X 275 - end of helix Processing helix chain 'X' and resid 290 through 292 No H-bonds generated for 'chain 'X' and resid 290 through 292' Processing sheet with id= A, first strand: chain '0' and resid 2 through 4 Processing sheet with id= B, first strand: chain '0' and resid 174 through 176 removed outlier: 4.001A pdb=" N GLY 0 107 " --> pdb=" O PHE 0 176 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE 0 205 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE 0 69 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR 0 208 " --> pdb=" O ILE 0 69 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR 0 71 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE 0 231 " --> pdb=" O ILE 0 70 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N CYS 0 72 " --> pdb=" O ILE 0 231 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE 0 233 " --> pdb=" O CYS 0 72 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 478 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN 0 480 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLU 0 41 " --> pdb=" O GLN 0 480 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER 0 482 " --> pdb=" O GLU 0 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 250 through 253 Processing sheet with id= D, first strand: chain '0' and resid 492 through 497 removed outlier: 7.232A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N MET 0 495 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE 0 497 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU 0 681 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR 0 619 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA 0 596 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL 0 539 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 4 through 9 Processing sheet with id= F, first strand: chain '1' and resid 86 through 90 removed outlier: 3.549A pdb=" N ILE 1 63 " --> pdb=" O LYS 1 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS 1 47 " --> pdb=" O ILE 1 63 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '2' and resid 87 through 92 Processing sheet with id= H, first strand: chain '2' and resid 259 through 261 Processing sheet with id= I, first strand: chain '2' and resid 339 through 341 removed outlier: 5.926A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '2' and resid 456 through 459 removed outlier: 6.351A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 28 through 31 removed outlier: 3.980A pdb=" N ASN 3 31 " --> pdb=" O HIS 3 36 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS 3 36 " --> pdb=" O ASN 3 31 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 82 through 87 removed outlier: 6.243A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ALA 4 74 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU 4 179 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '5' and resid 8 through 11 Processing sheet with id= N, first strand: chain '6' and resid 178 through 183 removed outlier: 6.582A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '6' and resid 326 through 328 removed outlier: 3.528A pdb=" N THR 6 326 " --> pdb=" O PHE 6 348 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE 6 328 " --> pdb=" O GLY 6 346 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY 6 346 " --> pdb=" O ILE 6 328 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '7' and resid 132 through 134 removed outlier: 6.601A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '7' and resid 224 through 228 removed outlier: 4.332A pdb=" N TYR 7 232 " --> pdb=" O ILE 7 318 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE 7 316 " --> pdb=" O VAL 7 234 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '7' and resid 435 through 437 removed outlier: 6.147A pdb=" N LEU 7 452 " --> pdb=" O ALA 7 436 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL 7 385 " --> pdb=" O PRO 7 533 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU 7 535 " --> pdb=" O VAL 7 385 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '7' and resid 734 through 736 removed outlier: 3.761A pdb=" N TRP 7 558 " --> pdb=" O ILE 7 736 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ALA 7 703 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA 7 555 " --> pdb=" O ALA 7 703 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE 7 705 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL 7 557 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N SER 7 707 " --> pdb=" O VAL 7 557 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS 7 559 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL 7 709 " --> pdb=" O CYS 7 559 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= U, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= V, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.674A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.765A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.399A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.666A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.751A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= AB, first strand: chain 'A' and resid 1115 through 1119 removed outlier: 3.641A pdb=" N ARG A1289 " --> pdb=" O GLU A1301 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.482A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 68 through 73 Processing sheet with id= AE, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= AF, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= AG, first strand: chain 'B' and resid 125 through 127 Processing sheet with id= AH, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= AI, first strand: chain 'B' and resid 404 through 407 Processing sheet with id= AJ, first strand: chain 'B' and resid 224 through 227 removed outlier: 6.926A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.516A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 634 through 638 Processing sheet with id= AM, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.734A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 990 through 994 removed outlier: 6.849A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= AP, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= AQ, first strand: chain 'C' and resid 176 through 179 removed outlier: 6.482A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 97 through 104 removed outlier: 6.058A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AT, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AU, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.741A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'E' and resid 152 through 155 Processing sheet with id= AW, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AX, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.300A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'G' and resid 142 through 146 removed outlier: 6.783A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ILE G 157 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N PHE G 109 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA G 159 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR G 111 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLY G 161 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.676A pdb=" N THR G 120 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.592A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.734A pdb=" N ASP I 19 " --> pdb=" O ARG I 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 69 through 71 removed outlier: 3.528A pdb=" N PHE I 85 " --> pdb=" O PRO I 69 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= BE, first strand: chain 'L' and resid 37 through 40 removed outlier: 3.754A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.451A pdb=" N CYS M 45 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL M 51 " --> pdb=" O CYS M 45 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'O' and resid 155 through 157 removed outlier: 4.319A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 192 through 196 removed outlier: 4.122A pdb=" N LYS O 211 " --> pdb=" O PHE O 207 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY O 216 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE O 160 " --> pdb=" O GLY O 216 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN O 69 " --> pdb=" O VAL O 161 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Q' and resid 103 through 105 removed outlier: 5.853A pdb=" N PHE Q 384 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Q' and resid 117 through 122 removed outlier: 6.563A pdb=" N LYS Q 391 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LYS Q 120 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR Q 393 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLN Q 122 " --> pdb=" O TYR Q 393 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE Q 395 " --> pdb=" O GLN Q 122 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL Q 392 " --> pdb=" O GLU Q 366 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'R' and resid 93 through 97 removed outlier: 4.307A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU R 70 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU R 221 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ARG R 72 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN R 223 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'R' and resid 337 through 340 removed outlier: 3.612A pdb=" N VAL R 340 " --> pdb=" O LYS R 348 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS R 348 " --> pdb=" O VAL R 340 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'R' and resid 133 through 138 removed outlier: 3.777A pdb=" N GLY R 216 " --> pdb=" O VAL R 134 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR R 136 " --> pdb=" O ILE R 214 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ILE R 214 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN R 138 " --> pdb=" O THR R 212 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR R 212 " --> pdb=" O GLN R 138 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'U' and resid 243 through 245 Processing sheet with id= BO, first strand: chain 'U' and resid 278 through 284 removed outlier: 3.913A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'V' and resid 60 through 63 removed outlier: 3.742A pdb=" N VAL V 87 " --> pdb=" O SER V 104 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER V 104 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'V' and resid 110 through 116 removed outlier: 5.939A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'W' and resid 68 through 74 removed outlier: 3.510A pdb=" N VAL W 82 " --> pdb=" O GLU W 74 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'X' and resid 169 through 172 Processing sheet with id= BT, first strand: chain 'X' and resid 230 through 232 2630 hydrogen bonds defined for protein. 7305 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 153 hydrogen bonds 306 hydrogen bond angles 0 basepair planarities 63 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 34.80 Time building geometry restraints manager: 23.40 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: 30972 1.43 - 1.64: 43736 1.64 - 1.85: 628 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 75348 Sorted by residual: bond pdb=" C4 ADP 7 903 " pdb=" C5 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" BE BEF 7 901 " pdb=" F2 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C5 ADP 7 903 " pdb=" C6 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" BE BEF 7 901 " pdb=" F3 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" BE BEF 7 901 " pdb=" F1 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.535 -0.059 2.00e-02 2.50e+03 8.85e+00 ... (remaining 75343 not shown) Histogram of bond angle deviations from ideal: 73.68 - 85.75: 12 85.75 - 97.82: 1 97.82 - 109.89: 10253 109.89 - 121.96: 76571 121.96 - 134.03: 15424 Bond angle restraints: 102261 Sorted by residual: angle pdb=" CA LEU D 15 " pdb=" C LEU D 15 " pdb=" N LYS D 16 " ideal model delta sigma weight residual 119.98 115.28 4.70 8.50e-01 1.38e+00 3.06e+01 angle pdb=" N ARG D 14 " pdb=" CA ARG D 14 " pdb=" C ARG D 14 " ideal model delta sigma weight residual 108.31 115.46 -7.15 1.52e+00 4.33e-01 2.21e+01 angle pdb=" C LEU D 15 " pdb=" CA LEU D 15 " pdb=" CB LEU D 15 " ideal model delta sigma weight residual 117.23 111.37 5.86 1.36e+00 5.41e-01 1.86e+01 angle pdb=" C1' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C3' ADP 7 903 " ideal model delta sigma weight residual 111.00 98.63 12.37 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N TYR A 465 " pdb=" CA TYR A 465 " pdb=" CB TYR A 465 " ideal model delta sigma weight residual 110.49 117.27 -6.78 1.69e+00 3.50e-01 1.61e+01 ... (remaining 102256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.88: 44616 32.88 - 65.75: 1237 65.75 - 98.63: 100 98.63 - 131.51: 2 131.51 - 164.39: 1 Dihedral angle restraints: 45956 sinusoidal: 19972 harmonic: 25984 Sorted by residual: dihedral pdb=" O1B ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PB ADP 7 903 " pdb=" PA ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 104.38 -164.39 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O2A ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 70.76 -130.76 1 2.00e+01 2.50e-03 3.97e+01 dihedral pdb=" C5' ADP 7 903 " pdb=" O5' ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" O2A ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 -171.95 111.95 1 2.00e+01 2.50e-03 3.30e+01 ... (remaining 45953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 10918 0.091 - 0.182: 636 0.182 - 0.274: 2 0.274 - 0.365: 0 0.365 - 0.456: 2 Chirality restraints: 11558 Sorted by residual: chirality pdb=" CA TYR A 465 " pdb=" N TYR A 465 " pdb=" C TYR A 465 " pdb=" CB TYR A 465 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CA ARG D 14 " pdb=" N ARG D 14 " pdb=" C ARG D 14 " pdb=" CB ARG D 14 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C3' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C4' ADP 7 903 " pdb=" O3' ADP 7 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 11555 not shown) Planarity restraints: 12672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 464 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C PRO A 464 " -0.056 2.00e-02 2.50e+03 pdb=" O PRO A 464 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR A 465 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS 7 676 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C HIS 7 676 " -0.039 2.00e-02 2.50e+03 pdb=" O HIS 7 676 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR 7 677 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP 5 13 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO 5 14 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO 5 14 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO 5 14 " -0.029 5.00e-02 4.00e+02 ... (remaining 12669 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 302 2.49 - 3.09: 53257 3.09 - 3.70: 109068 3.70 - 4.30: 162506 4.30 - 4.90: 267152 Nonbonded interactions: 592285 Sorted by model distance: nonbonded pdb=" OG1 THR X 235 " pdb=" O ASP X 238 " model vdw 1.888 2.440 nonbonded pdb=" OE2 GLU A 846 " pdb=" OG SER A1425 " model vdw 1.986 2.440 nonbonded pdb=" OD1 ASP A 481 " pdb="MG MG A1803 " model vdw 1.991 2.170 nonbonded pdb=" F1 BEF 7 901 " pdb="MG MG 7 902 " model vdw 2.000 2.120 nonbonded pdb="MG MG 7 902 " pdb=" O3B ADP 7 903 " model vdw 2.002 2.170 ... (remaining 592280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.060 Extract box with map and model: 13.250 Check model and map are aligned: 0.850 Set scattering table: 0.510 Process input model: 186.910 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.220 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 209.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.002 0.109 75348 Z= 0.148 Angle : 0.443 12.368 102261 Z= 0.254 Chirality : 0.039 0.456 11558 Planarity : 0.002 0.052 12672 Dihedral : 14.447 164.386 29078 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.19 % Favored : 97.79 % Rotamer: Outliers : 0.01 % Allowed : 0.08 % Favored : 99.91 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.51 % 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: 1.66 (0.09), residues: 8748 helix: 2.32 (0.09), residues: 3453 sheet: 0.60 (0.14), residues: 1348 loop : 0.27 (0.10), residues: 3947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 245 HIS 0.004 0.000 HIS R 234 PHE 0.014 0.001 PHE C 62 TYR 0.017 0.001 TYR A 465 ARG 0.002 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1826 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1825 time to evaluate : 6.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 458 ILE cc_start: 0.8820 (mt) cc_final: 0.8513 (tt) REVERT: 0 553 MET cc_start: 0.8325 (mmm) cc_final: 0.7864 (mmm) REVERT: 0 557 MET cc_start: 0.7333 (mtp) cc_final: 0.7107 (mtp) REVERT: 0 657 ASP cc_start: 0.8611 (t0) cc_final: 0.8280 (t0) REVERT: 1 97 MET cc_start: 0.8562 (ttt) cc_final: 0.8354 (ttt) REVERT: 1 266 VAL cc_start: 0.8946 (t) cc_final: 0.8739 (m) REVERT: 1 270 TYR cc_start: 0.8324 (t80) cc_final: 0.8115 (t80) REVERT: 2 150 MET cc_start: 0.8170 (tpt) cc_final: 0.7928 (tpt) REVERT: 2 360 LEU cc_start: 0.9443 (mm) cc_final: 0.9224 (mt) REVERT: 2 365 HIS cc_start: 0.8411 (t-90) cc_final: 0.7959 (t70) REVERT: 3 21 TYR cc_start: 0.6777 (t80) cc_final: 0.6249 (t80) REVERT: 3 45 ARG cc_start: 0.8482 (ptt90) cc_final: 0.8061 (ptp90) REVERT: 3 87 ARG cc_start: 0.8676 (ptp-170) cc_final: 0.8458 (ptm-80) REVERT: 3 110 LEU cc_start: 0.9172 (mt) cc_final: 0.8933 (tt) REVERT: 3 116 ILE cc_start: 0.9219 (mt) cc_final: 0.9012 (mt) REVERT: 4 81 GLN cc_start: 0.9140 (mm110) cc_final: 0.8856 (mm-40) REVERT: 4 142 GLN cc_start: 0.8844 (tp-100) cc_final: 0.8542 (tm-30) REVERT: 4 153 MET cc_start: 0.9061 (mtp) cc_final: 0.8585 (mpp) REVERT: 4 159 TYR cc_start: 0.8979 (t80) cc_final: 0.8659 (t80) REVERT: 4 181 CYS cc_start: 0.8572 (t) cc_final: 0.7834 (t) REVERT: 4 235 TYR cc_start: 0.8112 (t80) cc_final: 0.7612 (t80) REVERT: 4 247 TYR cc_start: 0.8576 (m-80) cc_final: 0.8273 (m-80) REVERT: 5 15 SER cc_start: 0.8899 (m) cc_final: 0.8389 (p) REVERT: 6 250 THR cc_start: 0.9309 (m) cc_final: 0.9040 (p) REVERT: 6 300 LEU cc_start: 0.8565 (mm) cc_final: 0.8016 (mm) REVERT: A 62 ASP cc_start: 0.7453 (t0) cc_final: 0.6877 (m-30) REVERT: A 83 HIS cc_start: 0.8491 (p-80) cc_final: 0.8232 (p-80) REVERT: A 109 HIS cc_start: 0.8434 (t-90) cc_final: 0.8152 (t70) REVERT: A 112 LYS cc_start: 0.8132 (tttp) cc_final: 0.7784 (tttm) REVERT: A 119 ASN cc_start: 0.8639 (t0) cc_final: 0.8411 (t0) REVERT: A 268 ASP cc_start: 0.7017 (m-30) cc_final: 0.6807 (m-30) REVERT: A 332 LYS cc_start: 0.8001 (tttp) cc_final: 0.7724 (ttmm) REVERT: A 451 HIS cc_start: 0.7911 (p-80) cc_final: 0.7575 (p-80) REVERT: A 453 MET cc_start: 0.8358 (mpp) cc_final: 0.7898 (mpp) REVERT: A 700 ASN cc_start: 0.9225 (t0) cc_final: 0.8814 (t0) REVERT: A 710 LEU cc_start: 0.8792 (mp) cc_final: 0.8511 (tt) REVERT: A 770 VAL cc_start: 0.8738 (t) cc_final: 0.8344 (m) REVERT: A 939 ASP cc_start: 0.6924 (m-30) cc_final: 0.6595 (m-30) REVERT: A 960 ILE cc_start: 0.8422 (mm) cc_final: 0.8213 (mm) REVERT: A 992 ASP cc_start: 0.7729 (p0) cc_final: 0.7499 (p0) REVERT: A 1033 GLN cc_start: 0.7933 (tt0) cc_final: 0.7673 (tt0) REVERT: A 1043 ASP cc_start: 0.7902 (t70) cc_final: 0.7666 (t0) REVERT: A 1195 LEU cc_start: 0.8870 (mm) cc_final: 0.8567 (mm) REVERT: A 1284 MET cc_start: 0.6619 (mtp) cc_final: 0.5797 (mtp) REVERT: A 1285 MET cc_start: 0.6951 (mmm) cc_final: 0.6510 (mmm) REVERT: A 1323 ASP cc_start: 0.8224 (t0) cc_final: 0.7874 (t0) REVERT: A 1328 TYR cc_start: 0.7448 (t80) cc_final: 0.6997 (t80) REVERT: B 216 GLU cc_start: 0.7535 (tt0) cc_final: 0.7241 (tt0) REVERT: B 278 GLN cc_start: 0.7994 (tt0) cc_final: 0.7710 (tt0) REVERT: B 348 ARG cc_start: 0.7937 (tpp80) cc_final: 0.7462 (tpp80) REVERT: B 358 LYS cc_start: 0.8491 (mtmt) cc_final: 0.7922 (mtmt) REVERT: B 398 ARG cc_start: 0.7535 (mmm-85) cc_final: 0.7303 (mmm-85) REVERT: B 426 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8208 (mmmt) REVERT: B 430 ARG cc_start: 0.7436 (ttm110) cc_final: 0.6983 (ttm110) REVERT: B 459 TYR cc_start: 0.7780 (t80) cc_final: 0.7531 (t80) REVERT: B 662 MET cc_start: 0.8082 (mtp) cc_final: 0.7460 (mtm) REVERT: B 730 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7798 (mmt90) REVERT: B 809 MET cc_start: 0.8406 (ttm) cc_final: 0.8146 (ttm) REVERT: B 914 LYS cc_start: 0.8307 (ttpp) cc_final: 0.7689 (ttpp) REVERT: B 1072 MET cc_start: 0.9005 (mtt) cc_final: 0.8704 (mtt) REVERT: B 1170 THR cc_start: 0.9087 (p) cc_final: 0.8813 (p) REVERT: B 1172 ILE cc_start: 0.9198 (mt) cc_final: 0.8842 (mt) REVERT: B 1174 LYS cc_start: 0.8323 (mttt) cc_final: 0.7917 (mtmt) REVERT: C 15 LYS cc_start: 0.8080 (ptmm) cc_final: 0.7793 (ptmt) REVERT: C 25 VAL cc_start: 0.9165 (p) cc_final: 0.8934 (t) REVERT: C 75 MET cc_start: 0.7877 (tpt) cc_final: 0.7631 (tpt) REVERT: C 154 LYS cc_start: 0.8502 (tttt) cc_final: 0.8062 (ttmm) REVERT: D 26 THR cc_start: 0.8973 (m) cc_final: 0.8180 (p) REVERT: D 38 ILE cc_start: 0.8548 (mt) cc_final: 0.7794 (mp) REVERT: D 53 SER cc_start: 0.9020 (m) cc_final: 0.8748 (p) REVERT: D 68 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7684 (mtm110) REVERT: D 146 GLN cc_start: 0.8978 (tt0) cc_final: 0.8579 (tt0) REVERT: D 149 THR cc_start: 0.8830 (m) cc_final: 0.8494 (p) REVERT: D 159 THR cc_start: 0.8199 (m) cc_final: 0.7325 (t) REVERT: D 164 ILE cc_start: 0.8721 (mt) cc_final: 0.7435 (mm) REVERT: D 189 ASP cc_start: 0.8720 (t70) cc_final: 0.8304 (t70) REVERT: D 200 ASN cc_start: 0.8345 (t0) cc_final: 0.7849 (t0) REVERT: D 201 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8148 (mmtp) REVERT: E 31 THR cc_start: 0.8450 (p) cc_final: 0.8213 (t) REVERT: E 41 ASP cc_start: 0.8702 (m-30) cc_final: 0.7717 (m-30) REVERT: E 99 HIS cc_start: 0.8334 (t70) cc_final: 0.8067 (t-170) REVERT: E 106 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7782 (tp40) REVERT: E 109 ILE cc_start: 0.8291 (mt) cc_final: 0.8068 (mm) REVERT: G 42 PHE cc_start: 0.8016 (m-80) cc_final: 0.6630 (m-80) REVERT: G 100 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7260 (mt-10) REVERT: G 131 GLN cc_start: 0.7911 (mt0) cc_final: 0.7663 (mt0) REVERT: G 167 TYR cc_start: 0.8581 (m-80) cc_final: 0.8380 (m-80) REVERT: H 86 ASP cc_start: 0.7196 (m-30) cc_final: 0.6810 (m-30) REVERT: H 94 ASP cc_start: 0.7898 (m-30) cc_final: 0.7624 (m-30) REVERT: I 5 ARG cc_start: 0.7495 (mtt180) cc_final: 0.7261 (mtt180) REVERT: I 13 MET cc_start: 0.8319 (ptp) cc_final: 0.8115 (ptt) REVERT: I 46 HIS cc_start: 0.7723 (t70) cc_final: 0.7397 (t70) REVERT: I 50 THR cc_start: 0.8759 (t) cc_final: 0.8189 (p) REVERT: I 51 ASN cc_start: 0.8422 (m-40) cc_final: 0.7373 (t0) REVERT: I 73 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7476 (ttm110) REVERT: I 113 ASP cc_start: 0.6060 (t0) cc_final: 0.5410 (t70) REVERT: K 84 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7831 (mtpt) REVERT: M 135 MET cc_start: 0.7674 (tmm) cc_final: 0.7441 (tmm) REVERT: M 208 ASN cc_start: 0.8805 (t0) cc_final: 0.8523 (m110) REVERT: M 243 CYS cc_start: 0.8858 (m) cc_final: 0.8341 (m) REVERT: M 275 ILE cc_start: 0.8866 (mt) cc_final: 0.8567 (mp) REVERT: M 300 GLN cc_start: 0.8332 (tt0) cc_final: 0.7774 (tp-100) REVERT: O 95 ASN cc_start: 0.7730 (t0) cc_final: 0.7446 (t0) REVERT: O 98 ARG cc_start: 0.8255 (mtm180) cc_final: 0.7873 (mtp180) REVERT: O 121 MET cc_start: 0.6931 (ttp) cc_final: 0.6431 (ttp) REVERT: O 193 LEU cc_start: 0.8298 (tt) cc_final: 0.7789 (pp) REVERT: Q 117 HIS cc_start: 0.8057 (m-70) cc_final: 0.7171 (m-70) REVERT: Q 140 HIS cc_start: 0.7224 (m-70) cc_final: 0.6864 (m-70) REVERT: Q 358 TYR cc_start: 0.7884 (t80) cc_final: 0.7447 (t80) REVERT: Q 365 TYR cc_start: 0.8316 (t80) cc_final: 0.8036 (t80) REVERT: Q 384 PHE cc_start: 0.8539 (m-80) cc_final: 0.7846 (m-80) REVERT: R 222 CYS cc_start: 0.6755 (m) cc_final: 0.5218 (m) REVERT: U 254 THR cc_start: 0.8477 (m) cc_final: 0.7898 (p) REVERT: V 79 ILE cc_start: 0.8838 (mt) cc_final: 0.8396 (mm) REVERT: W 42 ASP cc_start: 0.8536 (m-30) cc_final: 0.7871 (m-30) REVERT: W 63 SER cc_start: 0.8622 (t) cc_final: 0.8273 (m) REVERT: W 67 ILE cc_start: 0.9091 (mt) cc_final: 0.8729 (tp) REVERT: W 139 LEU cc_start: 0.8248 (mt) cc_final: 0.7937 (tp) REVERT: X 222 ASN cc_start: 0.8953 (t0) cc_final: 0.7395 (t0) REVERT: X 262 MET cc_start: 0.7492 (mtt) cc_final: 0.6416 (mtt) REVERT: X 293 ILE cc_start: 0.7586 (mt) cc_final: 0.7327 (tt) outliers start: 1 outliers final: 1 residues processed: 1826 average time/residue: 0.7438 time to fit residues: 2281.3324 Evaluate side-chains 1326 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1325 time to evaluate : 6.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 15 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 20.0000 chunk 673 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 454 optimal weight: 6.9990 chunk 359 optimal weight: 0.9990 chunk 696 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 423 optimal weight: 0.3980 chunk 518 optimal weight: 5.9990 chunk 806 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 164 ASN 0 283 GLN 0 350 HIS 0 362 HIS 1 92 ASN ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 165 ASN ** 2 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 261 GLN 2 407 GLN 3 90 ASN ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN 7 468 HIS 7 641 GLN 7 646 ASN 7 761 GLN A 18 GLN A 118 HIS A 427 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN A1106 ASN A1218 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN B 178 ASN B 357 GLN ** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B1040 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN D 34 GLN E 8 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN J 64 ASN K 52 ASN M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 144 GLN ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 GLN ** V 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 288 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 75348 Z= 0.451 Angle : 0.651 12.269 102261 Z= 0.341 Chirality : 0.045 0.213 11558 Planarity : 0.005 0.056 12672 Dihedral : 11.765 162.065 11075 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.86 % Allowed : 8.62 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.88 (0.09), residues: 8748 helix: 1.40 (0.09), residues: 3512 sheet: 0.38 (0.14), residues: 1312 loop : 0.00 (0.10), residues: 3924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 7 133 HIS 0.021 0.001 HIS O 88 PHE 0.036 0.002 PHE A 219 TYR 0.035 0.002 TYR U 10 ARG 0.012 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1530 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1382 time to evaluate : 7.585 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: 0 106 LEU cc_start: 0.7946 (mm) cc_final: 0.7731 (mm) REVERT: 0 366 LEU cc_start: 0.8771 (tp) cc_final: 0.8552 (tt) REVERT: 0 557 MET cc_start: 0.7424 (mtp) cc_final: 0.7189 (mtp) REVERT: 0 642 MET cc_start: 0.8787 (mmm) cc_final: 0.8570 (mmm) REVERT: 0 657 ASP cc_start: 0.8662 (t0) cc_final: 0.8405 (t70) REVERT: 1 1 MET cc_start: 0.7456 (ttp) cc_final: 0.6834 (tmm) REVERT: 1 11 LYS cc_start: 0.7868 (tptt) cc_final: 0.7586 (tppt) REVERT: 1 58 MET cc_start: 0.8652 (mmm) cc_final: 0.8432 (mmm) REVERT: 1 358 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8166 (mmp) REVERT: 2 50 MET cc_start: 0.8744 (ppp) cc_final: 0.8494 (ppp) REVERT: 2 150 MET cc_start: 0.8186 (tpt) cc_final: 0.7668 (tpt) REVERT: 2 165 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8660 (t0) REVERT: 2 216 MET cc_start: 0.6104 (mmt) cc_final: 0.5771 (ttm) REVERT: 2 365 HIS cc_start: 0.8522 (t-90) cc_final: 0.8078 (t70) REVERT: 3 45 ARG cc_start: 0.8440 (ptt90) cc_final: 0.8017 (ttp-110) REVERT: 3 64 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.7514 (mmt180) REVERT: 3 89 PHE cc_start: 0.8445 (m-80) cc_final: 0.8181 (m-80) REVERT: 4 37 TRP cc_start: 0.8296 (m100) cc_final: 0.7761 (m100) REVERT: 4 130 TYR cc_start: 0.8761 (t80) cc_final: 0.8373 (t80) REVERT: 4 153 MET cc_start: 0.8846 (mtp) cc_final: 0.8518 (mtt) REVERT: 4 159 TYR cc_start: 0.9041 (t80) cc_final: 0.8741 (t80) REVERT: 4 179 LEU cc_start: 0.9316 (mm) cc_final: 0.9038 (mt) REVERT: 4 206 MET cc_start: 0.8620 (ppp) cc_final: 0.7639 (ppp) REVERT: 5 15 SER cc_start: 0.9076 (m) cc_final: 0.8645 (p) REVERT: 6 136 MET cc_start: 0.8291 (tpp) cc_final: 0.8012 (mmp) REVERT: 6 250 THR cc_start: 0.9277 (m) cc_final: 0.8990 (p) REVERT: 6 300 LEU cc_start: 0.8428 (mm) cc_final: 0.7902 (mm) REVERT: 6 303 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8110 (mt-10) REVERT: A 62 ASP cc_start: 0.7571 (t0) cc_final: 0.7092 (m-30) REVERT: A 64 ASN cc_start: 0.7575 (t0) cc_final: 0.7369 (t0) REVERT: A 85 ASP cc_start: 0.6656 (m-30) cc_final: 0.6440 (t0) REVERT: A 109 HIS cc_start: 0.8613 (t-90) cc_final: 0.8265 (t-90) REVERT: A 112 LYS cc_start: 0.8187 (tttp) cc_final: 0.7876 (tttm) REVERT: A 119 ASN cc_start: 0.8700 (t0) cc_final: 0.8289 (t0) REVERT: A 268 ASP cc_start: 0.7199 (m-30) cc_final: 0.6878 (m-30) REVERT: A 453 MET cc_start: 0.8467 (mpp) cc_final: 0.7961 (mpp) REVERT: A 700 ASN cc_start: 0.9236 (t0) cc_final: 0.8857 (t0) REVERT: A 736 ASN cc_start: 0.7011 (t0) cc_final: 0.6766 (t0) REVERT: A 913 LEU cc_start: 0.8734 (pt) cc_final: 0.8516 (pt) REVERT: A 939 ASP cc_start: 0.6975 (m-30) cc_final: 0.6719 (m-30) REVERT: A 992 ASP cc_start: 0.7751 (p0) cc_final: 0.7507 (p0) REVERT: A 1033 GLN cc_start: 0.7942 (tt0) cc_final: 0.7675 (tt0) REVERT: A 1039 LYS cc_start: 0.8652 (tptt) cc_final: 0.8301 (tppt) REVERT: A 1043 ASP cc_start: 0.7957 (t70) cc_final: 0.7732 (t0) REVERT: A 1054 LEU cc_start: 0.9259 (mt) cc_final: 0.9032 (mt) REVERT: A 1135 ARG cc_start: 0.8909 (tmm-80) cc_final: 0.8242 (ttp80) REVERT: A 1195 LEU cc_start: 0.8774 (mm) cc_final: 0.8525 (mm) REVERT: A 1218 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8549 (pp30) REVERT: A 1285 MET cc_start: 0.7051 (mmm) cc_final: 0.6625 (mmm) REVERT: A 1287 TYR cc_start: 0.7618 (m-80) cc_final: 0.7413 (m-80) REVERT: A 1290 LYS cc_start: 0.8313 (mttm) cc_final: 0.8053 (mtpp) REVERT: A 1323 ASP cc_start: 0.8320 (t0) cc_final: 0.8058 (t0) REVERT: A 1328 TYR cc_start: 0.7570 (t80) cc_final: 0.7145 (t80) REVERT: A 1393 ASN cc_start: 0.8090 (p0) cc_final: 0.7720 (p0) REVERT: B 216 GLU cc_start: 0.7498 (tt0) cc_final: 0.7258 (tt0) REVERT: B 226 PHE cc_start: 0.7963 (m-10) cc_final: 0.7754 (m-10) REVERT: B 227 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8133 (mttm) REVERT: B 267 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7421 (mtm180) REVERT: B 278 GLN cc_start: 0.8049 (tt0) cc_final: 0.7824 (tt0) REVERT: B 348 ARG cc_start: 0.7624 (tpp80) cc_final: 0.7231 (tpp80) REVERT: B 358 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8022 (mtmt) REVERT: B 430 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7013 (ttp80) REVERT: B 434 ARG cc_start: 0.8407 (ttm110) cc_final: 0.8024 (mtm110) REVERT: B 445 LYS cc_start: 0.8805 (mttp) cc_final: 0.8466 (mtmt) REVERT: B 531 GLN cc_start: 0.7541 (pp30) cc_final: 0.6926 (pp30) REVERT: B 642 ASP cc_start: 0.7364 (t0) cc_final: 0.7149 (t0) REVERT: B 730 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7789 (mmt90) REVERT: B 863 GLU cc_start: 0.7455 (tt0) cc_final: 0.7188 (tt0) REVERT: B 873 THR cc_start: 0.8245 (p) cc_final: 0.7714 (m) REVERT: B 876 LYS cc_start: 0.8109 (ptpp) cc_final: 0.7584 (ptpp) REVERT: B 1174 LYS cc_start: 0.8452 (mttt) cc_final: 0.8081 (mtmt) REVERT: C 15 LYS cc_start: 0.8220 (ptmm) cc_final: 0.7975 (ptmt) REVERT: C 121 VAL cc_start: 0.8686 (p) cc_final: 0.8461 (m) REVERT: C 154 LYS cc_start: 0.8573 (tttt) cc_final: 0.8177 (ttpt) REVERT: C 253 LYS cc_start: 0.8289 (tppt) cc_final: 0.8081 (ttpp) REVERT: D 26 THR cc_start: 0.8996 (m) cc_final: 0.8561 (p) REVERT: D 189 ASP cc_start: 0.8540 (t70) cc_final: 0.8244 (t70) REVERT: D 200 ASN cc_start: 0.8424 (t0) cc_final: 0.7959 (t0) REVERT: D 216 ASN cc_start: 0.9336 (t0) cc_final: 0.9073 (t0) REVERT: E 61 GLN cc_start: 0.8358 (tm-30) cc_final: 0.8107 (tm-30) REVERT: E 99 HIS cc_start: 0.8437 (t70) cc_final: 0.8009 (t-170) REVERT: E 109 ILE cc_start: 0.8412 (mt) cc_final: 0.8186 (mm) REVERT: E 121 MET cc_start: 0.8046 (tpt) cc_final: 0.7822 (tpt) REVERT: G 22 MET cc_start: 0.7391 (ppp) cc_final: 0.7132 (ppp) REVERT: G 41 LYS cc_start: 0.8164 (ptmt) cc_final: 0.7905 (ptmm) REVERT: G 42 PHE cc_start: 0.8090 (m-80) cc_final: 0.7790 (m-80) REVERT: G 142 ARG cc_start: 0.7494 (ttm110) cc_final: 0.7204 (ttm-80) REVERT: G 143 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8928 (tp) REVERT: G 167 TYR cc_start: 0.8699 (m-80) cc_final: 0.8425 (m-80) REVERT: H 86 ASP cc_start: 0.7534 (m-30) cc_final: 0.7064 (m-30) REVERT: H 87 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6974 (mmm160) REVERT: I 9 ASP cc_start: 0.9025 (m-30) cc_final: 0.8357 (m-30) REVERT: I 34 TYR cc_start: 0.7851 (t80) cc_final: 0.7616 (t80) REVERT: I 46 HIS cc_start: 0.7940 (t70) cc_final: 0.7719 (t70) REVERT: I 50 THR cc_start: 0.9001 (t) cc_final: 0.8576 (p) REVERT: I 94 ASP cc_start: 0.8112 (t0) cc_final: 0.7885 (t0) REVERT: J 55 ASP cc_start: 0.7635 (p0) cc_final: 0.7285 (p0) REVERT: J 58 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7347 (mm-30) REVERT: L 36 SER cc_start: 0.8797 (t) cc_final: 0.8228 (p) REVERT: M 182 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7918 (mmm-85) REVERT: M 188 THR cc_start: 0.8443 (p) cc_final: 0.8225 (p) REVERT: M 243 CYS cc_start: 0.8741 (m) cc_final: 0.8378 (m) REVERT: M 300 GLN cc_start: 0.8237 (tt0) cc_final: 0.7292 (tm-30) REVERT: M 316 LEU cc_start: 0.8633 (mt) cc_final: 0.8384 (mt) REVERT: O 68 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7564 (tp-100) REVERT: O 95 ASN cc_start: 0.7838 (t0) cc_final: 0.7575 (t0) REVERT: O 193 LEU cc_start: 0.8204 (tt) cc_final: 0.8003 (tt) REVERT: O 240 MET cc_start: 0.8119 (tmm) cc_final: 0.7881 (tmm) REVERT: Q 117 HIS cc_start: 0.7827 (m-70) cc_final: 0.7124 (m-70) REVERT: Q 140 HIS cc_start: 0.7655 (m-70) cc_final: 0.7138 (m-70) REVERT: Q 147 LEU cc_start: 0.7906 (tt) cc_final: 0.7682 (tp) REVERT: Q 158 GLN cc_start: 0.8330 (pp30) cc_final: 0.8058 (pp30) REVERT: Q 348 TYR cc_start: 0.8044 (m-80) cc_final: 0.7530 (m-80) REVERT: Q 365 TYR cc_start: 0.8396 (t80) cc_final: 0.8144 (t80) REVERT: Q 373 TYR cc_start: 0.7958 (m-10) cc_final: 0.7672 (m-10) REVERT: Q 384 PHE cc_start: 0.8243 (m-80) cc_final: 0.7712 (m-80) REVERT: R 222 CYS cc_start: 0.6527 (m) cc_final: 0.5606 (m) REVERT: R 283 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7600 (pp20) REVERT: U 258 TRP cc_start: 0.8516 (m100) cc_final: 0.7955 (m-10) REVERT: U 262 LEU cc_start: 0.8214 (mt) cc_final: 0.8011 (mt) REVERT: W 38 LEU cc_start: 0.7587 (tp) cc_final: 0.7339 (tt) REVERT: W 63 SER cc_start: 0.8654 (t) cc_final: 0.8352 (m) REVERT: W 67 ILE cc_start: 0.9090 (mt) cc_final: 0.8699 (tp) REVERT: W 139 LEU cc_start: 0.8242 (mt) cc_final: 0.7918 (tp) REVERT: X 180 TYR cc_start: 0.8132 (t80) cc_final: 0.7890 (m-80) REVERT: X 227 ASP cc_start: 0.8167 (m-30) cc_final: 0.7957 (t0) REVERT: X 261 LYS cc_start: 0.8377 (pptt) cc_final: 0.7849 (ptpp) REVERT: X 293 ILE cc_start: 0.7958 (mt) cc_final: 0.7694 (tt) outliers start: 148 outliers final: 96 residues processed: 1452 average time/residue: 0.7145 time to fit residues: 1750.3181 Evaluate side-chains 1335 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1234 time to evaluate : 6.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 311 VAL Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 463 ILE Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 1 residue 358 MET Chi-restraints excluded: chain 1 residue 424 LEU Chi-restraints excluded: chain 2 residue 165 ASN Chi-restraints excluded: chain 3 residue 26 VAL Chi-restraints excluded: chain 3 residue 64 ARG Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 5 residue 53 GLU Chi-restraints excluded: chain 6 residue 199 ILE Chi-restraints excluded: chain 6 residue 240 SER Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1078 GLN Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1218 GLN Chi-restraints excluded: chain A residue 1383 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 909 ASP Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 334 VAL Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain U residue 252 THR Chi-restraints excluded: chain W residue 197 ASN Chi-restraints excluded: chain W residue 277 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 448 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 671 optimal weight: 0.8980 chunk 549 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 807 optimal weight: 0.9980 chunk 872 optimal weight: 50.0000 chunk 719 optimal weight: 0.5980 chunk 801 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 648 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 342 ASN ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 165 ASN 2 498 ASN 3 122 HIS A 118 HIS A 427 GLN ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 103 ASN B 592 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN G 113 HIS G 131 GLN H 137 GLN K 52 ASN M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 328 HIS U 43 GLN ** V 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 84 GLN W 104 GLN ** X 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 75348 Z= 0.233 Angle : 0.563 10.889 102261 Z= 0.291 Chirality : 0.042 0.196 11558 Planarity : 0.004 0.059 12672 Dihedral : 11.706 141.745 11075 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.80 % Allowed : 11.19 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.73 (0.09), residues: 8748 helix: 1.28 (0.09), residues: 3524 sheet: 0.28 (0.14), residues: 1310 loop : -0.07 (0.10), residues: 3914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 69 HIS 0.013 0.001 HIS O 88 PHE 0.028 0.002 PHE U 276 TYR 0.022 0.001 TYR 6 118 ARG 0.008 0.000 ARG 0 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1307 time to evaluate : 7.003 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: 0 61 MET cc_start: 0.8519 (mmp) cc_final: 0.8297 (mmp) REVERT: 0 106 LEU cc_start: 0.8103 (mm) cc_final: 0.7889 (mt) REVERT: 0 136 MET cc_start: 0.7771 (tpp) cc_final: 0.7458 (mmm) REVERT: 0 258 ARG cc_start: 0.7369 (ttp80) cc_final: 0.7105 (ttp80) REVERT: 0 346 MET cc_start: 0.7771 (tpp) cc_final: 0.7443 (tpp) REVERT: 0 366 LEU cc_start: 0.8761 (tp) cc_final: 0.8519 (tt) REVERT: 0 553 MET cc_start: 0.8268 (mmm) cc_final: 0.7814 (mmm) REVERT: 0 642 MET cc_start: 0.8783 (mmm) cc_final: 0.8516 (mmm) REVERT: 1 1 MET cc_start: 0.7475 (ttp) cc_final: 0.7181 (tmm) REVERT: 1 11 LYS cc_start: 0.7915 (tptt) cc_final: 0.7600 (tppt) REVERT: 1 97 MET cc_start: 0.8113 (ttm) cc_final: 0.7596 (ttt) REVERT: 1 266 VAL cc_start: 0.8811 (m) cc_final: 0.8610 (p) REVERT: 1 318 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: 1 328 MET cc_start: 0.8049 (tmm) cc_final: 0.7790 (ppp) REVERT: 1 358 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8219 (mmp) REVERT: 1 469 MET cc_start: 0.8428 (ttt) cc_final: 0.7649 (mmm) REVERT: 2 50 MET cc_start: 0.8680 (ppp) cc_final: 0.8416 (ppp) REVERT: 2 150 MET cc_start: 0.7960 (tpt) cc_final: 0.7585 (tpt) REVERT: 2 201 TRP cc_start: 0.8474 (t-100) cc_final: 0.8210 (t-100) REVERT: 2 216 MET cc_start: 0.7090 (mmt) cc_final: 0.6772 (ttt) REVERT: 2 249 MET cc_start: 0.8476 (mtp) cc_final: 0.8044 (ptp) REVERT: 2 365 HIS cc_start: 0.8496 (t-90) cc_final: 0.8138 (t70) REVERT: 3 64 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7439 (mmt180) REVERT: 3 89 PHE cc_start: 0.8297 (m-80) cc_final: 0.7922 (m-80) REVERT: 4 37 TRP cc_start: 0.8307 (m100) cc_final: 0.7796 (m100) REVERT: 4 130 TYR cc_start: 0.8755 (t80) cc_final: 0.8312 (t80) REVERT: 4 153 MET cc_start: 0.8783 (mtp) cc_final: 0.8482 (mtm) REVERT: 4 159 TYR cc_start: 0.9042 (t80) cc_final: 0.8687 (t80) REVERT: 4 179 LEU cc_start: 0.9345 (mm) cc_final: 0.9067 (mt) REVERT: 4 206 MET cc_start: 0.8842 (ppp) cc_final: 0.7674 (ppp) REVERT: 4 225 GLN cc_start: 0.9120 (mt0) cc_final: 0.8666 (mt0) REVERT: 4 247 TYR cc_start: 0.8440 (m-80) cc_final: 0.8188 (m-10) REVERT: 5 15 SER cc_start: 0.9022 (m) cc_final: 0.8604 (p) REVERT: 6 136 MET cc_start: 0.8208 (tpp) cc_final: 0.7978 (mmp) REVERT: 6 250 THR cc_start: 0.9271 (m) cc_final: 0.8951 (p) REVERT: 6 300 LEU cc_start: 0.8399 (mm) cc_final: 0.7823 (mm) REVERT: 6 303 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8116 (mt-10) REVERT: 6 448 LEU cc_start: 0.9691 (mt) cc_final: 0.9410 (mm) REVERT: 7 561 MET cc_start: 0.5948 (tmm) cc_final: 0.5565 (tmm) REVERT: A 12 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8159 (mtt-85) REVERT: A 62 ASP cc_start: 0.7624 (t0) cc_final: 0.7130 (m-30) REVERT: A 64 ASN cc_start: 0.7598 (t0) cc_final: 0.7353 (t0) REVERT: A 109 HIS cc_start: 0.8563 (t-90) cc_final: 0.8169 (t-90) REVERT: A 112 LYS cc_start: 0.8170 (tttp) cc_final: 0.7849 (tttm) REVERT: A 122 MET cc_start: 0.8619 (tpp) cc_final: 0.8379 (tpp) REVERT: A 453 MET cc_start: 0.8439 (mpp) cc_final: 0.7954 (mpp) REVERT: A 700 ASN cc_start: 0.9217 (t0) cc_final: 0.8841 (t0) REVERT: A 705 LYS cc_start: 0.7517 (tmtt) cc_final: 0.7288 (tmtt) REVERT: A 736 ASN cc_start: 0.6978 (t0) cc_final: 0.6705 (t0) REVERT: A 939 ASP cc_start: 0.6877 (m-30) cc_final: 0.6647 (m-30) REVERT: A 992 ASP cc_start: 0.7650 (p0) cc_final: 0.7397 (p0) REVERT: A 1033 GLN cc_start: 0.7970 (tt0) cc_final: 0.7664 (tt0) REVERT: A 1043 ASP cc_start: 0.7876 (t70) cc_final: 0.7666 (t0) REVERT: A 1054 LEU cc_start: 0.9198 (mt) cc_final: 0.8970 (mt) REVERT: A 1135 ARG cc_start: 0.8888 (tmm-80) cc_final: 0.8197 (ttp80) REVERT: A 1195 LEU cc_start: 0.8773 (mm) cc_final: 0.8548 (mm) REVERT: A 1285 MET cc_start: 0.7117 (mmm) cc_final: 0.6682 (mmm) REVERT: A 1287 TYR cc_start: 0.7617 (m-80) cc_final: 0.7388 (m-80) REVERT: A 1289 ARG cc_start: 0.6724 (ttp80) cc_final: 0.6265 (ttm170) REVERT: A 1290 LYS cc_start: 0.8384 (mttm) cc_final: 0.8005 (mtpp) REVERT: A 1328 TYR cc_start: 0.7469 (t80) cc_final: 0.7006 (t80) REVERT: A 1393 ASN cc_start: 0.8086 (p0) cc_final: 0.7637 (p0) REVERT: B 216 GLU cc_start: 0.7439 (tt0) cc_final: 0.7181 (tt0) REVERT: B 267 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7443 (mtm180) REVERT: B 312 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 348 ARG cc_start: 0.7503 (tpp80) cc_final: 0.6990 (tpp80) REVERT: B 358 LYS cc_start: 0.8358 (mtmt) cc_final: 0.7996 (mtmt) REVERT: B 430 ARG cc_start: 0.7422 (ttm110) cc_final: 0.6979 (ttp80) REVERT: B 434 ARG cc_start: 0.8374 (ttm110) cc_final: 0.7939 (mtm110) REVERT: B 445 LYS cc_start: 0.8788 (mttp) cc_final: 0.8486 (mtmt) REVERT: B 531 GLN cc_start: 0.7416 (pp30) cc_final: 0.6847 (pp30) REVERT: B 598 GLU cc_start: 0.7371 (tp30) cc_final: 0.7128 (tp30) REVERT: B 730 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7785 (mmt90) REVERT: B 863 GLU cc_start: 0.7489 (tt0) cc_final: 0.7209 (tt0) REVERT: B 876 LYS cc_start: 0.8083 (ptpp) cc_final: 0.7845 (ptpp) REVERT: B 885 MET cc_start: 0.7019 (ptp) cc_final: 0.6786 (ptp) REVERT: B 1041 GLU cc_start: 0.7239 (pm20) cc_final: 0.7033 (pm20) REVERT: B 1174 LYS cc_start: 0.8361 (mttt) cc_final: 0.8017 (mtmt) REVERT: C 15 LYS cc_start: 0.8203 (ptmm) cc_final: 0.7997 (ptmt) REVERT: C 121 VAL cc_start: 0.8653 (p) cc_final: 0.8407 (m) REVERT: C 154 LYS cc_start: 0.8656 (tttt) cc_final: 0.8256 (ttpt) REVERT: C 253 LYS cc_start: 0.8304 (tppt) cc_final: 0.8067 (ttpp) REVERT: D 34 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7674 (tm-30) REVERT: D 54 GLU cc_start: 0.8434 (tp30) cc_final: 0.8053 (tp30) REVERT: D 189 ASP cc_start: 0.8510 (t70) cc_final: 0.8250 (t70) REVERT: D 200 ASN cc_start: 0.8444 (t0) cc_final: 0.7975 (t0) REVERT: D 216 ASN cc_start: 0.9304 (t0) cc_final: 0.9067 (t0) REVERT: D 217 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8103 (pt) REVERT: E 32 GLN cc_start: 0.7993 (pm20) cc_final: 0.7680 (pp30) REVERT: E 61 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8159 (tm-30) REVERT: E 94 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8961 (tptp) REVERT: E 99 HIS cc_start: 0.8404 (t70) cc_final: 0.8015 (t70) REVERT: E 109 ILE cc_start: 0.8445 (mt) cc_final: 0.8193 (mm) REVERT: G 41 LYS cc_start: 0.8146 (ptmt) cc_final: 0.7590 (ptmm) REVERT: G 42 PHE cc_start: 0.8029 (m-80) cc_final: 0.7750 (m-80) REVERT: G 143 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8897 (tp) REVERT: G 167 TYR cc_start: 0.8730 (m-80) cc_final: 0.8492 (m-80) REVERT: H 86 ASP cc_start: 0.7606 (m-30) cc_final: 0.7182 (m-30) REVERT: I 18 GLU cc_start: 0.7564 (pm20) cc_final: 0.7345 (pm20) REVERT: I 34 TYR cc_start: 0.7267 (t80) cc_final: 0.6841 (t80) REVERT: I 46 HIS cc_start: 0.7943 (t70) cc_final: 0.7726 (t70) REVERT: I 50 THR cc_start: 0.8914 (t) cc_final: 0.8489 (p) REVERT: I 94 ASP cc_start: 0.8134 (t0) cc_final: 0.7801 (t0) REVERT: J 55 ASP cc_start: 0.7670 (p0) cc_final: 0.7354 (p0) REVERT: J 58 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7173 (mm-30) REVERT: K 54 ARG cc_start: 0.7705 (tpp80) cc_final: 0.7463 (tpp80) REVERT: L 36 SER cc_start: 0.8788 (t) cc_final: 0.8419 (m) REVERT: L 47 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7437 (mmm-85) REVERT: M 182 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7873 (tpp80) REVERT: M 188 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8174 (p) REVERT: M 208 ASN cc_start: 0.8986 (t0) cc_final: 0.8557 (m-40) REVERT: M 275 ILE cc_start: 0.9034 (mt) cc_final: 0.8736 (mp) REVERT: M 300 GLN cc_start: 0.8097 (tt0) cc_final: 0.7581 (tp-100) REVERT: O 68 GLN cc_start: 0.7804 (tp-100) cc_final: 0.7499 (tp-100) REVERT: O 95 ASN cc_start: 0.7798 (t0) cc_final: 0.7540 (t0) REVERT: O 188 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7515 (mt-10) REVERT: O 193 LEU cc_start: 0.8078 (tt) cc_final: 0.7855 (tt) REVERT: O 195 TYR cc_start: 0.7285 (t80) cc_final: 0.7069 (t80) REVERT: O 240 MET cc_start: 0.8113 (tmm) cc_final: 0.7734 (tmm) REVERT: Q 117 HIS cc_start: 0.7812 (m-70) cc_final: 0.7108 (m-70) REVERT: Q 140 HIS cc_start: 0.7600 (m-70) cc_final: 0.7051 (m-70) REVERT: Q 158 GLN cc_start: 0.8297 (pp30) cc_final: 0.7935 (pp30) REVERT: Q 348 TYR cc_start: 0.8054 (m-80) cc_final: 0.7608 (m-80) REVERT: Q 373 TYR cc_start: 0.8124 (m-10) cc_final: 0.7881 (m-10) REVERT: Q 384 PHE cc_start: 0.8183 (m-80) cc_final: 0.7922 (m-80) REVERT: R 222 CYS cc_start: 0.6942 (m) cc_final: 0.6210 (m) REVERT: U 258 TRP cc_start: 0.8643 (m100) cc_final: 0.8134 (m-90) REVERT: W 63 SER cc_start: 0.8635 (t) cc_final: 0.8341 (m) REVERT: W 67 ILE cc_start: 0.9066 (mt) cc_final: 0.8709 (tp) REVERT: W 139 LEU cc_start: 0.8241 (mt) cc_final: 0.7922 (tp) REVERT: X 180 TYR cc_start: 0.8108 (t80) cc_final: 0.7860 (m-80) REVERT: X 261 LYS cc_start: 0.8379 (pptt) cc_final: 0.7789 (pttp) REVERT: X 264 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7288 (mp0) REVERT: X 280 ASP cc_start: 0.7895 (m-30) cc_final: 0.7691 (m-30) REVERT: X 293 ILE cc_start: 0.7952 (mt) cc_final: 0.7703 (tt) outliers start: 143 outliers final: 101 residues processed: 1381 average time/residue: 0.7038 time to fit residues: 1645.9451 Evaluate side-chains 1324 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1217 time to evaluate : 6.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 209 SER Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 358 MET Chi-restraints excluded: chain 1 residue 371 THR Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 444 LYS Chi-restraints excluded: chain 2 residue 125 VAL Chi-restraints excluded: chain 2 residue 143 TRP Chi-restraints excluded: chain 3 residue 26 VAL Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 64 ARG Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 438 VAL Chi-restraints excluded: chain 7 residue 554 CYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 738 LYS Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1383 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 841 MET Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain Q residue 334 VAL Chi-restraints excluded: chain Q residue 338 ASN Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain V residue 67 ASP Chi-restraints excluded: chain V residue 110 LYS Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain W residue 197 ASN Chi-restraints excluded: chain W residue 273 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 798 optimal weight: 7.9990 chunk 607 optimal weight: 3.9990 chunk 419 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 385 optimal weight: 3.9990 chunk 542 optimal weight: 0.0270 chunk 810 optimal weight: 30.0000 chunk 858 optimal weight: 20.0000 chunk 423 optimal weight: 1.9990 chunk 768 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 overall best weight: 2.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 169 HIS ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS A 427 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS A 736 ASN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 136 ASN G 131 GLN I 22 ASN K 52 ASN M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 328 HIS ** V 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 HIS X 316 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 75348 Z= 0.324 Angle : 0.578 11.128 102261 Z= 0.299 Chirality : 0.042 0.200 11558 Planarity : 0.004 0.116 12672 Dihedral : 11.731 123.576 11075 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.61 % Allowed : 12.03 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.09), residues: 8748 helix: 1.19 (0.09), residues: 3514 sheet: 0.09 (0.14), residues: 1355 loop : -0.17 (0.10), residues: 3879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 69 HIS 0.016 0.001 HIS G 113 PHE 0.052 0.002 PHE 2 226 TYR 0.019 0.001 TYR 4 79 ARG 0.011 0.000 ARG 0 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1244 time to evaluate : 6.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 106 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7930 (mm) REVERT: 0 258 ARG cc_start: 0.7427 (ttp80) cc_final: 0.7163 (ttp80) REVERT: 0 553 MET cc_start: 0.8307 (mmm) cc_final: 0.7868 (mmm) REVERT: 0 642 MET cc_start: 0.8816 (mmm) cc_final: 0.8515 (mmm) REVERT: 1 97 MET cc_start: 0.8330 (ttm) cc_final: 0.8096 (ttt) REVERT: 1 358 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8258 (mmp) REVERT: 1 383 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7943 (mt-10) REVERT: 1 469 MET cc_start: 0.8404 (ttt) cc_final: 0.7649 (mmm) REVERT: 2 112 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8887 (tp) REVERT: 2 150 MET cc_start: 0.7886 (tpt) cc_final: 0.7529 (tpt) REVERT: 2 201 TRP cc_start: 0.8469 (t-100) cc_final: 0.8218 (t-100) REVERT: 2 249 MET cc_start: 0.8507 (mtp) cc_final: 0.8119 (mtp) REVERT: 2 365 HIS cc_start: 0.8536 (t-90) cc_final: 0.8178 (t70) REVERT: 3 22 LEU cc_start: 0.8998 (mt) cc_final: 0.8658 (pp) REVERT: 3 89 PHE cc_start: 0.8275 (m-80) cc_final: 0.7861 (m-80) REVERT: 4 37 TRP cc_start: 0.8380 (m100) cc_final: 0.7832 (m100) REVERT: 4 114 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.5943 (mmt) REVERT: 4 130 TYR cc_start: 0.8836 (t80) cc_final: 0.8370 (t80) REVERT: 4 142 GLN cc_start: 0.9254 (tp40) cc_final: 0.8667 (tm-30) REVERT: 4 153 MET cc_start: 0.8798 (mtp) cc_final: 0.8521 (mtm) REVERT: 4 159 TYR cc_start: 0.9041 (t80) cc_final: 0.8729 (t80) REVERT: 4 179 LEU cc_start: 0.9359 (mm) cc_final: 0.9139 (mt) REVERT: 4 206 MET cc_start: 0.8970 (ppp) cc_final: 0.7875 (ppp) REVERT: 4 225 GLN cc_start: 0.8927 (mt0) cc_final: 0.8401 (mt0) REVERT: 4 235 TYR cc_start: 0.8119 (t80) cc_final: 0.7852 (t80) REVERT: 4 247 TYR cc_start: 0.8427 (m-80) cc_final: 0.8138 (m-10) REVERT: 5 15 SER cc_start: 0.9057 (m) cc_final: 0.8597 (p) REVERT: 5 53 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7587 (mm-30) REVERT: 6 250 THR cc_start: 0.9286 (m) cc_final: 0.9051 (p) REVERT: 6 300 LEU cc_start: 0.8459 (mm) cc_final: 0.7822 (mm) REVERT: 6 303 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8049 (mt-10) REVERT: 6 442 VAL cc_start: 0.8957 (t) cc_final: 0.8434 (p) REVERT: 7 561 MET cc_start: 0.6067 (tmm) cc_final: 0.5580 (tmm) REVERT: A 62 ASP cc_start: 0.7656 (t0) cc_final: 0.7183 (m-30) REVERT: A 63 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7587 (ttp-170) REVERT: A 109 HIS cc_start: 0.8608 (t-90) cc_final: 0.8211 (t-90) REVERT: A 112 LYS cc_start: 0.8198 (tttp) cc_final: 0.7888 (tttt) REVERT: A 119 ASN cc_start: 0.8768 (t0) cc_final: 0.8386 (t0) REVERT: A 453 MET cc_start: 0.8409 (mpp) cc_final: 0.7959 (mpp) REVERT: A 470 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7988 (pp) REVERT: A 700 ASN cc_start: 0.9250 (t0) cc_final: 0.8965 (t0) REVERT: A 705 LYS cc_start: 0.7530 (tmtt) cc_final: 0.7312 (tmtt) REVERT: A 736 ASN cc_start: 0.6927 (t0) cc_final: 0.6699 (t0) REVERT: A 939 ASP cc_start: 0.6804 (m-30) cc_final: 0.6589 (m-30) REVERT: A 991 LYS cc_start: 0.8462 (mmmm) cc_final: 0.8172 (mmmm) REVERT: A 992 ASP cc_start: 0.7629 (p0) cc_final: 0.7371 (p0) REVERT: A 1033 GLN cc_start: 0.7959 (tt0) cc_final: 0.7659 (tt0) REVERT: A 1043 ASP cc_start: 0.7861 (t70) cc_final: 0.7635 (t0) REVERT: A 1054 LEU cc_start: 0.9232 (mt) cc_final: 0.8979 (mt) REVERT: A 1135 ARG cc_start: 0.8913 (tmm-80) cc_final: 0.8256 (ttp80) REVERT: A 1195 LEU cc_start: 0.8784 (mm) cc_final: 0.8559 (mm) REVERT: A 1284 MET cc_start: 0.7239 (mtp) cc_final: 0.6069 (mtp) REVERT: A 1285 MET cc_start: 0.7130 (mmm) cc_final: 0.6766 (mmm) REVERT: A 1287 TYR cc_start: 0.7664 (m-80) cc_final: 0.7387 (m-80) REVERT: A 1290 LYS cc_start: 0.8409 (mttm) cc_final: 0.7968 (mtpp) REVERT: A 1328 TYR cc_start: 0.7530 (t80) cc_final: 0.7040 (t80) REVERT: A 1393 ASN cc_start: 0.8193 (p0) cc_final: 0.7761 (p0) REVERT: B 72 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: B 216 GLU cc_start: 0.7478 (tt0) cc_final: 0.7217 (tt0) REVERT: B 226 PHE cc_start: 0.7956 (m-10) cc_final: 0.7748 (m-10) REVERT: B 267 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7614 (mtm180) REVERT: B 303 TYR cc_start: 0.7896 (m-80) cc_final: 0.7668 (m-80) REVERT: B 358 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7942 (mtmt) REVERT: B 390 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8133 (tt) REVERT: B 430 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7032 (ttp80) REVERT: B 434 ARG cc_start: 0.8362 (ttm110) cc_final: 0.7925 (mtm110) REVERT: B 531 GLN cc_start: 0.7457 (pp30) cc_final: 0.6894 (pp30) REVERT: B 573 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7574 (tm-30) REVERT: B 595 ARG cc_start: 0.8059 (ptm160) cc_final: 0.7812 (mtp-110) REVERT: B 598 GLU cc_start: 0.7411 (tp30) cc_final: 0.7152 (tp30) REVERT: B 730 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7764 (mmt90) REVERT: B 863 GLU cc_start: 0.7540 (tt0) cc_final: 0.7269 (tt0) REVERT: B 876 LYS cc_start: 0.8313 (ptpp) cc_final: 0.7918 (ptpp) REVERT: B 1174 LYS cc_start: 0.8401 (mttt) cc_final: 0.8084 (mtmt) REVERT: C 121 VAL cc_start: 0.8668 (p) cc_final: 0.8371 (m) REVERT: C 154 LYS cc_start: 0.8748 (tttt) cc_final: 0.8292 (ttmm) REVERT: C 253 LYS cc_start: 0.8269 (tppt) cc_final: 0.8062 (ttpp) REVERT: D 54 GLU cc_start: 0.8478 (tp30) cc_final: 0.8058 (tp30) REVERT: D 157 GLN cc_start: 0.8306 (mm110) cc_final: 0.8045 (mm110) REVERT: D 189 ASP cc_start: 0.8522 (t70) cc_final: 0.8255 (t70) REVERT: D 200 ASN cc_start: 0.8484 (t0) cc_final: 0.8091 (t0) REVERT: D 204 ASP cc_start: 0.8352 (t0) cc_final: 0.8112 (m-30) REVERT: D 216 ASN cc_start: 0.9323 (t0) cc_final: 0.9085 (t0) REVERT: D 217 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8239 (pt) REVERT: E 61 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8204 (tm-30) REVERT: E 68 SER cc_start: 0.8511 (t) cc_final: 0.8298 (p) REVERT: E 99 HIS cc_start: 0.8430 (t70) cc_final: 0.8006 (t-170) REVERT: E 109 ILE cc_start: 0.8464 (mt) cc_final: 0.8221 (mm) REVERT: G 25 TYR cc_start: 0.6412 (m-80) cc_final: 0.6049 (m-80) REVERT: G 41 LYS cc_start: 0.8199 (ptmt) cc_final: 0.7972 (ptmm) REVERT: G 42 PHE cc_start: 0.8101 (m-80) cc_final: 0.7868 (m-80) REVERT: G 60 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7824 (ttt-90) REVERT: G 143 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8899 (tp) REVERT: G 167 TYR cc_start: 0.8787 (m-80) cc_final: 0.8556 (m-80) REVERT: H 8 ASP cc_start: 0.6883 (m-30) cc_final: 0.6627 (m-30) REVERT: H 86 ASP cc_start: 0.7495 (m-30) cc_final: 0.7209 (m-30) REVERT: I 46 HIS cc_start: 0.7935 (t70) cc_final: 0.7730 (t70) REVERT: I 83 ASN cc_start: 0.7922 (p0) cc_final: 0.7610 (p0) REVERT: I 94 ASP cc_start: 0.8226 (t0) cc_final: 0.7871 (t0) REVERT: J 58 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7395 (mm-30) REVERT: K 54 ARG cc_start: 0.7699 (tpp80) cc_final: 0.7445 (tpp80) REVERT: L 36 SER cc_start: 0.8813 (t) cc_final: 0.8460 (m) REVERT: M 275 ILE cc_start: 0.9057 (mt) cc_final: 0.8813 (mp) REVERT: M 277 ILE cc_start: 0.8329 (tt) cc_final: 0.8099 (tp) REVERT: M 300 GLN cc_start: 0.8050 (tt0) cc_final: 0.7709 (mm-40) REVERT: O 68 GLN cc_start: 0.7813 (tp-100) cc_final: 0.7463 (tp-100) REVERT: O 121 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6588 (tmm) REVERT: O 193 LEU cc_start: 0.8151 (tt) cc_final: 0.7947 (tt) REVERT: Q 117 HIS cc_start: 0.7811 (m-70) cc_final: 0.7161 (m-70) REVERT: Q 140 HIS cc_start: 0.7622 (m-70) cc_final: 0.7062 (m-70) REVERT: Q 150 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.6287 (tp40) REVERT: Q 158 GLN cc_start: 0.8338 (pp30) cc_final: 0.7922 (pp30) REVERT: Q 348 TYR cc_start: 0.8120 (m-80) cc_final: 0.7666 (m-80) REVERT: Q 384 PHE cc_start: 0.8151 (m-80) cc_final: 0.7894 (m-80) REVERT: R 265 HIS cc_start: 0.7102 (t-170) cc_final: 0.6808 (t-170) REVERT: U 253 ARG cc_start: 0.6432 (tpt-90) cc_final: 0.5268 (tpt-90) REVERT: U 258 TRP cc_start: 0.8618 (m100) cc_final: 0.7979 (m-90) REVERT: V 78 PHE cc_start: 0.8456 (m-10) cc_final: 0.8192 (m-10) REVERT: W 63 SER cc_start: 0.8642 (t) cc_final: 0.8356 (m) REVERT: W 67 ILE cc_start: 0.9050 (mt) cc_final: 0.8697 (tp) REVERT: W 123 MET cc_start: 0.7765 (mmp) cc_final: 0.7113 (mmm) REVERT: W 139 LEU cc_start: 0.8276 (mt) cc_final: 0.7948 (tp) REVERT: X 129 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8279 (mm) REVERT: X 180 TYR cc_start: 0.8116 (t80) cc_final: 0.7856 (m-80) REVERT: X 227 ASP cc_start: 0.7915 (t0) cc_final: 0.7560 (t0) REVERT: X 261 LYS cc_start: 0.8417 (pptt) cc_final: 0.7866 (pttp) REVERT: X 264 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7289 (pt0) REVERT: X 280 ASP cc_start: 0.7873 (m-30) cc_final: 0.7578 (m-30) outliers start: 207 outliers final: 143 residues processed: 1357 average time/residue: 0.6986 time to fit residues: 1608.2423 Evaluate side-chains 1336 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1181 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 106 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 209 SER Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 632 SER Chi-restraints excluded: chain 1 residue 259 ILE Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 358 MET Chi-restraints excluded: chain 1 residue 371 THR Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 424 LEU Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain 2 residue 125 VAL Chi-restraints excluded: chain 2 residue 143 TRP Chi-restraints excluded: chain 2 residue 165 ASN Chi-restraints excluded: chain 3 residue 26 VAL Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 81 GLU Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 5 residue 31 VAL Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 214 LEU Chi-restraints excluded: chain 6 residue 221 LEU Chi-restraints excluded: chain 6 residue 240 SER Chi-restraints excluded: chain 6 residue 269 GLN Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 438 VAL Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 554 CYS Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1383 SER Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 881 ASN Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 30 ARG Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 320 ARG Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 121 MET Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 150 GLN Chi-restraints excluded: chain Q residue 334 VAL Chi-restraints excluded: chain Q residue 338 ASN Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 183 ILE Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain W residue 197 ASN Chi-restraints excluded: chain W residue 273 GLN Chi-restraints excluded: chain X residue 118 ASP Chi-restraints excluded: chain X residue 129 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 714 optimal weight: 0.8980 chunk 487 optimal weight: 0.4980 chunk 12 optimal weight: 9.9990 chunk 639 optimal weight: 0.8980 chunk 354 optimal weight: 0.7980 chunk 732 optimal weight: 2.9990 chunk 593 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 438 optimal weight: 9.9990 chunk 770 optimal weight: 10.0000 chunk 216 optimal weight: 50.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 142 GLN ** 6 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 349 ASN A 256 GLN A 427 GLN A 493 GLN ** A 994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN I 22 ASN K 52 ASN M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 ASN W 104 GLN W 294 HIS ** X 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 75348 Z= 0.181 Angle : 0.544 16.737 102261 Z= 0.279 Chirality : 0.041 0.188 11558 Planarity : 0.004 0.060 12672 Dihedral : 11.709 113.738 11075 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.05 % Allowed : 13.58 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.09), residues: 8748 helix: 1.25 (0.09), residues: 3524 sheet: 0.16 (0.14), residues: 1312 loop : -0.18 (0.10), residues: 3912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1304 HIS 0.016 0.001 HIS 2 169 PHE 0.037 0.001 PHE 2 226 TYR 0.021 0.001 TYR 6 344 ARG 0.006 0.000 ARG 0 513 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1254 time to evaluate : 6.345 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: 0 106 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7938 (mm) REVERT: 0 136 MET cc_start: 0.7897 (tpp) cc_final: 0.7556 (mmt) REVERT: 0 553 MET cc_start: 0.8342 (mmm) cc_final: 0.7895 (mmm) REVERT: 0 642 MET cc_start: 0.8849 (mmm) cc_final: 0.8542 (mmm) REVERT: 0 649 ARG cc_start: 0.6937 (mmp-170) cc_final: 0.6517 (mmp-170) REVERT: 0 664 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7931 (pp30) REVERT: 1 58 MET cc_start: 0.7607 (mmm) cc_final: 0.7097 (mmp) REVERT: 1 88 MET cc_start: 0.7646 (mmp) cc_final: 0.7323 (mmp) REVERT: 1 97 MET cc_start: 0.8313 (ttm) cc_final: 0.7866 (ttt) REVERT: 1 318 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: 1 469 MET cc_start: 0.8396 (ttt) cc_final: 0.7666 (mmm) REVERT: 2 112 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8870 (tp) REVERT: 2 150 MET cc_start: 0.7814 (tpt) cc_final: 0.7431 (tpt) REVERT: 2 201 TRP cc_start: 0.8473 (t-100) cc_final: 0.8216 (t-100) REVERT: 2 365 HIS cc_start: 0.8473 (t-90) cc_final: 0.8109 (t70) REVERT: 3 22 LEU cc_start: 0.8965 (mt) cc_final: 0.8648 (pp) REVERT: 3 64 ARG cc_start: 0.7606 (mmt180) cc_final: 0.7142 (mmt90) REVERT: 3 89 PHE cc_start: 0.8274 (m-80) cc_final: 0.7818 (m-80) REVERT: 4 37 TRP cc_start: 0.8511 (m100) cc_final: 0.7933 (m100) REVERT: 4 114 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.5816 (mmt) REVERT: 4 130 TYR cc_start: 0.8836 (t80) cc_final: 0.8338 (t80) REVERT: 4 153 MET cc_start: 0.8765 (mtp) cc_final: 0.8542 (ptp) REVERT: 4 159 TYR cc_start: 0.9020 (t80) cc_final: 0.8691 (t80) REVERT: 4 179 LEU cc_start: 0.9351 (mm) cc_final: 0.9124 (mt) REVERT: 4 206 MET cc_start: 0.8977 (ppp) cc_final: 0.7839 (ppp) REVERT: 4 225 GLN cc_start: 0.8946 (mt0) cc_final: 0.8457 (mt0) REVERT: 4 235 TYR cc_start: 0.8268 (t80) cc_final: 0.8012 (t80) REVERT: 4 247 TYR cc_start: 0.8485 (m-80) cc_final: 0.8224 (m-10) REVERT: 5 15 SER cc_start: 0.9027 (m) cc_final: 0.8557 (p) REVERT: 5 53 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7628 (mm-30) REVERT: 6 250 THR cc_start: 0.9283 (m) cc_final: 0.9049 (p) REVERT: 6 303 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8101 (mt-10) REVERT: 7 561 MET cc_start: 0.6005 (tmm) cc_final: 0.5521 (tmm) REVERT: A 12 ARG cc_start: 0.8496 (mtp85) cc_final: 0.8050 (mtt-85) REVERT: A 41 MET cc_start: 0.7055 (mmm) cc_final: 0.6809 (mmm) REVERT: A 62 ASP cc_start: 0.7705 (t0) cc_final: 0.7290 (m-30) REVERT: A 63 ARG cc_start: 0.8098 (ttm170) cc_final: 0.7681 (ttp-170) REVERT: A 109 HIS cc_start: 0.8636 (t-90) cc_final: 0.8287 (t-90) REVERT: A 112 LYS cc_start: 0.8159 (tttp) cc_final: 0.7835 (tttm) REVERT: A 123 ARG cc_start: 0.8884 (ttm110) cc_final: 0.8304 (ttm110) REVERT: A 414 ASP cc_start: 0.8242 (t0) cc_final: 0.7958 (t0) REVERT: A 451 HIS cc_start: 0.8213 (p-80) cc_final: 0.7486 (p90) REVERT: A 453 MET cc_start: 0.8358 (mpp) cc_final: 0.7742 (mpp) REVERT: A 526 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8092 (t70) REVERT: A 705 LYS cc_start: 0.7548 (tmtt) cc_final: 0.7284 (tmtt) REVERT: A 801 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 939 ASP cc_start: 0.6846 (m-30) cc_final: 0.6622 (m-30) REVERT: A 991 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8126 (mmmm) REVERT: A 992 ASP cc_start: 0.7580 (p0) cc_final: 0.7326 (p0) REVERT: A 1033 GLN cc_start: 0.7956 (tt0) cc_final: 0.7673 (tt0) REVERT: A 1043 ASP cc_start: 0.7775 (t70) cc_final: 0.7535 (t0) REVERT: A 1054 LEU cc_start: 0.9159 (mt) cc_final: 0.8890 (mt) REVERT: A 1135 ARG cc_start: 0.8995 (tmm-80) cc_final: 0.8345 (ttp80) REVERT: A 1195 LEU cc_start: 0.8790 (mm) cc_final: 0.8562 (mm) REVERT: A 1284 MET cc_start: 0.7250 (mtp) cc_final: 0.6132 (mtp) REVERT: A 1285 MET cc_start: 0.7123 (mmm) cc_final: 0.6795 (mmm) REVERT: A 1287 TYR cc_start: 0.7630 (m-80) cc_final: 0.7259 (m-10) REVERT: A 1290 LYS cc_start: 0.8323 (mttm) cc_final: 0.7930 (mtpp) REVERT: A 1328 TYR cc_start: 0.7441 (t80) cc_final: 0.6930 (t80) REVERT: A 1393 ASN cc_start: 0.8093 (p0) cc_final: 0.7644 (p0) REVERT: B 69 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.6787 (mp) REVERT: B 70 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7469 (pt) REVERT: B 72 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7621 (pp20) REVERT: B 216 GLU cc_start: 0.7455 (tt0) cc_final: 0.7200 (tt0) REVERT: B 267 ARG cc_start: 0.7902 (mtm-85) cc_final: 0.7646 (mtm180) REVERT: B 358 LYS cc_start: 0.8307 (mtmt) cc_final: 0.7882 (mtmt) REVERT: B 390 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8121 (tt) REVERT: B 430 ARG cc_start: 0.7424 (ttm110) cc_final: 0.6944 (ttp80) REVERT: B 434 ARG cc_start: 0.8311 (ttm110) cc_final: 0.7940 (ttm110) REVERT: B 531 GLN cc_start: 0.7362 (pp30) cc_final: 0.6818 (pp30) REVERT: B 573 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7548 (tm-30) REVERT: B 592 ASN cc_start: 0.7698 (t0) cc_final: 0.6860 (t0) REVERT: B 595 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7696 (mtp-110) REVERT: B 598 GLU cc_start: 0.7421 (tp30) cc_final: 0.7148 (tp30) REVERT: B 729 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.7986 (mt) REVERT: B 730 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7763 (mmt90) REVERT: B 863 GLU cc_start: 0.7524 (tt0) cc_final: 0.7229 (tt0) REVERT: B 876 LYS cc_start: 0.8295 (ptpp) cc_final: 0.7775 (ptpp) REVERT: B 1174 LYS cc_start: 0.8340 (mttt) cc_final: 0.8033 (mtmt) REVERT: C 75 MET cc_start: 0.7934 (tpt) cc_final: 0.7702 (tpt) REVERT: C 121 VAL cc_start: 0.8645 (p) cc_final: 0.8338 (m) REVERT: C 154 LYS cc_start: 0.8760 (tttt) cc_final: 0.8281 (ttmm) REVERT: C 253 LYS cc_start: 0.8195 (tppt) cc_final: 0.7993 (ttpp) REVERT: D 54 GLU cc_start: 0.8453 (tp30) cc_final: 0.7972 (tp30) REVERT: D 157 GLN cc_start: 0.8246 (mm110) cc_final: 0.7971 (mm110) REVERT: D 189 ASP cc_start: 0.8490 (t70) cc_final: 0.8233 (t70) REVERT: D 200 ASN cc_start: 0.8481 (t0) cc_final: 0.8095 (t0) REVERT: D 204 ASP cc_start: 0.8210 (t0) cc_final: 0.7886 (m-30) REVERT: D 216 ASN cc_start: 0.9299 (t0) cc_final: 0.8998 (t0) REVERT: D 217 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8242 (pt) REVERT: E 61 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8270 (tm-30) REVERT: E 68 SER cc_start: 0.8465 (t) cc_final: 0.8250 (p) REVERT: E 99 HIS cc_start: 0.8387 (t70) cc_final: 0.8052 (t70) REVERT: E 109 ILE cc_start: 0.8465 (mt) cc_final: 0.8211 (mm) REVERT: G 41 LYS cc_start: 0.8204 (ptmt) cc_final: 0.7872 (ptmm) REVERT: G 42 PHE cc_start: 0.8050 (m-80) cc_final: 0.7700 (m-80) REVERT: G 87 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8145 (p) REVERT: G 119 LEU cc_start: 0.8631 (mp) cc_final: 0.7724 (tt) REVERT: G 130 TYR cc_start: 0.6490 (m-10) cc_final: 0.6276 (m-10) REVERT: G 143 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8917 (tp) REVERT: G 167 TYR cc_start: 0.8769 (m-80) cc_final: 0.8529 (m-80) REVERT: H 8 ASP cc_start: 0.6841 (m-30) cc_final: 0.6604 (m-30) REVERT: H 86 ASP cc_start: 0.7522 (m-30) cc_final: 0.7313 (m-30) REVERT: I 46 HIS cc_start: 0.7953 (t70) cc_final: 0.7727 (t70) REVERT: I 83 ASN cc_start: 0.7485 (p0) cc_final: 0.7239 (p0) REVERT: I 94 ASP cc_start: 0.8190 (t0) cc_final: 0.7819 (t0) REVERT: J 55 ASP cc_start: 0.7594 (p0) cc_final: 0.7129 (p0) REVERT: J 58 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7154 (mm-30) REVERT: K 54 ARG cc_start: 0.7683 (tpp80) cc_final: 0.7458 (tpp80) REVERT: L 36 SER cc_start: 0.8796 (t) cc_final: 0.8444 (m) REVERT: L 47 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.7469 (mmm-85) REVERT: M 90 ASN cc_start: 0.5489 (OUTLIER) cc_final: 0.4743 (m-40) REVERT: M 208 ASN cc_start: 0.8946 (t0) cc_final: 0.8518 (m-40) REVERT: M 238 TYR cc_start: 0.8374 (m-10) cc_final: 0.8151 (m-10) REVERT: M 275 ILE cc_start: 0.9048 (mt) cc_final: 0.8734 (mp) REVERT: M 300 GLN cc_start: 0.8032 (tt0) cc_final: 0.7665 (mm-40) REVERT: O 68 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7422 (tp-100) REVERT: O 121 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6420 (tmm) REVERT: O 188 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7487 (tt0) REVERT: Q 117 HIS cc_start: 0.7780 (m-70) cc_final: 0.7143 (m-70) REVERT: Q 140 HIS cc_start: 0.7447 (m-70) cc_final: 0.6949 (m-70) REVERT: Q 150 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.6226 (tp40) REVERT: Q 158 GLN cc_start: 0.8357 (pp30) cc_final: 0.7958 (pp30) REVERT: Q 348 TYR cc_start: 0.8145 (m-80) cc_final: 0.7666 (m-80) REVERT: Q 373 TYR cc_start: 0.8176 (m-10) cc_final: 0.7933 (m-10) REVERT: Q 375 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8282 (tp) REVERT: Q 384 PHE cc_start: 0.8121 (m-80) cc_final: 0.7638 (m-80) REVERT: R 265 HIS cc_start: 0.7164 (t-170) cc_final: 0.6889 (t-170) REVERT: R 278 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8685 (mm) REVERT: U 243 LEU cc_start: 0.6712 (tp) cc_final: 0.6004 (mp) REVERT: U 252 THR cc_start: 0.5941 (t) cc_final: 0.5584 (m) REVERT: U 258 TRP cc_start: 0.8600 (m100) cc_final: 0.7865 (m-10) REVERT: V 78 PHE cc_start: 0.8506 (m-10) cc_final: 0.6845 (m-10) REVERT: W 63 SER cc_start: 0.8633 (t) cc_final: 0.8339 (m) REVERT: W 67 ILE cc_start: 0.9052 (mt) cc_final: 0.8713 (tp) REVERT: W 123 MET cc_start: 0.7806 (mmp) cc_final: 0.7046 (mmm) REVERT: W 139 LEU cc_start: 0.8262 (mt) cc_final: 0.7920 (tp) REVERT: X 180 TYR cc_start: 0.8102 (t80) cc_final: 0.7873 (m-80) REVERT: X 261 LYS cc_start: 0.8430 (pptt) cc_final: 0.7869 (pptt) REVERT: X 280 ASP cc_start: 0.7727 (m-30) cc_final: 0.7440 (m-30) outliers start: 163 outliers final: 110 residues processed: 1343 average time/residue: 0.6986 time to fit residues: 1594.3674 Evaluate side-chains 1309 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1181 time to evaluate : 6.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 106 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 209 SER Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 424 LEU Chi-restraints excluded: chain 1 residue 444 LYS Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain 2 residue 125 VAL Chi-restraints excluded: chain 2 residue 143 TRP Chi-restraints excluded: chain 3 residue 26 VAL Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 81 GLU Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 4 residue 160 VAL Chi-restraints excluded: chain 5 residue 31 VAL Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 214 LEU Chi-restraints excluded: chain 6 residue 221 LEU Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 438 VAL Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 554 CYS Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 751 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1383 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 90 ASN Chi-restraints excluded: chain M residue 320 ARG Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain O residue 121 MET Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain Q residue 150 GLN Chi-restraints excluded: chain Q residue 334 VAL Chi-restraints excluded: chain Q residue 338 ASN Chi-restraints excluded: chain Q residue 375 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 183 ILE Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain W residue 197 ASN Chi-restraints excluded: chain W residue 273 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 288 optimal weight: 10.0000 chunk 772 optimal weight: 4.9990 chunk 169 optimal weight: 50.0000 chunk 503 optimal weight: 2.9990 chunk 211 optimal weight: 8.9990 chunk 859 optimal weight: 7.9990 chunk 713 optimal weight: 1.9990 chunk 397 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 284 optimal weight: 50.0000 chunk 451 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 555 GLN 1 359 GLN ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 610 ASN 4 232 ASN 5 39 HIS ** 6 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 GLN ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 113 GLN E 136 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN I 22 ASN K 40 HIS K 52 ASN M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 ASN W 294 HIS X 123 HIS ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 75348 Z= 0.549 Angle : 0.670 11.941 102261 Z= 0.345 Chirality : 0.046 0.229 11558 Planarity : 0.005 0.063 12672 Dihedral : 11.877 104.192 11075 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.50 % Favored : 96.49 % Rotamer: Outliers : 2.92 % Allowed : 14.57 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.29 (0.09), residues: 8748 helix: 1.01 (0.09), residues: 3511 sheet: -0.13 (0.14), residues: 1342 loop : -0.34 (0.10), residues: 3895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 130 HIS 0.009 0.001 HIS R 328 PHE 0.043 0.002 PHE C 178 TYR 0.028 0.002 TYR B 797 ARG 0.013 0.001 ARG B 904 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1189 time to evaluate : 6.329 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: 0 72 CYS cc_start: 0.8170 (m) cc_final: 0.7832 (m) REVERT: 0 106 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8022 (mm) REVERT: 0 423 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7955 (p90) REVERT: 0 553 MET cc_start: 0.8385 (mmm) cc_final: 0.7994 (mmm) REVERT: 0 642 MET cc_start: 0.8836 (mmm) cc_final: 0.8490 (mmm) REVERT: 0 657 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8395 (t0) REVERT: 1 88 MET cc_start: 0.7620 (mmp) cc_final: 0.7264 (mmp) REVERT: 1 97 MET cc_start: 0.8376 (ttm) cc_final: 0.8063 (ttt) REVERT: 1 469 MET cc_start: 0.8391 (ttt) cc_final: 0.7635 (mmm) REVERT: 1 477 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8710 (mmt) REVERT: 2 112 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8939 (tp) REVERT: 2 201 TRP cc_start: 0.8481 (t-100) cc_final: 0.8263 (t-100) REVERT: 2 365 HIS cc_start: 0.8582 (t-90) cc_final: 0.8228 (t70) REVERT: 3 22 LEU cc_start: 0.8993 (mt) cc_final: 0.8681 (pp) REVERT: 3 64 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7366 (mmt-90) REVERT: 3 89 PHE cc_start: 0.8310 (m-80) cc_final: 0.7832 (m-80) REVERT: 4 37 TRP cc_start: 0.8572 (m100) cc_final: 0.7958 (m100) REVERT: 4 114 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.5971 (mmt) REVERT: 4 130 TYR cc_start: 0.8881 (t80) cc_final: 0.8437 (t80) REVERT: 4 142 GLN cc_start: 0.9253 (tp-100) cc_final: 0.8934 (tm-30) REVERT: 4 153 MET cc_start: 0.8778 (mtp) cc_final: 0.8523 (mtm) REVERT: 4 159 TYR cc_start: 0.9044 (t80) cc_final: 0.8441 (t80) REVERT: 4 179 LEU cc_start: 0.9368 (mm) cc_final: 0.9166 (mm) REVERT: 4 206 MET cc_start: 0.9033 (ppp) cc_final: 0.7961 (ppp) REVERT: 4 225 GLN cc_start: 0.9002 (mt0) cc_final: 0.8519 (mt0) REVERT: 4 247 TYR cc_start: 0.8564 (m-80) cc_final: 0.8327 (m-10) REVERT: 5 15 SER cc_start: 0.9088 (m) cc_final: 0.8657 (p) REVERT: 5 53 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7629 (mm-30) REVERT: 6 250 THR cc_start: 0.9300 (m) cc_final: 0.9063 (p) REVERT: 6 280 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8000 (p) REVERT: 6 303 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7974 (mt-10) REVERT: 6 442 VAL cc_start: 0.8842 (p) cc_final: 0.8478 (m) REVERT: A 28 ARG cc_start: 0.7838 (mtt90) cc_final: 0.7570 (mtt90) REVERT: A 62 ASP cc_start: 0.7763 (t0) cc_final: 0.7444 (m-30) REVERT: A 63 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7850 (ttp-170) REVERT: A 109 HIS cc_start: 0.8757 (t-90) cc_final: 0.8412 (t-90) REVERT: A 112 LYS cc_start: 0.8239 (tttp) cc_final: 0.7955 (tttt) REVERT: A 119 ASN cc_start: 0.8793 (t0) cc_final: 0.8414 (t0) REVERT: A 453 MET cc_start: 0.8451 (mpp) cc_final: 0.7996 (mpp) REVERT: A 470 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8337 (pp) REVERT: A 526 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8200 (t70) REVERT: A 705 LYS cc_start: 0.7683 (tmtt) cc_final: 0.7457 (tmtt) REVERT: A 991 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8153 (mmmm) REVERT: A 992 ASP cc_start: 0.7765 (p0) cc_final: 0.7494 (p0) REVERT: A 1033 GLN cc_start: 0.7893 (tt0) cc_final: 0.7556 (tt0) REVERT: A 1043 ASP cc_start: 0.7912 (t70) cc_final: 0.7649 (t0) REVERT: A 1135 ARG cc_start: 0.8987 (tmm-80) cc_final: 0.8317 (ttp80) REVERT: A 1195 LEU cc_start: 0.8743 (mm) cc_final: 0.8524 (mm) REVERT: A 1285 MET cc_start: 0.7175 (mmm) cc_final: 0.6876 (mmm) REVERT: A 1287 TYR cc_start: 0.7692 (m-80) cc_final: 0.7267 (m-10) REVERT: A 1290 LYS cc_start: 0.8411 (mttm) cc_final: 0.7981 (mtpp) REVERT: A 1328 TYR cc_start: 0.7544 (t80) cc_final: 0.7050 (t80) REVERT: A 1393 ASN cc_start: 0.8327 (p0) cc_final: 0.7894 (p0) REVERT: B 72 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7609 (pp20) REVERT: B 216 GLU cc_start: 0.7473 (tt0) cc_final: 0.7246 (tt0) REVERT: B 358 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7872 (mtmt) REVERT: B 415 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7290 (tp-100) REVERT: B 418 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7865 (ttpt) REVERT: B 430 ARG cc_start: 0.7557 (ttm110) cc_final: 0.7158 (ttp80) REVERT: B 434 ARG cc_start: 0.8349 (ttm110) cc_final: 0.7910 (ttm110) REVERT: B 531 GLN cc_start: 0.7517 (pp30) cc_final: 0.6980 (pp30) REVERT: B 573 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7635 (tm-30) REVERT: B 592 ASN cc_start: 0.7772 (t0) cc_final: 0.7497 (t0) REVERT: B 598 GLU cc_start: 0.7478 (tp30) cc_final: 0.7205 (tp30) REVERT: B 729 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8153 (mp) REVERT: B 730 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7659 (mmt90) REVERT: B 863 GLU cc_start: 0.7604 (tt0) cc_final: 0.7392 (tt0) REVERT: B 876 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7861 (ptpp) REVERT: B 1174 LYS cc_start: 0.8538 (mttt) cc_final: 0.8232 (mtmt) REVERT: C 154 LYS cc_start: 0.8832 (tttt) cc_final: 0.8362 (ttmt) REVERT: D 150 ASN cc_start: 0.8815 (m-40) cc_final: 0.8489 (t0) REVERT: D 157 GLN cc_start: 0.8333 (mm110) cc_final: 0.8132 (mm110) REVERT: D 189 ASP cc_start: 0.8551 (t70) cc_final: 0.8336 (t70) REVERT: D 204 ASP cc_start: 0.8455 (t0) cc_final: 0.8117 (m-30) REVERT: D 216 ASN cc_start: 0.9326 (t0) cc_final: 0.9073 (t0) REVERT: E 61 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8298 (tm-30) REVERT: E 68 SER cc_start: 0.8635 (t) cc_final: 0.8404 (p) REVERT: E 99 HIS cc_start: 0.8396 (t70) cc_final: 0.8082 (t70) REVERT: E 109 ILE cc_start: 0.8562 (mt) cc_final: 0.8311 (mm) REVERT: E 121 MET cc_start: 0.7970 (tpt) cc_final: 0.7557 (mpp) REVERT: G 21 ARG cc_start: 0.7365 (ptm160) cc_final: 0.6993 (ptt90) REVERT: G 57 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7601 (mm110) REVERT: G 67 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8973 (p) REVERT: G 87 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8210 (p) REVERT: G 130 TYR cc_start: 0.6475 (m-10) cc_final: 0.6208 (m-10) REVERT: H 8 ASP cc_start: 0.7047 (m-30) cc_final: 0.6725 (m-30) REVERT: H 52 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8268 (mm-40) REVERT: H 87 ARG cc_start: 0.7576 (mmm160) cc_final: 0.7364 (mmm160) REVERT: I 83 ASN cc_start: 0.8032 (p0) cc_final: 0.7724 (p0) REVERT: I 94 ASP cc_start: 0.8286 (t0) cc_final: 0.7924 (t0) REVERT: K 54 ARG cc_start: 0.7735 (tpp80) cc_final: 0.7489 (tpp80) REVERT: L 36 SER cc_start: 0.8867 (t) cc_final: 0.8532 (m) REVERT: M 90 ASN cc_start: 0.5778 (OUTLIER) cc_final: 0.4979 (m110) REVERT: M 238 TYR cc_start: 0.8558 (m-10) cc_final: 0.8350 (m-10) REVERT: M 275 ILE cc_start: 0.9097 (mt) cc_final: 0.8861 (mp) REVERT: M 300 GLN cc_start: 0.8096 (tt0) cc_final: 0.7614 (mm-40) REVERT: O 68 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7519 (tp-100) REVERT: O 121 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6525 (tmm) REVERT: Q 117 HIS cc_start: 0.7860 (m-70) cc_final: 0.7330 (m-70) REVERT: Q 140 HIS cc_start: 0.7532 (m-70) cc_final: 0.7053 (m-70) REVERT: Q 150 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.6245 (tp40) REVERT: Q 158 GLN cc_start: 0.8358 (pp30) cc_final: 0.7907 (pp30) REVERT: Q 348 TYR cc_start: 0.8228 (m-80) cc_final: 0.7757 (m-80) REVERT: Q 375 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8289 (tp) REVERT: Q 384 PHE cc_start: 0.8179 (m-80) cc_final: 0.7572 (m-80) REVERT: Q 387 ILE cc_start: 0.8824 (mt) cc_final: 0.8535 (mp) REVERT: R 265 HIS cc_start: 0.7160 (t-170) cc_final: 0.6903 (t-170) REVERT: U 258 TRP cc_start: 0.8630 (m100) cc_final: 0.7913 (m-90) REVERT: V 78 PHE cc_start: 0.8550 (m-10) cc_final: 0.8231 (m-10) REVERT: V 110 LYS cc_start: 0.6045 (pptt) cc_final: 0.5466 (pptt) REVERT: W 38 LEU cc_start: 0.7646 (tp) cc_final: 0.7396 (tt) REVERT: W 63 SER cc_start: 0.8673 (t) cc_final: 0.8299 (m) REVERT: W 67 ILE cc_start: 0.9030 (mt) cc_final: 0.8702 (tp) REVERT: W 123 MET cc_start: 0.7942 (mmp) cc_final: 0.7152 (mmm) REVERT: W 139 LEU cc_start: 0.8340 (mt) cc_final: 0.7999 (tp) REVERT: X 134 TYR cc_start: 0.7937 (t80) cc_final: 0.7702 (t80) REVERT: X 180 TYR cc_start: 0.8111 (t80) cc_final: 0.7830 (m-80) REVERT: X 227 ASP cc_start: 0.7917 (t0) cc_final: 0.7538 (t0) REVERT: X 261 LYS cc_start: 0.8480 (pptt) cc_final: 0.7898 (pptt) REVERT: X 264 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7306 (pt0) REVERT: X 277 LYS cc_start: 0.8303 (mttt) cc_final: 0.7841 (ttmm) REVERT: X 280 ASP cc_start: 0.7864 (m-30) cc_final: 0.7568 (m-30) outliers start: 232 outliers final: 156 residues processed: 1325 average time/residue: 0.7373 time to fit residues: 1670.5323 Evaluate side-chains 1323 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1148 time to evaluate : 6.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 17 ILE Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 106 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 423 TYR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 435 MET Chi-restraints excluded: chain 0 residue 463 ILE Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 632 SER Chi-restraints excluded: chain 0 residue 657 ASP Chi-restraints excluded: chain 1 residue 259 ILE Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 358 MET Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 2 residue 112 LEU Chi-restraints excluded: chain 2 residue 125 VAL Chi-restraints excluded: chain 2 residue 143 TRP Chi-restraints excluded: chain 2 residue 216 MET Chi-restraints excluded: chain 3 residue 26 VAL Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 64 ARG Chi-restraints excluded: chain 3 residue 81 GLU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 5 residue 31 VAL Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 214 LEU Chi-restraints excluded: chain 6 residue 240 SER Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 438 VAL Chi-restraints excluded: chain 7 residue 448 THR Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 554 CYS Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 876 LYS Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 90 ASN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 121 MET Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 150 GLN Chi-restraints excluded: chain Q residue 334 VAL Chi-restraints excluded: chain Q residue 338 ASN Chi-restraints excluded: chain Q residue 375 LEU Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 183 ILE Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain W residue 197 ASN Chi-restraints excluded: chain W residue 273 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 828 optimal weight: 40.0000 chunk 96 optimal weight: 8.9990 chunk 489 optimal weight: 1.9990 chunk 627 optimal weight: 10.0000 chunk 486 optimal weight: 0.0470 chunk 723 optimal weight: 0.7980 chunk 479 optimal weight: 20.0000 chunk 855 optimal weight: 1.9990 chunk 535 optimal weight: 0.5980 chunk 521 optimal weight: 0.9980 chunk 395 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 113 GLN G 24 GLN G 113 HIS ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN K 52 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 331 GLN W 120 ASN W 294 HIS X 123 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 75348 Z= 0.181 Angle : 0.570 16.746 102261 Z= 0.291 Chirality : 0.041 0.272 11558 Planarity : 0.004 0.061 12672 Dihedral : 11.752 98.191 11075 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.67 % Favored : 97.31 % Rotamer: Outliers : 1.97 % Allowed : 15.80 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.49 (0.09), residues: 8748 helix: 1.19 (0.09), residues: 3516 sheet: 0.00 (0.14), residues: 1344 loop : -0.27 (0.10), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1304 HIS 0.007 0.001 HIS X 123 PHE 0.024 0.001 PHE R 304 TYR 0.024 0.001 TYR 5 63 ARG 0.012 0.000 ARG B 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1224 time to evaluate : 6.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 106 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8001 (mt) REVERT: 0 423 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7876 (p90) REVERT: 0 487 LEU cc_start: 0.7650 (pt) cc_final: 0.7355 (pp) REVERT: 0 553 MET cc_start: 0.8315 (mmm) cc_final: 0.7829 (mmm) REVERT: 0 642 MET cc_start: 0.8764 (mmm) cc_final: 0.8467 (mmm) REVERT: 0 664 GLN cc_start: 0.8461 (tm-30) cc_final: 0.7883 (pp30) REVERT: 1 88 MET cc_start: 0.7290 (mmp) cc_final: 0.6946 (mmp) REVERT: 1 97 MET cc_start: 0.8292 (ttm) cc_final: 0.8004 (ttt) REVERT: 1 318 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8151 (m-30) REVERT: 1 469 MET cc_start: 0.8365 (ttt) cc_final: 0.7854 (mmm) REVERT: 2 201 TRP cc_start: 0.8472 (t-100) cc_final: 0.8256 (t-100) REVERT: 2 365 HIS cc_start: 0.8516 (t-90) cc_final: 0.8191 (t70) REVERT: 3 22 LEU cc_start: 0.8912 (mt) cc_final: 0.8640 (pp) REVERT: 3 64 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6868 (mmt90) REVERT: 3 89 PHE cc_start: 0.8248 (m-80) cc_final: 0.7693 (m-80) REVERT: 4 37 TRP cc_start: 0.8588 (m100) cc_final: 0.8047 (m100) REVERT: 4 114 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5851 (mmt) REVERT: 4 130 TYR cc_start: 0.8862 (t80) cc_final: 0.8323 (t80) REVERT: 4 142 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8939 (tm-30) REVERT: 4 153 MET cc_start: 0.8750 (mtp) cc_final: 0.8516 (mtt) REVERT: 4 159 TYR cc_start: 0.9011 (t80) cc_final: 0.8338 (t80) REVERT: 4 206 MET cc_start: 0.9012 (ppp) cc_final: 0.7959 (ppp) REVERT: 4 225 GLN cc_start: 0.8950 (mt0) cc_final: 0.8551 (mt0) REVERT: 4 235 TYR cc_start: 0.8097 (t80) cc_final: 0.7877 (t80) REVERT: 4 247 TYR cc_start: 0.8501 (m-80) cc_final: 0.8197 (m-10) REVERT: 5 22 GLN cc_start: 0.8773 (mp10) cc_final: 0.8528 (mp10) REVERT: 6 250 THR cc_start: 0.9255 (m) cc_final: 0.9040 (p) REVERT: 6 303 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7987 (mt-10) REVERT: A 62 ASP cc_start: 0.7742 (t0) cc_final: 0.7395 (m-30) REVERT: A 63 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7824 (ttp-170) REVERT: A 65 LEU cc_start: 0.8238 (mt) cc_final: 0.8026 (mm) REVERT: A 109 HIS cc_start: 0.8668 (t-90) cc_final: 0.8237 (t-90) REVERT: A 112 LYS cc_start: 0.8205 (tttp) cc_final: 0.7901 (tttt) REVERT: A 119 ASN cc_start: 0.8750 (t0) cc_final: 0.8505 (t0) REVERT: A 268 ASP cc_start: 0.7151 (m-30) cc_final: 0.6899 (m-30) REVERT: A 453 MET cc_start: 0.8366 (mpp) cc_final: 0.7899 (mpp) REVERT: A 526 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7948 (t70) REVERT: A 705 LYS cc_start: 0.7653 (tmtt) cc_final: 0.7380 (tmtt) REVERT: A 801 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7402 (tm-30) REVERT: A 991 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8098 (mmmm) REVERT: A 992 ASP cc_start: 0.7615 (p0) cc_final: 0.7360 (p0) REVERT: A 1033 GLN cc_start: 0.7919 (tt0) cc_final: 0.7611 (tt0) REVERT: A 1043 ASP cc_start: 0.7789 (t70) cc_final: 0.7566 (t0) REVERT: A 1054 LEU cc_start: 0.9175 (mt) cc_final: 0.8938 (mt) REVERT: A 1135 ARG cc_start: 0.9032 (tmm-80) cc_final: 0.8359 (ttp80) REVERT: A 1284 MET cc_start: 0.7224 (mtp) cc_final: 0.6244 (mtm) REVERT: A 1285 MET cc_start: 0.7096 (mmm) cc_final: 0.6815 (mmm) REVERT: A 1287 TYR cc_start: 0.7622 (m-80) cc_final: 0.7279 (m-10) REVERT: A 1290 LYS cc_start: 0.8326 (mttm) cc_final: 0.7971 (mtpp) REVERT: A 1328 TYR cc_start: 0.7457 (t80) cc_final: 0.6951 (t80) REVERT: A 1393 ASN cc_start: 0.8188 (p0) cc_final: 0.7729 (p0) REVERT: B 72 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7624 (pp20) REVERT: B 94 LYS cc_start: 0.7620 (mmpt) cc_final: 0.7362 (mmmt) REVERT: B 216 GLU cc_start: 0.7453 (tt0) cc_final: 0.7202 (tt0) REVERT: B 277 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8483 (ttpt) REVERT: B 358 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7845 (mtmt) REVERT: B 418 LYS cc_start: 0.8091 (ttpt) cc_final: 0.7769 (ttpt) REVERT: B 430 ARG cc_start: 0.7532 (ttm110) cc_final: 0.7077 (ttp80) REVERT: B 434 ARG cc_start: 0.8301 (ttm110) cc_final: 0.7712 (ttp-110) REVERT: B 531 GLN cc_start: 0.7409 (pp30) cc_final: 0.6881 (pp30) REVERT: B 573 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7472 (tm-30) REVERT: B 592 ASN cc_start: 0.7688 (t0) cc_final: 0.6952 (t0) REVERT: B 595 ARG cc_start: 0.8110 (ptm160) cc_final: 0.7695 (mtp-110) REVERT: B 598 GLU cc_start: 0.7431 (tp30) cc_final: 0.7157 (tp30) REVERT: B 729 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.7982 (mt) REVERT: B 730 ARG cc_start: 0.8173 (tpp80) cc_final: 0.7959 (mmt90) REVERT: B 876 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7918 (ptpp) REVERT: B 1101 ASP cc_start: 0.7382 (t0) cc_final: 0.7010 (t0) REVERT: B 1174 LYS cc_start: 0.8417 (mttt) cc_final: 0.8116 (mtmt) REVERT: C 154 LYS cc_start: 0.8701 (tttt) cc_final: 0.8243 (ttmm) REVERT: D 150 ASN cc_start: 0.8752 (m-40) cc_final: 0.8403 (t0) REVERT: D 204 ASP cc_start: 0.8374 (t0) cc_final: 0.8071 (m-30) REVERT: E 56 LYS cc_start: 0.8753 (mmtp) cc_final: 0.8290 (mmmm) REVERT: E 61 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8319 (tm-30) REVERT: E 68 SER cc_start: 0.8519 (t) cc_final: 0.8308 (p) REVERT: E 99 HIS cc_start: 0.8349 (t70) cc_final: 0.8056 (t70) REVERT: E 109 ILE cc_start: 0.8504 (mt) cc_final: 0.8231 (mm) REVERT: E 113 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: E 115 ASN cc_start: 0.8268 (p0) cc_final: 0.7958 (t0) REVERT: E 121 MET cc_start: 0.8007 (tpt) cc_final: 0.7534 (mpp) REVERT: F 127 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7107 (tm-30) REVERT: F 129 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7634 (mttm) REVERT: G 21 ARG cc_start: 0.7451 (ptm160) cc_final: 0.6998 (ptt90) REVERT: G 57 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7495 (mm110) REVERT: G 67 SER cc_start: 0.9140 (p) cc_final: 0.8936 (p) REVERT: G 87 VAL cc_start: 0.8373 (m) cc_final: 0.8172 (p) REVERT: G 119 LEU cc_start: 0.8636 (mp) cc_final: 0.7666 (tt) REVERT: H 8 ASP cc_start: 0.6935 (m-30) cc_final: 0.6559 (m-30) REVERT: I 13 MET cc_start: 0.8182 (ptp) cc_final: 0.7972 (ptt) REVERT: I 18 GLU cc_start: 0.7463 (pm20) cc_final: 0.7093 (pm20) REVERT: I 34 TYR cc_start: 0.6701 (t80) cc_final: 0.6335 (t80) REVERT: I 83 ASN cc_start: 0.7574 (p0) cc_final: 0.7315 (p0) REVERT: I 94 ASP cc_start: 0.8182 (t0) cc_final: 0.7849 (t0) REVERT: J 55 ASP cc_start: 0.7593 (p0) cc_final: 0.7275 (p0) REVERT: J 58 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7212 (mm-30) REVERT: L 36 SER cc_start: 0.8842 (t) cc_final: 0.8512 (m) REVERT: L 38 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8691 (tp) REVERT: M 190 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7452 (ttmt) REVERT: M 208 ASN cc_start: 0.8946 (t0) cc_final: 0.8517 (m-40) REVERT: M 275 ILE cc_start: 0.9018 (mt) cc_final: 0.8710 (mp) REVERT: M 300 GLN cc_start: 0.7959 (tt0) cc_final: 0.7607 (mm-40) REVERT: O 68 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7371 (tp-100) REVERT: O 121 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6450 (tmm) REVERT: Q 117 HIS cc_start: 0.7818 (m-70) cc_final: 0.7279 (m-70) REVERT: Q 140 HIS cc_start: 0.7408 (m-70) cc_final: 0.6948 (m-70) REVERT: Q 150 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6254 (tp40) REVERT: Q 158 GLN cc_start: 0.8398 (pp30) cc_final: 0.7957 (pp30) REVERT: Q 348 TYR cc_start: 0.8203 (m-80) cc_final: 0.7686 (m-80) REVERT: Q 365 TYR cc_start: 0.8244 (t80) cc_final: 0.7990 (t80) REVERT: Q 375 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8354 (tp) REVERT: Q 384 PHE cc_start: 0.8259 (m-80) cc_final: 0.7758 (m-80) REVERT: Q 387 ILE cc_start: 0.8832 (mt) cc_final: 0.8544 (mp) REVERT: R 67 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7528 (mm-40) REVERT: R 87 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8295 (tt) REVERT: R 263 MET cc_start: 0.8378 (mmm) cc_final: 0.8168 (mmm) REVERT: R 265 HIS cc_start: 0.7262 (t-170) cc_final: 0.7001 (t-170) REVERT: R 270 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.6096 (tmm) REVERT: U 258 TRP cc_start: 0.8625 (m100) cc_final: 0.7873 (m-10) REVERT: V 78 PHE cc_start: 0.8559 (m-10) cc_final: 0.6843 (m-10) REVERT: V 110 LYS cc_start: 0.6263 (pptt) cc_final: 0.5832 (pptt) REVERT: W 38 LEU cc_start: 0.7483 (tp) cc_final: 0.7253 (tt) REVERT: W 63 SER cc_start: 0.8656 (t) cc_final: 0.8267 (m) REVERT: W 67 ILE cc_start: 0.9024 (mt) cc_final: 0.8693 (tp) REVERT: W 123 MET cc_start: 0.7720 (mmp) cc_final: 0.7408 (mmm) REVERT: W 139 LEU cc_start: 0.8265 (mt) cc_final: 0.7942 (tp) REVERT: X 134 TYR cc_start: 0.7969 (t80) cc_final: 0.7685 (t80) REVERT: X 199 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8219 (mp10) REVERT: X 227 ASP cc_start: 0.7872 (t0) cc_final: 0.7488 (t0) REVERT: X 261 LYS cc_start: 0.8485 (pptt) cc_final: 0.7823 (pptt) REVERT: X 264 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7225 (pt0) REVERT: X 277 LYS cc_start: 0.8264 (mttt) cc_final: 0.7828 (ttmm) REVERT: X 280 ASP cc_start: 0.7684 (m-30) cc_final: 0.7386 (m-30) outliers start: 156 outliers final: 103 residues processed: 1313 average time/residue: 0.6995 time to fit residues: 1555.8422 Evaluate side-chains 1303 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1183 time to evaluate : 6.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 106 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 423 TYR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 632 SER Chi-restraints excluded: chain 1 residue 259 ILE Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 444 LYS Chi-restraints excluded: chain 2 residue 125 VAL Chi-restraints excluded: chain 2 residue 165 ASN Chi-restraints excluded: chain 3 residue 26 VAL Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 64 ARG Chi-restraints excluded: chain 3 residue 81 GLU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 214 LEU Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 7 residue 448 THR Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 554 CYS Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 876 LYS Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 113 HIS Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain O residue 121 MET Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain O residue 206 ILE Chi-restraints excluded: chain Q residue 150 GLN Chi-restraints excluded: chain Q residue 338 ASN Chi-restraints excluded: chain Q residue 375 LEU Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain R residue 270 MET Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 183 ILE Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain W residue 197 ASN Chi-restraints excluded: chain W residue 273 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 529 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 chunk 511 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 168 optimal weight: 30.0000 chunk 165 optimal weight: 7.9990 chunk 544 optimal weight: 0.4980 chunk 583 optimal weight: 3.9990 chunk 423 optimal weight: 4.9990 chunk 79 optimal weight: 40.0000 chunk 672 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 39 HIS ** 5 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 551 ASN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 113 GLN E 136 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 HIS ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 75348 Z= 0.389 Angle : 0.629 15.159 102261 Z= 0.320 Chirality : 0.044 0.278 11558 Planarity : 0.004 0.062 12672 Dihedral : 11.801 91.431 11075 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.45 % Favored : 96.54 % Rotamer: Outliers : 2.36 % Allowed : 15.86 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.35 (0.09), residues: 8748 helix: 1.10 (0.09), residues: 3519 sheet: -0.13 (0.14), residues: 1357 loop : -0.35 (0.10), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1304 HIS 0.010 0.001 HIS 0 747 PHE 0.057 0.002 PHE 2 226 TYR 0.037 0.001 TYR O 224 ARG 0.009 0.000 ARG 0 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1191 time to evaluate : 8.027 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: 0 61 MET cc_start: 0.8630 (mmp) cc_final: 0.8213 (mmp) REVERT: 0 106 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8015 (mm) REVERT: 0 136 MET cc_start: 0.8063 (tpp) cc_final: 0.7837 (tpp) REVERT: 0 423 TYR cc_start: 0.8185 (OUTLIER) cc_final: 0.7874 (p90) REVERT: 0 553 MET cc_start: 0.8364 (mmm) cc_final: 0.7855 (mmm) REVERT: 0 642 MET cc_start: 0.8780 (mmm) cc_final: 0.8444 (mmm) REVERT: 0 660 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7368 (ptm160) REVERT: 0 664 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8251 (tm-30) REVERT: 1 88 MET cc_start: 0.7334 (mmp) cc_final: 0.6988 (mmp) REVERT: 1 328 MET cc_start: 0.8088 (ppp) cc_final: 0.7795 (ppp) REVERT: 1 469 MET cc_start: 0.8367 (ttt) cc_final: 0.7846 (mmm) REVERT: 1 477 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8738 (mmt) REVERT: 2 201 TRP cc_start: 0.8481 (t-100) cc_final: 0.8276 (t-100) REVERT: 2 365 HIS cc_start: 0.8523 (t-90) cc_final: 0.8184 (t70) REVERT: 3 22 LEU cc_start: 0.8944 (mt) cc_final: 0.8651 (pp) REVERT: 3 64 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6793 (mmt90) REVERT: 3 89 PHE cc_start: 0.8281 (m-80) cc_final: 0.7755 (m-80) REVERT: 4 37 TRP cc_start: 0.8636 (m100) cc_final: 0.8065 (m100) REVERT: 4 114 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.5919 (mmt) REVERT: 4 130 TYR cc_start: 0.8885 (t80) cc_final: 0.8474 (t80) REVERT: 4 153 MET cc_start: 0.8754 (mtp) cc_final: 0.8551 (mtt) REVERT: 4 159 TYR cc_start: 0.9037 (t80) cc_final: 0.8369 (t80) REVERT: 4 206 MET cc_start: 0.9050 (ppp) cc_final: 0.8148 (ppp) REVERT: 4 225 GLN cc_start: 0.8964 (mt0) cc_final: 0.8579 (mt0) REVERT: 4 235 TYR cc_start: 0.8111 (t80) cc_final: 0.7882 (t80) REVERT: 4 247 TYR cc_start: 0.8504 (m-80) cc_final: 0.8281 (m-10) REVERT: 5 22 GLN cc_start: 0.8731 (mp10) cc_final: 0.8370 (mp10) REVERT: 6 250 THR cc_start: 0.9263 (m) cc_final: 0.9045 (p) REVERT: 6 280 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.7924 (p) REVERT: 6 303 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7947 (mt-10) REVERT: 7 445 MET cc_start: 0.4782 (mpp) cc_final: 0.4517 (mpp) REVERT: 7 561 MET cc_start: 0.6320 (tmm) cc_final: 0.5845 (ppp) REVERT: A 62 ASP cc_start: 0.7829 (t0) cc_final: 0.7497 (m-30) REVERT: A 63 ARG cc_start: 0.8277 (ttm170) cc_final: 0.7894 (ttp-170) REVERT: A 65 LEU cc_start: 0.8432 (mt) cc_final: 0.8182 (mm) REVERT: A 109 HIS cc_start: 0.8678 (t-90) cc_final: 0.8365 (t-90) REVERT: A 112 LYS cc_start: 0.8220 (tttp) cc_final: 0.7920 (tttt) REVERT: A 119 ASN cc_start: 0.8799 (t0) cc_final: 0.8507 (t0) REVERT: A 186 LYS cc_start: 0.8222 (tppt) cc_final: 0.7900 (tptt) REVERT: A 453 MET cc_start: 0.8405 (mpp) cc_final: 0.8007 (mpp) REVERT: A 470 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8236 (pp) REVERT: A 501 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8270 (mp) REVERT: A 526 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8100 (t70) REVERT: A 801 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 991 LYS cc_start: 0.8476 (mmmm) cc_final: 0.8119 (mmmm) REVERT: A 992 ASP cc_start: 0.7704 (p0) cc_final: 0.7439 (p0) REVERT: A 1033 GLN cc_start: 0.7932 (tt0) cc_final: 0.7621 (tt0) REVERT: A 1043 ASP cc_start: 0.7873 (t70) cc_final: 0.7617 (t0) REVERT: A 1054 LEU cc_start: 0.9240 (mt) cc_final: 0.9030 (mt) REVERT: A 1135 ARG cc_start: 0.9036 (tmm-80) cc_final: 0.8360 (ttp80) REVERT: A 1285 MET cc_start: 0.7108 (mmm) cc_final: 0.6798 (mmm) REVERT: A 1287 TYR cc_start: 0.7655 (m-80) cc_final: 0.7249 (m-10) REVERT: A 1290 LYS cc_start: 0.8337 (mttm) cc_final: 0.7920 (mtpp) REVERT: A 1328 TYR cc_start: 0.7541 (t80) cc_final: 0.7026 (t80) REVERT: A 1393 ASN cc_start: 0.8285 (p0) cc_final: 0.7874 (p0) REVERT: B 72 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7750 (pp20) REVERT: B 216 GLU cc_start: 0.7477 (tt0) cc_final: 0.7231 (tt0) REVERT: B 277 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8488 (ttpt) REVERT: B 358 LYS cc_start: 0.8316 (mtmt) cc_final: 0.7787 (mtmt) REVERT: B 415 GLN cc_start: 0.7434 (tm-30) cc_final: 0.7174 (tp40) REVERT: B 418 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7891 (ttpt) REVERT: B 430 ARG cc_start: 0.7585 (ttm110) cc_final: 0.7159 (ttp80) REVERT: B 434 ARG cc_start: 0.8327 (ttm110) cc_final: 0.7794 (ttp-110) REVERT: B 531 GLN cc_start: 0.7516 (pp30) cc_final: 0.6995 (pp30) REVERT: B 592 ASN cc_start: 0.7760 (t0) cc_final: 0.7496 (t0) REVERT: B 598 GLU cc_start: 0.7435 (tp30) cc_final: 0.7143 (tp30) REVERT: B 729 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.7987 (mt) REVERT: B 865 LYS cc_start: 0.8995 (ptpt) cc_final: 0.8405 (pttp) REVERT: B 876 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7947 (ptpp) REVERT: B 1101 ASP cc_start: 0.7288 (t0) cc_final: 0.6913 (t0) REVERT: B 1174 LYS cc_start: 0.8488 (mttt) cc_final: 0.8172 (mtmt) REVERT: C 154 LYS cc_start: 0.8813 (tttt) cc_final: 0.8266 (ttmm) REVERT: C 155 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9002 (pp) REVERT: D 150 ASN cc_start: 0.8802 (m-40) cc_final: 0.8488 (t0) REVERT: D 204 ASP cc_start: 0.8382 (t0) cc_final: 0.8035 (m-30) REVERT: E 56 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8362 (mmmm) REVERT: E 61 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8171 (tm-30) REVERT: E 109 ILE cc_start: 0.8512 (mt) cc_final: 0.8250 (mm) REVERT: E 113 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7302 (mt0) REVERT: E 121 MET cc_start: 0.7986 (tpt) cc_final: 0.7511 (mpp) REVERT: G 21 ARG cc_start: 0.7450 (ptm160) cc_final: 0.6999 (ptt90) REVERT: G 57 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7571 (mm110) REVERT: G 67 SER cc_start: 0.9205 (p) cc_final: 0.8954 (p) REVERT: G 87 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8212 (p) REVERT: G 130 TYR cc_start: 0.6145 (m-10) cc_final: 0.5846 (m-10) REVERT: H 8 ASP cc_start: 0.6961 (m-30) cc_final: 0.6685 (m-30) REVERT: H 52 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8291 (mm-40) REVERT: I 13 MET cc_start: 0.8025 (ptp) cc_final: 0.7740 (ptt) REVERT: I 18 GLU cc_start: 0.7573 (pm20) cc_final: 0.7245 (pm20) REVERT: I 34 TYR cc_start: 0.6664 (t80) cc_final: 0.6277 (t80) REVERT: I 83 ASN cc_start: 0.7737 (p0) cc_final: 0.7421 (p0) REVERT: I 94 ASP cc_start: 0.8231 (t0) cc_final: 0.7892 (t0) REVERT: K 54 ARG cc_start: 0.7678 (tpp80) cc_final: 0.7457 (tpp80) REVERT: L 36 SER cc_start: 0.8876 (t) cc_final: 0.8548 (m) REVERT: M 119 MET cc_start: 0.6966 (ppp) cc_final: 0.6645 (ppp) REVERT: M 190 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7512 (ttmt) REVERT: M 208 ASN cc_start: 0.8989 (t0) cc_final: 0.8546 (m-40) REVERT: M 290 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7836 (mp10) REVERT: M 300 GLN cc_start: 0.8026 (tt0) cc_final: 0.7660 (mm-40) REVERT: O 68 GLN cc_start: 0.7800 (tp-100) cc_final: 0.7342 (tp-100) REVERT: O 121 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.6287 (tmm) REVERT: O 240 MET cc_start: 0.7857 (tmm) cc_final: 0.7352 (tmm) REVERT: Q 117 HIS cc_start: 0.7839 (m-70) cc_final: 0.7281 (m-70) REVERT: Q 140 HIS cc_start: 0.7523 (m-70) cc_final: 0.7073 (m-70) REVERT: Q 150 GLN cc_start: 0.6513 (OUTLIER) cc_final: 0.6312 (tp40) REVERT: Q 158 GLN cc_start: 0.8418 (pp30) cc_final: 0.7972 (pp30) REVERT: Q 348 TYR cc_start: 0.8238 (m-80) cc_final: 0.7735 (m-80) REVERT: Q 365 TYR cc_start: 0.8261 (t80) cc_final: 0.8015 (t80) REVERT: Q 375 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8350 (tp) REVERT: Q 384 PHE cc_start: 0.8069 (m-80) cc_final: 0.7524 (m-80) REVERT: Q 387 ILE cc_start: 0.8855 (mt) cc_final: 0.8578 (mp) REVERT: R 87 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8261 (tt) REVERT: R 265 HIS cc_start: 0.7187 (t-170) cc_final: 0.6941 (t-170) REVERT: R 270 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.6079 (tmm) REVERT: V 78 PHE cc_start: 0.8583 (m-10) cc_final: 0.8210 (m-10) REVERT: V 110 LYS cc_start: 0.6404 (pptt) cc_final: 0.6076 (pptt) REVERT: W 38 LEU cc_start: 0.7545 (tp) cc_final: 0.7280 (tt) REVERT: W 63 SER cc_start: 0.8667 (t) cc_final: 0.8294 (m) REVERT: W 67 ILE cc_start: 0.9032 (mt) cc_final: 0.8706 (tp) REVERT: W 123 MET cc_start: 0.7809 (mmp) cc_final: 0.6811 (mmm) REVERT: W 139 LEU cc_start: 0.8315 (mt) cc_final: 0.7974 (tp) REVERT: X 134 TYR cc_start: 0.8002 (t80) cc_final: 0.7676 (t80) REVERT: X 227 ASP cc_start: 0.7872 (t0) cc_final: 0.7485 (t0) REVERT: X 261 LYS cc_start: 0.8483 (pptt) cc_final: 0.7845 (pptt) REVERT: X 264 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7272 (pt0) REVERT: X 277 LYS cc_start: 0.8277 (mttt) cc_final: 0.7856 (ttmm) REVERT: X 280 ASP cc_start: 0.7665 (m-30) cc_final: 0.7363 (m-30) REVERT: X 293 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8293 (pt) outliers start: 187 outliers final: 142 residues processed: 1289 average time/residue: 0.7047 time to fit residues: 1541.6496 Evaluate side-chains 1336 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1171 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 106 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 250 LEU Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 423 TYR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 632 SER Chi-restraints excluded: chain 0 residue 660 ARG Chi-restraints excluded: chain 1 residue 259 ILE Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 419 LEU Chi-restraints excluded: chain 1 residue 444 LYS Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 2 residue 125 VAL Chi-restraints excluded: chain 2 residue 143 TRP Chi-restraints excluded: chain 2 residue 408 MET Chi-restraints excluded: chain 3 residue 26 VAL Chi-restraints excluded: chain 3 residue 64 ARG Chi-restraints excluded: chain 3 residue 81 GLU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 214 LEU Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 438 VAL Chi-restraints excluded: chain 7 residue 448 THR Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 554 CYS Chi-restraints excluded: chain 7 residue 740 HIS Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 255 GLN Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 876 LYS Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain O residue 121 MET Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain Q residue 150 GLN Chi-restraints excluded: chain Q residue 338 ASN Chi-restraints excluded: chain Q residue 375 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 118 HIS Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain R residue 270 MET Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 183 ILE Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain W residue 197 ASN Chi-restraints excluded: chain W residue 273 GLN Chi-restraints excluded: chain X residue 293 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 778 optimal weight: 6.9990 chunk 819 optimal weight: 20.0000 chunk 748 optimal weight: 20.0000 chunk 797 optimal weight: 5.9990 chunk 480 optimal weight: 0.7980 chunk 347 optimal weight: 2.9990 chunk 626 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 720 optimal weight: 1.9990 chunk 754 optimal weight: 30.0000 chunk 794 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 113 GLN G 113 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN K 52 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 GLN X 123 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 75348 Z= 0.471 Angle : 0.668 15.117 102261 Z= 0.342 Chirality : 0.045 0.273 11558 Planarity : 0.004 0.064 12672 Dihedral : 11.889 81.572 11075 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.64 % Favored : 96.35 % Rotamer: Outliers : 2.48 % Allowed : 16.07 % Favored : 81.45 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.51 % 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: 0.17 (0.09), residues: 8748 helix: 0.97 (0.09), residues: 3521 sheet: -0.26 (0.14), residues: 1356 loop : -0.46 (0.10), residues: 3871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1304 HIS 0.016 0.001 HIS 5 39 PHE 0.055 0.002 PHE 2 226 TYR 0.039 0.002 TYR O 224 ARG 0.014 0.001 ARG A 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1195 time to evaluate : 6.490 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: 0 61 MET cc_start: 0.8627 (mmp) cc_final: 0.8227 (mmp) REVERT: 0 72 CYS cc_start: 0.8076 (m) cc_final: 0.7757 (m) REVERT: 0 106 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8067 (mm) REVERT: 0 346 MET cc_start: 0.8056 (tpp) cc_final: 0.7595 (tmm) REVERT: 0 423 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.7890 (p90) REVERT: 0 553 MET cc_start: 0.8363 (mmm) cc_final: 0.7855 (mmm) REVERT: 0 642 MET cc_start: 0.8782 (mmm) cc_final: 0.8441 (mmm) REVERT: 0 660 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7307 (ptm160) REVERT: 0 664 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8342 (tm-30) REVERT: 1 88 MET cc_start: 0.7340 (mmp) cc_final: 0.6973 (mmp) REVERT: 1 318 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8180 (m-30) REVERT: 1 328 MET cc_start: 0.8157 (ppp) cc_final: 0.7856 (ppp) REVERT: 1 469 MET cc_start: 0.8394 (ttt) cc_final: 0.7867 (mmm) REVERT: 1 477 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8738 (mmt) REVERT: 2 50 MET cc_start: 0.8865 (ppp) cc_final: 0.8653 (ppp) REVERT: 2 365 HIS cc_start: 0.8558 (t-90) cc_final: 0.8222 (t70) REVERT: 3 22 LEU cc_start: 0.8926 (mt) cc_final: 0.8640 (pp) REVERT: 3 64 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6919 (mmt90) REVERT: 3 89 PHE cc_start: 0.8308 (m-80) cc_final: 0.7759 (m-80) REVERT: 4 37 TRP cc_start: 0.8690 (m100) cc_final: 0.8099 (m100) REVERT: 4 79 TYR cc_start: 0.8524 (p90) cc_final: 0.8315 (p90) REVERT: 4 114 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6017 (mmt) REVERT: 4 130 TYR cc_start: 0.8897 (t80) cc_final: 0.8604 (t80) REVERT: 4 153 MET cc_start: 0.8767 (mtp) cc_final: 0.8519 (mtt) REVERT: 4 159 TYR cc_start: 0.8992 (t80) cc_final: 0.8361 (t80) REVERT: 4 206 MET cc_start: 0.9021 (ppp) cc_final: 0.8178 (ppp) REVERT: 4 225 GLN cc_start: 0.8985 (mt0) cc_final: 0.8455 (mt0) REVERT: 4 226 GLN cc_start: 0.8918 (mm110) cc_final: 0.8416 (mm110) REVERT: 4 235 TYR cc_start: 0.8155 (t80) cc_final: 0.7921 (t80) REVERT: 4 247 TYR cc_start: 0.8513 (m-80) cc_final: 0.8310 (m-10) REVERT: 5 15 SER cc_start: 0.8997 (m) cc_final: 0.8576 (p) REVERT: 5 22 GLN cc_start: 0.8741 (mp10) cc_final: 0.8452 (mp10) REVERT: 6 250 THR cc_start: 0.9270 (m) cc_final: 0.9060 (p) REVERT: 6 280 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.7983 (p) REVERT: 6 303 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7930 (mt-10) REVERT: 7 445 MET cc_start: 0.5123 (mpp) cc_final: 0.4836 (mpp) REVERT: 7 561 MET cc_start: 0.6510 (tmm) cc_final: 0.6029 (ppp) REVERT: A 28 ARG cc_start: 0.7814 (mtt90) cc_final: 0.7543 (mtt90) REVERT: A 63 ARG cc_start: 0.8363 (ttm170) cc_final: 0.8091 (ttp-170) REVERT: A 109 HIS cc_start: 0.8749 (t-90) cc_final: 0.8388 (t-90) REVERT: A 112 LYS cc_start: 0.8217 (tttp) cc_final: 0.7945 (tttt) REVERT: A 119 ASN cc_start: 0.8824 (t0) cc_final: 0.8527 (t0) REVERT: A 186 LYS cc_start: 0.8331 (tppt) cc_final: 0.7990 (tptt) REVERT: A 453 MET cc_start: 0.8405 (mpp) cc_final: 0.8015 (mpp) REVERT: A 470 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8281 (pp) REVERT: A 526 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8140 (t70) REVERT: A 708 MET cc_start: 0.8155 (mtp) cc_final: 0.7929 (ptp) REVERT: A 991 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8120 (mmmm) REVERT: A 992 ASP cc_start: 0.7754 (p0) cc_final: 0.7501 (p0) REVERT: A 1043 ASP cc_start: 0.7911 (t70) cc_final: 0.7667 (t0) REVERT: A 1135 ARG cc_start: 0.9051 (tmm-80) cc_final: 0.8363 (ttp80) REVERT: A 1285 MET cc_start: 0.7141 (mmm) cc_final: 0.6864 (mmm) REVERT: A 1287 TYR cc_start: 0.7675 (m-80) cc_final: 0.7269 (m-10) REVERT: A 1290 LYS cc_start: 0.8299 (mttm) cc_final: 0.7850 (mtpp) REVERT: A 1328 TYR cc_start: 0.7565 (t80) cc_final: 0.7079 (t80) REVERT: A 1393 ASN cc_start: 0.8311 (p0) cc_final: 0.7903 (p0) REVERT: B 72 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7707 (pp20) REVERT: B 216 GLU cc_start: 0.7479 (tt0) cc_final: 0.7227 (tt0) REVERT: B 277 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8454 (ttpt) REVERT: B 320 ASP cc_start: 0.8155 (t70) cc_final: 0.7911 (t0) REVERT: B 337 ARG cc_start: 0.8135 (mmt180) cc_final: 0.7864 (mmt180) REVERT: B 358 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7871 (mtmt) REVERT: B 398 ARG cc_start: 0.7609 (mmm-85) cc_final: 0.7401 (mmm-85) REVERT: B 418 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7933 (ttpt) REVERT: B 430 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7257 (ttp80) REVERT: B 434 ARG cc_start: 0.8328 (ttm110) cc_final: 0.7793 (ttp-110) REVERT: B 531 GLN cc_start: 0.7532 (pp30) cc_final: 0.7026 (pp30) REVERT: B 592 ASN cc_start: 0.7760 (t0) cc_final: 0.7544 (t0) REVERT: B 598 GLU cc_start: 0.7449 (tp30) cc_final: 0.7156 (tp30) REVERT: B 601 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7704 (mtp85) REVERT: B 729 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8155 (mt) REVERT: B 1101 ASP cc_start: 0.7328 (t0) cc_final: 0.6965 (t0) REVERT: B 1174 LYS cc_start: 0.8547 (mttt) cc_final: 0.8227 (mtmt) REVERT: C 154 LYS cc_start: 0.8830 (tttt) cc_final: 0.8296 (ttmm) REVERT: C 155 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.9006 (pp) REVERT: D 150 ASN cc_start: 0.8819 (m-40) cc_final: 0.8426 (t0) REVERT: D 204 ASP cc_start: 0.8469 (t0) cc_final: 0.8122 (m-30) REVERT: E 56 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8408 (mmmm) REVERT: E 61 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8293 (tm-30) REVERT: E 109 ILE cc_start: 0.8500 (mt) cc_final: 0.8232 (mm) REVERT: E 113 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7434 (mt0) REVERT: E 121 MET cc_start: 0.8020 (tpt) cc_final: 0.7537 (mpp) REVERT: G 6 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6255 (p0) REVERT: G 21 ARG cc_start: 0.7470 (ptm160) cc_final: 0.7026 (ptt90) REVERT: G 57 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7586 (mt0) REVERT: G 67 SER cc_start: 0.9193 (p) cc_final: 0.8942 (p) REVERT: G 87 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8238 (p) REVERT: H 8 ASP cc_start: 0.6991 (m-30) cc_final: 0.6693 (m-30) REVERT: H 52 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8248 (mm-40) REVERT: H 136 LYS cc_start: 0.7743 (pttm) cc_final: 0.6962 (pttm) REVERT: I 13 MET cc_start: 0.8075 (ptp) cc_final: 0.7763 (ptt) REVERT: I 18 GLU cc_start: 0.7643 (pm20) cc_final: 0.7356 (pm20) REVERT: I 34 TYR cc_start: 0.6651 (t80) cc_final: 0.6373 (t80) REVERT: I 83 ASN cc_start: 0.7859 (p0) cc_final: 0.7527 (p0) REVERT: I 94 ASP cc_start: 0.8249 (t0) cc_final: 0.7934 (t0) REVERT: K 1 MET cc_start: 0.6124 (mmm) cc_final: 0.5883 (tpt) REVERT: L 36 SER cc_start: 0.8936 (t) cc_final: 0.8586 (m) REVERT: L 47 ARG cc_start: 0.7985 (mmm-85) cc_final: 0.7778 (mmm-85) REVERT: M 119 MET cc_start: 0.6976 (ppp) cc_final: 0.6648 (ppp) REVERT: M 300 GLN cc_start: 0.7981 (tt0) cc_final: 0.7588 (mm-40) REVERT: O 94 TYR cc_start: 0.8076 (t80) cc_final: 0.7618 (t80) REVERT: O 121 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.6152 (tmm) REVERT: O 240 MET cc_start: 0.7877 (tmm) cc_final: 0.7367 (tmm) REVERT: Q 117 HIS cc_start: 0.7917 (m-70) cc_final: 0.7445 (m-70) REVERT: Q 140 HIS cc_start: 0.7542 (m-70) cc_final: 0.7102 (m-70) REVERT: Q 158 GLN cc_start: 0.8367 (pp30) cc_final: 0.7916 (pp30) REVERT: Q 348 TYR cc_start: 0.8269 (m-80) cc_final: 0.7753 (m-80) REVERT: Q 365 TYR cc_start: 0.8302 (t80) cc_final: 0.8087 (t80) REVERT: Q 375 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8395 (tp) REVERT: Q 384 PHE cc_start: 0.8149 (m-80) cc_final: 0.7597 (m-80) REVERT: Q 387 ILE cc_start: 0.8839 (mt) cc_final: 0.8562 (mp) REVERT: R 87 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8301 (tt) REVERT: R 220 HIS cc_start: 0.7038 (m90) cc_final: 0.6689 (m90) REVERT: R 270 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7237 (tmm) REVERT: V 78 PHE cc_start: 0.8606 (m-10) cc_final: 0.8181 (m-10) REVERT: W 38 LEU cc_start: 0.7611 (tp) cc_final: 0.7381 (tt) REVERT: W 63 SER cc_start: 0.8688 (t) cc_final: 0.8314 (m) REVERT: W 67 ILE cc_start: 0.9005 (mt) cc_final: 0.8703 (tp) REVERT: W 123 MET cc_start: 0.7890 (mmp) cc_final: 0.6739 (mmm) REVERT: X 134 TYR cc_start: 0.8054 (t80) cc_final: 0.7698 (t80) REVERT: X 199 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7899 (mp10) REVERT: X 227 ASP cc_start: 0.7882 (t0) cc_final: 0.7468 (t0) REVERT: X 261 LYS cc_start: 0.8505 (pptt) cc_final: 0.8035 (pptt) REVERT: X 262 MET cc_start: 0.7621 (mtt) cc_final: 0.7392 (mtp) REVERT: X 264 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7341 (pt0) REVERT: X 280 ASP cc_start: 0.7655 (m-30) cc_final: 0.7334 (m-30) outliers start: 197 outliers final: 153 residues processed: 1299 average time/residue: 0.7053 time to fit residues: 1551.7599 Evaluate side-chains 1336 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1162 time to evaluate : 6.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 106 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 423 TYR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 632 SER Chi-restraints excluded: chain 0 residue 660 ARG Chi-restraints excluded: chain 1 residue 259 ILE Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 374 ILE Chi-restraints excluded: chain 1 residue 444 LYS Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 2 residue 125 VAL Chi-restraints excluded: chain 2 residue 143 TRP Chi-restraints excluded: chain 2 residue 408 MET Chi-restraints excluded: chain 3 residue 26 VAL Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 64 ARG Chi-restraints excluded: chain 3 residue 81 GLU Chi-restraints excluded: chain 3 residue 95 THR Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 5 residue 52 HIS Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 214 LEU Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 438 VAL Chi-restraints excluded: chain 7 residue 448 THR Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 554 CYS Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1143 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1284 MET Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1066 SER Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 6 ASP Chi-restraints excluded: chain G residue 41 LYS Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 277 ILE Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain O residue 121 MET Chi-restraints excluded: chain O residue 124 THR Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain Q residue 338 ASN Chi-restraints excluded: chain Q residue 375 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain R residue 270 MET Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 183 ILE Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain W residue 197 ASN Chi-restraints excluded: chain W residue 261 HIS Chi-restraints excluded: chain W residue 273 GLN Chi-restraints excluded: chain X residue 317 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 523 optimal weight: 0.8980 chunk 843 optimal weight: 8.9990 chunk 514 optimal weight: 2.9990 chunk 400 optimal weight: 0.3980 chunk 586 optimal weight: 0.7980 chunk 884 optimal weight: 3.9990 chunk 814 optimal weight: 10.0000 chunk 704 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 chunk 544 optimal weight: 0.5980 chunk 431 optimal weight: 20.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 389 ASN ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 GLN A 427 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 592 ASN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN E 8 ASN E 113 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 HIS I 114 GLN K 52 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 331 GLN R 265 HIS R 328 HIS X 123 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 75348 Z= 0.178 Angle : 0.607 19.060 102261 Z= 0.306 Chirality : 0.042 0.245 11558 Planarity : 0.004 0.062 12672 Dihedral : 11.768 70.403 11075 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.85 % Favored : 97.14 % Rotamer: Outliers : 1.80 % Allowed : 16.99 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.38 (0.09), residues: 8748 helix: 1.16 (0.09), residues: 3520 sheet: -0.09 (0.14), residues: 1298 loop : -0.37 (0.10), residues: 3930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 2 201 HIS 0.015 0.001 HIS G 113 PHE 0.051 0.001 PHE 2 226 TYR 0.050 0.001 TYR O 224 ARG 0.024 0.000 ARG V 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17496 Ramachandran restraints generated. 8748 Oldfield, 0 Emsley, 8748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1215 time to evaluate : 6.430 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: 0 61 MET cc_start: 0.8560 (mmp) cc_final: 0.8165 (mmp) REVERT: 0 106 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7986 (mm) REVERT: 0 193 TYR cc_start: 0.8772 (t80) cc_final: 0.8361 (t80) REVERT: 0 346 MET cc_start: 0.7925 (tpp) cc_final: 0.7048 (tmm) REVERT: 0 423 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.7843 (p90) REVERT: 0 553 MET cc_start: 0.8272 (mmm) cc_final: 0.7822 (mmm) REVERT: 0 642 MET cc_start: 0.8717 (mmm) cc_final: 0.8420 (mmm) REVERT: 0 649 ARG cc_start: 0.6927 (mmp-170) cc_final: 0.6525 (mmp-170) REVERT: 0 664 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8307 (tm-30) REVERT: 0 668 ARG cc_start: 0.7789 (mmt90) cc_final: 0.7563 (mmp80) REVERT: 1 88 MET cc_start: 0.7282 (mmp) cc_final: 0.6951 (mmp) REVERT: 1 318 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: 1 328 MET cc_start: 0.8148 (ppp) cc_final: 0.7851 (ppp) REVERT: 1 469 MET cc_start: 0.8345 (ttt) cc_final: 0.7849 (mmm) REVERT: 1 477 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8715 (mmt) REVERT: 2 216 MET cc_start: 0.6811 (ppp) cc_final: 0.6414 (ppp) REVERT: 2 365 HIS cc_start: 0.8485 (t-90) cc_final: 0.8173 (t70) REVERT: 3 22 LEU cc_start: 0.8887 (mt) cc_final: 0.8592 (pp) REVERT: 3 64 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6674 (mmt90) REVERT: 3 89 PHE cc_start: 0.8274 (m-80) cc_final: 0.7688 (m-80) REVERT: 4 37 TRP cc_start: 0.8628 (m100) cc_final: 0.8162 (m100) REVERT: 4 114 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.5888 (mmt) REVERT: 4 125 LEU cc_start: 0.9663 (tp) cc_final: 0.9372 (mm) REVERT: 4 130 TYR cc_start: 0.8860 (t80) cc_final: 0.8586 (t80) REVERT: 4 153 MET cc_start: 0.8738 (mtp) cc_final: 0.8512 (mtt) REVERT: 4 159 TYR cc_start: 0.8947 (t80) cc_final: 0.8286 (t80) REVERT: 4 206 MET cc_start: 0.8994 (ppp) cc_final: 0.8204 (ppp) REVERT: 4 225 GLN cc_start: 0.8955 (mt0) cc_final: 0.8413 (mt0) REVERT: 4 226 GLN cc_start: 0.8890 (mm110) cc_final: 0.8341 (mm110) REVERT: 4 235 TYR cc_start: 0.8227 (t80) cc_final: 0.7991 (t80) REVERT: 4 247 TYR cc_start: 0.8495 (m-80) cc_final: 0.8284 (m-10) REVERT: 5 22 GLN cc_start: 0.8733 (mp10) cc_final: 0.8460 (mp10) REVERT: 5 63 TYR cc_start: 0.7979 (t80) cc_final: 0.7753 (t80) REVERT: 6 299 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7993 (mp0) REVERT: 6 303 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8031 (mt-10) REVERT: 6 384 MET cc_start: 0.8556 (pmm) cc_final: 0.7858 (pmm) REVERT: 7 445 MET cc_start: 0.5020 (mpp) cc_final: 0.4759 (mpp) REVERT: A 65 LEU cc_start: 0.8419 (mt) cc_final: 0.8144 (mm) REVERT: A 109 HIS cc_start: 0.8661 (t-90) cc_final: 0.8285 (t-90) REVERT: A 112 LYS cc_start: 0.8170 (tttp) cc_final: 0.7861 (tttt) REVERT: A 186 LYS cc_start: 0.8323 (tppt) cc_final: 0.7984 (tptt) REVERT: A 268 ASP cc_start: 0.7090 (m-30) cc_final: 0.6772 (m-30) REVERT: A 453 MET cc_start: 0.8355 (mpp) cc_final: 0.8000 (mpp) REVERT: A 526 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7950 (t70) REVERT: A 708 MET cc_start: 0.8157 (mtp) cc_final: 0.7927 (ptp) REVERT: A 801 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7403 (tm-30) REVERT: A 991 LYS cc_start: 0.8423 (mmmm) cc_final: 0.8078 (mmmm) REVERT: A 992 ASP cc_start: 0.7610 (p0) cc_final: 0.7375 (p0) REVERT: A 1003 LYS cc_start: 0.7937 (mmtm) cc_final: 0.7723 (mmtp) REVERT: A 1033 GLN cc_start: 0.7781 (tt0) cc_final: 0.7495 (tt0) REVERT: A 1043 ASP cc_start: 0.7792 (t70) cc_final: 0.7549 (t0) REVERT: A 1054 LEU cc_start: 0.9133 (mt) cc_final: 0.8885 (mt) REVERT: A 1135 ARG cc_start: 0.9029 (tmm-80) cc_final: 0.8365 (ttp80) REVERT: A 1284 MET cc_start: 0.7207 (mtp) cc_final: 0.6232 (mtm) REVERT: A 1285 MET cc_start: 0.7066 (mmm) cc_final: 0.6762 (mmm) REVERT: A 1287 TYR cc_start: 0.7628 (m-80) cc_final: 0.7310 (m-80) REVERT: A 1290 LYS cc_start: 0.8236 (mttm) cc_final: 0.7809 (mtpp) REVERT: A 1328 TYR cc_start: 0.7539 (t80) cc_final: 0.7040 (t80) REVERT: A 1393 ASN cc_start: 0.8201 (p0) cc_final: 0.7797 (p0) REVERT: B 72 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7675 (pp20) REVERT: B 94 LYS cc_start: 0.7597 (mmpt) cc_final: 0.7370 (mmmt) REVERT: B 216 GLU cc_start: 0.7427 (tt0) cc_final: 0.7214 (tt0) REVERT: B 226 PHE cc_start: 0.8108 (m-10) cc_final: 0.7808 (m-10) REVERT: B 267 ARG cc_start: 0.8029 (mtm180) cc_final: 0.7647 (mtm-85) REVERT: B 277 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8391 (ttpt) REVERT: B 320 ASP cc_start: 0.8077 (t70) cc_final: 0.7861 (t0) REVERT: B 337 ARG cc_start: 0.8018 (mmt180) cc_final: 0.7797 (mmt180) REVERT: B 358 LYS cc_start: 0.8306 (mtmt) cc_final: 0.7766 (mtmt) REVERT: B 430 ARG cc_start: 0.7563 (ttm110) cc_final: 0.7167 (ttp80) REVERT: B 434 ARG cc_start: 0.8310 (ttm110) cc_final: 0.7817 (ttp-110) REVERT: B 592 ASN cc_start: 0.7682 (t0) cc_final: 0.7461 (t0) REVERT: B 598 GLU cc_start: 0.7426 (tp30) cc_final: 0.7137 (tp30) REVERT: B 729 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.7998 (mt) REVERT: B 1101 ASP cc_start: 0.7303 (t0) cc_final: 0.6946 (t0) REVERT: B 1174 LYS cc_start: 0.8415 (mttt) cc_final: 0.8109 (mtmt) REVERT: C 154 LYS cc_start: 0.8776 (tttt) cc_final: 0.8212 (ttmm) REVERT: D 150 ASN cc_start: 0.8725 (m-40) cc_final: 0.8298 (t0) REVERT: D 204 ASP cc_start: 0.8346 (t0) cc_final: 0.8013 (m-30) REVERT: E 56 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8321 (mmmm) REVERT: E 61 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8147 (tm-30) REVERT: E 109 ILE cc_start: 0.8461 (mt) cc_final: 0.8178 (mm) REVERT: E 121 MET cc_start: 0.8036 (tpt) cc_final: 0.7512 (mpp) REVERT: G 21 ARG cc_start: 0.7480 (ptm160) cc_final: 0.7018 (ptt90) REVERT: G 87 VAL cc_start: 0.8373 (m) cc_final: 0.8167 (p) REVERT: H 8 ASP cc_start: 0.6922 (m-30) cc_final: 0.6521 (m-30) REVERT: I 18 GLU cc_start: 0.7687 (pm20) cc_final: 0.7377 (pm20) REVERT: I 83 ASN cc_start: 0.7574 (p0) cc_final: 0.7304 (p0) REVERT: I 94 ASP cc_start: 0.8100 (t0) cc_final: 0.7749 (t0) REVERT: L 36 SER cc_start: 0.8874 (t) cc_final: 0.8552 (m) REVERT: L 47 ARG cc_start: 0.7891 (mmm-85) cc_final: 0.7379 (mmm-85) REVERT: M 119 MET cc_start: 0.6896 (ppp) cc_final: 0.6548 (ppp) REVERT: M 208 ASN cc_start: 0.8980 (t0) cc_final: 0.8545 (m110) REVERT: M 300 GLN cc_start: 0.7887 (tt0) cc_final: 0.7374 (tm-30) REVERT: O 94 TYR cc_start: 0.8030 (t80) cc_final: 0.7612 (t80) REVERT: O 240 MET cc_start: 0.7791 (tmm) cc_final: 0.7270 (tmm) REVERT: Q 117 HIS cc_start: 0.7841 (m-70) cc_final: 0.7306 (m-70) REVERT: Q 140 HIS cc_start: 0.7437 (m-70) cc_final: 0.6992 (m-70) REVERT: Q 348 TYR cc_start: 0.8235 (m-80) cc_final: 0.7710 (m-80) REVERT: Q 375 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8364 (tp) REVERT: Q 387 ILE cc_start: 0.8857 (mt) cc_final: 0.8568 (mp) REVERT: R 87 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8317 (tt) REVERT: R 220 HIS cc_start: 0.6977 (m90) cc_final: 0.6643 (m90) REVERT: R 270 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7100 (tmm) REVERT: U 258 TRP cc_start: 0.8636 (m100) cc_final: 0.7793 (m-10) REVERT: V 78 PHE cc_start: 0.8393 (m-10) cc_final: 0.7300 (m-10) REVERT: W 63 SER cc_start: 0.8653 (t) cc_final: 0.8280 (m) REVERT: W 67 ILE cc_start: 0.9012 (mt) cc_final: 0.8717 (tp) REVERT: W 123 MET cc_start: 0.7706 (mmp) cc_final: 0.7411 (mmm) REVERT: X 134 TYR cc_start: 0.8063 (t80) cc_final: 0.7763 (t80) REVERT: X 199 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7782 (mp10) REVERT: X 222 ASN cc_start: 0.8896 (t0) cc_final: 0.8677 (t0) REVERT: X 227 ASP cc_start: 0.7838 (t0) cc_final: 0.7447 (t0) REVERT: X 261 LYS cc_start: 0.8506 (pptt) cc_final: 0.8045 (pptt) REVERT: X 277 LYS cc_start: 0.8256 (mttt) cc_final: 0.7960 (mmmm) REVERT: X 280 ASP cc_start: 0.7534 (m-30) cc_final: 0.7211 (m-30) outliers start: 143 outliers final: 112 residues processed: 1289 average time/residue: 0.7235 time to fit residues: 1589.7528 Evaluate side-chains 1307 residues out of total 7940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1182 time to evaluate : 6.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 50 VAL Chi-restraints excluded: chain 0 residue 106 LEU Chi-restraints excluded: chain 0 residue 113 ASN Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 324 ASN Chi-restraints excluded: chain 0 residue 423 TYR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 477 THR Chi-restraints excluded: chain 0 residue 525 MET Chi-restraints excluded: chain 0 residue 729 ASP Chi-restraints excluded: chain 1 residue 259 ILE Chi-restraints excluded: chain 1 residue 318 ASP Chi-restraints excluded: chain 1 residue 424 LEU Chi-restraints excluded: chain 1 residue 444 LYS Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 2 residue 125 VAL Chi-restraints excluded: chain 2 residue 143 TRP Chi-restraints excluded: chain 2 residue 408 MET Chi-restraints excluded: chain 3 residue 26 VAL Chi-restraints excluded: chain 3 residue 62 ILE Chi-restraints excluded: chain 3 residue 64 ARG Chi-restraints excluded: chain 3 residue 81 GLU Chi-restraints excluded: chain 4 residue 57 LEU Chi-restraints excluded: chain 4 residue 114 MET Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 214 LEU Chi-restraints excluded: chain 6 residue 240 SER Chi-restraints excluded: chain 6 residue 280 THR Chi-restraints excluded: chain 6 residue 438 VAL Chi-restraints excluded: chain 7 residue 501 VAL Chi-restraints excluded: chain 7 residue 554 CYS Chi-restraints excluded: chain 7 residue 637 MET Chi-restraints excluded: chain 7 residue 745 ILE Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 729 ILE Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 915 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 956 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1177 HIS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 162 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 84 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain O residue 153 THR Chi-restraints excluded: chain O residue 155 PHE Chi-restraints excluded: chain O residue 189 LEU Chi-restraints excluded: chain Q residue 338 ASN Chi-restraints excluded: chain Q residue 375 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 ASP Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 106 LEU Chi-restraints excluded: chain R residue 128 VAL Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain R residue 270 MET Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 83 CYS Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 98 ILE Chi-restraints excluded: chain W residue 183 ILE Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain W residue 197 ASN Chi-restraints excluded: chain W residue 273 GLN Chi-restraints excluded: chain X residue 123 HIS Chi-restraints excluded: chain X residue 317 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 559 optimal weight: 1.9990 chunk 750 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 649 optimal weight: 0.0370 chunk 104 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 705 optimal weight: 5.9990 chunk 295 optimal weight: 30.0000 chunk 724 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 129 optimal weight: 9.9990 overall best weight: 1.3064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 223 HIS ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN E 136 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 GLN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 225 GLN U 19 ASN X 123 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.191942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.127489 restraints weight = 120891.240| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 3.36 r_work: 0.2988 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 75348 Z= 0.239 Angle : 0.624 16.269 102261 Z= 0.313 Chirality : 0.042 0.265 11558 Planarity : 0.004 0.060 12672 Dihedral : 11.763 63.922 11075 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.78 % Allowed : 17.46 % Favored : 80.76 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.51 % 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: 0.38 (0.09), residues: 8748 helix: 1.17 (0.09), residues: 3521 sheet: -0.11 (0.14), residues: 1305 loop : -0.37 (0.10), residues: 3922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP 2 201 HIS 0.022 0.001 HIS X 123 PHE 0.053 0.001 PHE 2 226 TYR 0.057 0.001 TYR O 224 ARG 0.012 0.000 ARG 0 258 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24240.82 seconds wall clock time: 422 minutes 24.01 seconds (25344.01 seconds total)