Starting phenix.real_space_refine on Tue Mar 12 00:08:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceo_16611/03_2024/8ceo_16611_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceo_16611/03_2024/8ceo_16611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceo_16611/03_2024/8ceo_16611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceo_16611/03_2024/8ceo_16611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceo_16611/03_2024/8ceo_16611_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ceo_16611/03_2024/8ceo_16611_updated.pdb" } resolution = 3.6 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 416 5.49 5 Mg 1 5.21 5 S 512 5.16 5 C 70708 2.51 5 N 19680 2.21 5 O 22246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "7 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "L GLU 68": "OE1" <-> "OE2" Residue "O PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 186": "OE1" <-> "OE2" Residue "i GLU 193": "OE1" <-> "OE2" Residue "l PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 46": "OE1" <-> "OE2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r GLU 94": "OE1" <-> "OE2" Residue "s GLU 53": "OE1" <-> "OE2" Residue "s GLU 74": "OE1" <-> "OE2" Residue "t GLU 64": "OE1" <-> "OE2" Residue "v GLU 94": "OE1" <-> "OE2" Residue "x GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 113584 Number of models: 1 Model: "" Number of chains: 66 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4214 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 503} Chain breaks: 6 Chain: "2" Number of atoms: 3647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3647 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 17, 'TRANS': 434} Chain breaks: 1 Chain: "3" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2338 Classifications: {'peptide': 302} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 288} Chain breaks: 1 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3019 Classifications: {'peptide': 383} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 361} Chain breaks: 1 Chain: "7" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4954 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 24, 'TRANS': 590} Chain breaks: 2 Chain: "A" Number of atoms: 11815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1508, 11815 Classifications: {'peptide': 1508} Link IDs: {'PCIS': 3, 'PTRANS': 87, 'TRANS': 1417} Chain breaks: 6 Chain: "B" Number of atoms: 9404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9404 Classifications: {'peptide': 1180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "C" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2092 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1343 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 983 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain breaks: 1 Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2379 Classifications: {'peptide': 310} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 297} Chain breaks: 1 Chain: "N" Number of atoms: 4263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 4263 Classifications: {'DNA': 209} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 208} Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1422 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 172} Chain: "Q" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1871 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 211} Chain breaks: 2 Chain: "R" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2230 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain breaks: 1 Chain: "T" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 4300 Classifications: {'DNA': 209} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 208} Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 885 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain breaks: 2 Chain: "V" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'TRANS': 103} Chain breaks: 1 Chain: "W" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2473 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 3 Chain: "X" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1708 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain breaks: 1 Chain: "a" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1495 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 166} Chain breaks: 3 Chain: "b" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1407 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 8, 'TRANS': 163} Chain breaks: 1 Chain: "c" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 902 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "d" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 4063 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 19, 'TRANS': 481} Chain breaks: 9 Chain: "e" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2017 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Chain breaks: 1 Chain: "f" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1578 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 6, 'TRANS': 199} Chain breaks: 1 Chain: "g" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 815 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Chain: "h" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1394 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "i" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1512 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 13, 'TRANS': 167} Chain breaks: 2 Chain: "j" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 852 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain breaks: 1 Chain: "k" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1259 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain: "l" Number of atoms: 4385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4385 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 22, 'TRANS': 512} Chain breaks: 6 Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1068 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "n" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1095 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "o" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 922 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 101} Chain: "p" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1863 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 1 Chain: "r" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "s" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "t" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "u" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "v" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "x" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "y" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 938 SG CYS 0 115 72.952 104.003 184.727 1.00110.03 S ATOM 1265 SG CYS 0 156 68.052 103.807 189.217 1.00113.36 S ATOM 1080 SG CYS 0 133 70.219 109.433 186.966 1.00109.48 S ATOM 1566 SG CYS 0 191 73.175 106.120 191.072 1.00102.06 S ATOM 13991 SG CYS 3 13 61.190 136.730 141.454 1.00151.85 S ATOM 14012 SG CYS 3 16 62.248 136.337 137.804 1.00153.88 S ATOM 14207 SG CYS 3 39 63.487 139.138 139.782 1.00145.83 S ATOM 14228 SG CYS 3 42 60.038 139.387 138.642 1.00146.37 S ATOM 14160 SG CYS 3 34 53.003 139.955 151.068 1.00124.02 S ATOM 14318 SG CYS 3 54 52.704 140.530 147.107 1.00134.85 S ATOM 14356 SG CYS 3 59 49.621 140.473 149.395 1.00131.52 S ATOM 17084 SG CYS 4 289 117.922 60.994 202.806 1.00110.12 S ATOM 17103 SG CYS 4 292 121.321 61.487 204.373 1.00117.13 S ATOM 17195 SG CYS 4 305 118.648 59.878 206.243 1.00121.28 S ATOM 17213 SG CYS 4 308 118.388 63.816 205.330 1.00123.90 S ATOM 20040 SG CYS 6 349 119.602 43.895 188.825 1.00104.11 S ATOM 20061 SG CYS 6 352 117.348 41.670 186.663 1.00105.05 S ATOM 20140 SG CYS 6 363 117.954 45.189 185.671 1.00104.66 S ATOM 20159 SG CYS 6 366 115.810 44.607 188.617 1.00109.25 S ATOM 20461 SG CYS 6 403 149.874 75.754 200.547 1.00119.60 S ATOM 20484 SG CYS 6 406 151.353 74.874 196.909 1.00113.06 S ATOM 20743 SG CYS 6 437 149.096 77.658 197.259 1.00122.89 S ATOM 20764 SG CYS 6 440 147.685 74.262 197.983 1.00116.79 S ATOM 20676 SG CYS 6 429 139.511 75.070 206.979 1.00121.79 S ATOM 20699 SG CYS 6 432 142.527 73.379 208.558 1.00111.20 S ATOM 20857 SG CYS 6 451 141.559 72.350 205.180 1.00107.45 S ATOM 20874 SG CYS 6 454 139.156 71.507 208.030 1.00108.83 S ATOM 19939 SG CYS 6 336 123.252 44.785 175.502 1.00122.08 S ATOM 19951 SG CYS 6 338 122.278 47.530 178.064 1.00122.63 S ATOM 20099 SG CYS 6 357 125.806 47.352 176.692 1.00115.20 S ATOM 26686 SG CYS A 107 98.352 129.634 114.540 1.00158.21 S ATOM 26710 SG CYS A 110 97.896 131.326 117.934 1.00179.01 S ATOM 27015 SG CYS A 148 101.353 130.281 116.896 1.00186.59 S ATOM 27153 SG CYS A 167 98.778 127.648 117.696 1.00189.28 S ATOM 26381 SG CYS A 67 61.975 156.141 100.106 1.00109.63 S ATOM 26403 SG CYS A 70 62.709 159.810 100.780 1.00102.81 S ATOM 26456 SG CYS A 77 64.679 158.008 98.095 1.00 92.55 S ATOM 46591 SG CYS B1163 75.266 159.905 110.959 1.00 89.18 S ATOM 46609 SG CYS B1166 76.650 156.767 109.688 1.00 89.93 S ATOM 46734 SG CYS B1182 72.820 157.234 110.604 1.00103.11 S ATOM 46753 SG CYS B1185 75.600 156.696 113.219 1.00104.45 S ATOM 47738 SG CYS C 86 47.482 195.396 47.090 1.00 85.27 S ATOM 47755 SG CYS C 88 46.943 191.781 48.279 1.00 86.41 S ATOM 47788 SG CYS C 92 45.559 193.110 44.992 1.00 71.41 S ATOM 47811 SG CYS C 95 49.349 192.375 45.558 1.00 70.88 S ATOM 55767 SG CYS I 7 130.063 103.035 58.181 1.00 91.20 S ATOM 55792 SG CYS I 10 126.692 103.423 59.977 1.00 89.94 S ATOM 55958 SG CYS I 29 129.832 103.941 61.970 1.00 94.06 S ATOM 55982 SG CYS I 32 129.085 100.488 60.613 1.00 97.11 S ATOM 56309 SG CYS I 75 134.156 136.414 29.665 1.00119.16 S ATOM 56331 SG CYS I 78 133.844 133.593 26.730 1.00117.36 S ATOM 56547 SG CYS I 103 130.744 135.318 28.510 1.00108.25 S ATOM 56567 SG CYS I 106 133.090 132.745 29.832 1.00106.47 S ATOM 56712 SG CYS J 7 76.209 181.377 34.094 1.00 47.24 S ATOM 56735 SG CYS J 10 75.629 184.990 33.009 1.00 51.28 S ATOM 57015 SG CYS J 45 79.223 183.289 32.887 1.00 50.38 S ATOM 57021 SG CYS J 46 76.413 182.813 30.440 1.00 49.99 S ATOM 58201 SG CYS L 31 50.255 147.141 43.771 1.00 78.73 S ATOM 58221 SG CYS L 34 47.958 148.555 41.149 1.00 83.13 S ATOM 58325 SG CYS L 48 46.755 145.826 43.361 1.00 84.86 S ATOM 58348 SG CYS L 51 49.345 145.123 40.540 1.00 83.96 S ATOM 58592 SG CYS M 24 49.459 176.321 89.593 1.00 98.06 S ATOM 58614 SG CYS M 27 46.988 178.167 87.397 1.00104.06 S ATOM 58758 SG CYS M 45 49.223 175.453 85.863 1.00 87.16 S ATOM 58777 SG CYS M 48 50.686 178.754 87.020 1.00 80.65 S ATOM 77685 SG CYS W 124 48.097 154.882 109.298 1.00170.63 S ATOM 77706 SG CYS W 127 51.420 153.624 108.219 1.00172.84 S ATOM 77891 SG CYS W 149 50.833 157.427 108.521 1.00157.49 S ATOM 77911 SG CYS W 152 49.269 155.449 105.692 1.00161.20 S Time building chain proxies: 40.42, per 1000 atoms: 0.36 Number of scatterers: 113584 At special positions: 0 Unit cell: (295.05, 294, 258.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 512 16.00 P 416 15.00 Mg 1 11.99 O 22246 8.00 N 19680 7.00 C 70708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 32.94 Conformation dependent library (CDL) restraints added in 12.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 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=" NE2 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " 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 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 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 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " 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 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " Number of angles added : 93 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24954 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 481 helices and 101 sheets defined 52.5% alpha, 12.4% beta 193 base pairs and 368 stacking pairs defined. Time for finding SS restraints: 68.93 Creating SS restraints... Processing helix chain '0' and resid 18 through 35 Processing helix chain '0' and resid 47 through 63 Processing helix chain '0' and resid 75 through 98 Processing helix chain '0' and resid 110 through 115 removed outlier: 3.545A pdb=" N LEU 0 114 " --> pdb=" O SER 0 110 " (cutoff:3.500A) Processing helix chain '0' and resid 125 through 138 Processing helix chain '0' and resid 139 through 149 Proline residue: 0 149 - end of helix Processing helix chain '0' and resid 156 through 166 removed outlier: 3.877A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE 0 165 " --> pdb=" O ASN 0 161 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLU 0 166 " --> pdb=" O LEU 0 162 " (cutoff:3.500A) Processing helix chain '0' and resid 177 through 189 Processing helix chain '0' and resid 191 through 200 removed outlier: 3.509A pdb=" N ILE 0 200 " --> pdb=" O VAL 0 196 " (cutoff:3.500A) Processing helix chain '0' and resid 209 through 214 removed outlier: 3.925A pdb=" N LEU 0 213 " --> pdb=" O SER 0 209 " (cutoff:3.500A) Processing helix chain '0' and resid 218 through 227 removed outlier: 3.873A pdb=" N VAL 0 222 " --> pdb=" O ILE 0 218 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN 0 224 " --> pdb=" O GLU 0 220 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU 0 225 " --> pdb=" O ARG 0 221 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N SER 0 227 " --> pdb=" O SER 0 223 " (cutoff:3.500A) Processing helix chain '0' and resid 239 through 249 removed outlier: 3.612A pdb=" N VAL 0 243 " --> pdb=" O ASN 0 239 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 253 through 278 Processing helix chain '0' and resid 279 through 292 removed outlier: 4.376A pdb=" N GLU 0 285 " --> pdb=" O LYS 0 281 " (cutoff:3.500A) Processing helix chain '0' and resid 294 through 299 Processing helix chain '0' and resid 312 through 317 removed outlier: 5.860A pdb=" N LEU 0 317 " --> pdb=" O PRO 0 313 " (cutoff:3.500A) Processing helix chain '0' and resid 322 through 327 removed outlier: 6.617A pdb=" N ARG 0 326 " --> pdb=" O PRO 0 322 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG 0 327 " --> pdb=" O GLY 0 323 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 322 through 327' Processing helix chain '0' and resid 328 through 348 removed outlier: 5.352A pdb=" N VAL 0 348 " --> pdb=" O THR 0 344 " (cutoff:3.500A) Processing helix chain '0' and resid 355 through 367 Processing helix chain '0' and resid 370 through 389 removed outlier: 3.553A pdb=" N LEU 0 374 " --> pdb=" O GLU 0 370 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE 0 376 " --> pdb=" O LYS 0 372 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS 0 377 " --> pdb=" O PRO 0 373 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 396 through 412 Processing helix chain '0' and resid 441 through 454 removed outlier: 4.817A pdb=" N ALA 0 445 " --> pdb=" O ASP 0 441 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE 0 446 " --> pdb=" O ALA 0 442 " (cutoff:3.500A) Proline residue: 0 448 - end of helix removed outlier: 4.801A pdb=" N SER 0 454 " --> pdb=" O PHE 0 450 " (cutoff:3.500A) Processing helix chain '0' and resid 465 through 474 removed outlier: 4.494A pdb=" N TYR 0 469 " --> pdb=" O PRO 0 465 " (cutoff:3.500A) Proline residue: 0 470 - end of helix removed outlier: 4.330A pdb=" N ASN 0 474 " --> pdb=" O PRO 0 470 " (cutoff:3.500A) Processing helix chain '0' and resid 515 through 533 Processing helix chain '0' and resid 543 through 558 Processing helix chain '0' and resid 559 through 567 removed outlier: 3.782A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 575 through 593 removed outlier: 3.563A pdb=" N GLY 0 593 " --> pdb=" O ALA 0 589 " (cutoff:3.500A) Processing helix chain '0' and resid 604 through 610 removed outlier: 3.826A pdb=" N GLU 0 608 " --> pdb=" O GLY 0 604 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N GLY 0 609 " --> pdb=" O LYS 0 605 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE 0 610 " --> pdb=" O VAL 0 606 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 604 through 610' Processing helix chain '0' and resid 632 through 646 Processing helix chain '0' and resid 649 through 670 removed outlier: 3.967A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL 0 669 " --> pdb=" O CYS 0 665 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU 0 670 " --> pdb=" O LEU 0 666 " (cutoff:3.500A) Processing helix chain '0' and resid 685 through 690 removed outlier: 4.120A pdb=" N LYS 0 689 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG 0 690 " --> pdb=" O PHE 0 686 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 685 through 690' Processing helix chain '0' and resid 694 through 702 removed outlier: 5.065A pdb=" N SER 0 702 " --> pdb=" O ALA 0 698 " (cutoff:3.500A) Processing helix chain '0' and resid 709 through 726 removed outlier: 3.580A pdb=" N ALA 0 713 " --> pdb=" O SER 0 709 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN 0 726 " --> pdb=" O ARG 0 722 " (cutoff:3.500A) Processing helix chain '0' and resid 729 through 734 Processing helix chain '0' and resid 740 through 752 Processing helix chain '1' and resid 93 through 121 Processing helix chain '1' and resid 170 through 177 Processing helix chain '1' and resid 178 through 189 removed outlier: 5.045A pdb=" N LYS 1 189 " --> pdb=" O LEU 1 185 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 196 removed outlier: 4.287A pdb=" N VAL 1 194 " --> pdb=" O VAL 1 190 " (cutoff:3.500A) Processing helix chain '1' and resid 205 through 214 removed outlier: 3.868A pdb=" N THR 1 212 " --> pdb=" O GLU 1 208 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG 1 213 " --> pdb=" O PHE 1 209 " (cutoff:3.500A) Processing helix chain '1' and resid 215 through 225 removed outlier: 3.816A pdb=" N THR 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 232 through 238 removed outlier: 5.192A pdb=" N LYS 1 238 " --> pdb=" O LEU 1 234 " (cutoff:3.500A) Processing helix chain '1' and resid 252 through 263 Processing helix chain '1' and resid 264 through 276 removed outlier: 3.665A pdb=" N ASP 1 272 " --> pdb=" O LYS 1 268 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN 1 273 " --> pdb=" O ALA 1 269 " (cutoff:3.500A) Proline residue: 1 275 - end of helix Processing helix chain '1' and resid 279 through 290 removed outlier: 3.584A pdb=" N SER 1 289 " --> pdb=" O ALA 1 285 " (cutoff:3.500A) Processing helix chain '1' and resid 291 through 298 Processing helix chain '1' and resid 309 through 330 removed outlier: 3.921A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR 1 314 " --> pdb=" O ILE 1 310 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU 1 315 " --> pdb=" O ILE 1 311 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR 1 316 " --> pdb=" O ASP 1 312 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU 1 317 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP 1 327 " --> pdb=" O ARG 1 323 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET 1 328 " --> pdb=" O LYS 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 347 removed outlier: 3.798A pdb=" N ILE 1 343 " --> pdb=" O LEU 1 339 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP 1 346 " --> pdb=" O ASN 1 342 " (cutoff:3.500A) Proline residue: 1 347 - end of helix Processing helix chain '1' and resid 355 through 360 Proline residue: 1 360 - end of helix Processing helix chain '1' and resid 370 through 391 removed outlier: 3.688A pdb=" N ILE 1 374 " --> pdb=" O GLY 1 370 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU 1 375 " --> pdb=" O THR 1 371 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU 1 389 " --> pdb=" O MET 1 385 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS 1 390 " --> pdb=" O ILE 1 386 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASN 1 391 " --> pdb=" O MET 1 387 " (cutoff:3.500A) Processing helix chain '1' and resid 413 through 420 removed outlier: 3.561A pdb=" N ASN 1 417 " --> pdb=" O ASN 1 413 " (cutoff:3.500A) Processing helix chain '1' and resid 421 through 426 removed outlier: 3.525A pdb=" N ASN 1 425 " --> pdb=" O ILE 1 421 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLU 1 426 " --> pdb=" O ASP 1 422 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 421 through 426' Processing helix chain '1' and resid 465 through 483 removed outlier: 4.112A pdb=" N LYS 1 483 " --> pdb=" O ASN 1 479 " (cutoff:3.500A) Processing helix chain '1' and resid 492 through 517 removed outlier: 6.332A pdb=" N SER 1 496 " --> pdb=" O ASN 1 492 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN 1 497 " --> pdb=" O ASN 1 493 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS 1 498 " --> pdb=" O GLU 1 494 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N HIS 1 516 " --> pdb=" O LYS 1 512 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN 1 517 " --> pdb=" O GLN 1 513 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 571 removed outlier: 4.286A pdb=" N GLY 1 571 " --> pdb=" O HIS 1 567 " (cutoff:3.500A) Processing helix chain '1' and resid 572 through 604 removed outlier: 4.069A pdb=" N ALA 1 576 " --> pdb=" O GLU 1 572 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N SER 1 577 " --> pdb=" O GLN 1 573 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR 1 578 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) Processing helix chain '1' and resid 605 through 617 removed outlier: 6.362A pdb=" N SER 1 609 " --> pdb=" O GLY 1 605 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASN 1 610 " --> pdb=" O GLU 1 606 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N THR 1 611 " --> pdb=" O SER 1 607 " (cutoff:3.500A) Processing helix chain '1' and resid 618 through 639 Processing helix chain '1' and resid 485 through 490 removed outlier: 3.515A pdb=" N VAL 1 489 " --> pdb=" O LEU 1 486 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL 1 490 " --> pdb=" O ASN 1 487 " (cutoff:3.500A) Processing helix chain '1' and resid 197 through 203 Processing helix chain '2' and resid 5 through 18 removed outlier: 3.903A pdb=" N SER 2 9 " --> pdb=" O SER 2 5 " (cutoff:3.500A) Proline residue: 2 18 - end of helix Processing helix chain '2' and resid 19 through 28 removed outlier: 4.106A pdb=" N THR 2 27 " --> pdb=" O ASN 2 23 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N SER 2 28 " --> pdb=" O ARG 2 24 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 39 removed outlier: 3.702A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU 2 39 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 52 removed outlier: 4.498A pdb=" N PHE 2 52 " --> pdb=" O MET 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 58 through 67 removed outlier: 3.795A pdb=" N LEU 2 62 " --> pdb=" O PRO 2 58 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASN 2 67 " --> pdb=" O ASP 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 85 Processing helix chain '2' and resid 101 through 114 Processing helix chain '2' and resid 134 through 152 Processing helix chain '2' and resid 160 through 170 Processing helix chain '2' and resid 185 through 194 removed outlier: 3.727A pdb=" N LEU 2 192 " --> pdb=" O GLY 2 188 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU 2 193 " --> pdb=" O PHE 2 189 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN 2 194 " --> pdb=" O GLN 2 190 " (cutoff:3.500A) Processing helix chain '2' and resid 195 through 212 removed outlier: 5.511A pdb=" N GLU 2 212 " --> pdb=" O LEU 2 208 " (cutoff:3.500A) Processing helix chain '2' and resid 217 through 232 removed outlier: 5.715A pdb=" N GLU 2 232 " --> pdb=" O LEU 2 228 " (cutoff:3.500A) Processing helix chain '2' and resid 243 through 257 Processing helix chain '2' and resid 272 through 280 removed outlier: 3.833A pdb=" N LEU 2 276 " --> pdb=" O THR 2 272 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER 2 280 " --> pdb=" O LEU 2 276 " (cutoff:3.500A) Processing helix chain '2' and resid 353 through 364 removed outlier: 3.862A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE 2 363 " --> pdb=" O VAL 2 359 " (cutoff:3.500A) Processing helix chain '2' and resid 379 through 390 removed outlier: 3.538A pdb=" N GLY 2 390 " --> pdb=" O ALA 2 386 " (cutoff:3.500A) Processing helix chain '2' and resid 392 through 404 Processing helix chain '2' and resid 405 through 424 removed outlier: 3.581A pdb=" N LEU 2 422 " --> pdb=" O LYS 2 418 " (cutoff:3.500A) Proline residue: 2 424 - end of helix Processing helix chain '2' and resid 434 through 450 removed outlier: 3.532A pdb=" N VAL 2 438 " --> pdb=" O PRO 2 434 " (cutoff:3.500A) Processing helix chain '2' and resid 464 through 479 removed outlier: 3.702A pdb=" N TYR 2 468 " --> pdb=" O THR 2 464 " (cutoff:3.500A) Processing helix chain '2' and resid 494 through 507 removed outlier: 4.539A pdb=" N SER 2 499 " --> pdb=" O LYS 2 495 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLN 2 500 " --> pdb=" O GLU 2 496 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL 2 501 " --> pdb=" O GLY 2 497 " (cutoff:3.500A) Processing helix chain '3' and resid 39 through 50 removed outlier: 4.140A pdb=" N SER 3 48 " --> pdb=" O ASP 3 44 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N LEU 3 49 " --> pdb=" O ARG 3 45 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY 3 50 " --> pdb=" O ILE 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 75 through 93 removed outlier: 3.509A pdb=" N ASN 3 90 " --> pdb=" O LYS 3 86 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL 3 91 " --> pdb=" O ARG 3 87 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN 3 93 " --> pdb=" O PHE 3 89 " (cutoff:3.500A) Processing helix chain '3' and resid 95 through 100 Processing helix chain '3' and resid 102 through 123 Processing helix chain '3' and resid 125 through 139 removed outlier: 3.989A pdb=" N LEU 3 139 " --> pdb=" O THR 3 135 " (cutoff:3.500A) Processing helix chain '4' and resid 33 through 45 removed outlier: 4.632A pdb=" N ASN 4 45 " --> pdb=" O ASP 4 41 " (cutoff:3.500A) Processing helix chain '4' and resid 48 through 69 removed outlier: 3.891A pdb=" N LYS 4 52 " --> pdb=" O GLY 4 48 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN 4 68 " --> pdb=" O HIS 4 64 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N SER 4 69 " --> pdb=" O LEU 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 90 through 97 Processing helix chain '4' and resid 115 through 140 removed outlier: 3.842A pdb=" N VAL 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) Processing helix chain '4' and resid 148 through 167 Processing helix chain '4' and resid 189 through 207 removed outlier: 4.337A pdb=" N TYR 4 193 " --> pdb=" O GLU 4 189 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE 4 194 " --> pdb=" O ILE 4 190 " (cutoff:3.500A) Proline residue: 4 195 - end of helix Processing helix chain '4' and resid 221 through 232 Processing helix chain '4' and resid 243 through 251 removed outlier: 3.727A pdb=" N TYR 4 247 " --> pdb=" O GLY 4 243 " (cutoff:3.500A) Processing helix chain '4' and resid 258 through 263 removed outlier: 5.135A pdb=" N VAL 4 263 " --> pdb=" O ARG 4 259 " (cutoff:3.500A) Processing helix chain '4' and resid 313 through 322 Processing helix chain '5' and resid 13 through 28 removed outlier: 3.782A pdb=" N SER 5 28 " --> pdb=" O ASP 5 24 " (cutoff:3.500A) Processing helix chain '5' and resid 46 through 63 removed outlier: 4.052A pdb=" N ARG 5 56 " --> pdb=" O HIS 5 52 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER 5 59 " --> pdb=" O ASN 5 55 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASN 5 61 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE 5 62 " --> pdb=" O LEU 5 58 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR 5 63 " --> pdb=" O SER 5 59 " (cutoff:3.500A) Processing helix chain '6' and resid 74 through 79 removed outlier: 3.735A pdb=" N ASP 6 78 " --> pdb=" O TYR 6 74 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU 6 79 " --> pdb=" O ALA 6 75 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 74 through 79' Processing helix chain '6' and resid 82 through 88 removed outlier: 3.779A pdb=" N VAL 6 87 " --> pdb=" O SER 6 83 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LYS 6 88 " --> pdb=" O TRP 6 84 " (cutoff:3.500A) Processing helix chain '6' and resid 96 through 114 removed outlier: 3.914A pdb=" N GLU 6 104 " --> pdb=" O ALA 6 100 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASN 6 114 " --> pdb=" O THR 6 110 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 138 removed outlier: 4.148A pdb=" N LEU 6 137 " --> pdb=" O SER 6 133 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU 6 138 " --> pdb=" O GLU 6 134 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 133 through 138' Processing helix chain '6' and resid 144 through 164 removed outlier: 3.717A pdb=" N MET 6 148 " --> pdb=" O ASN 6 144 " (cutoff:3.500A) Processing helix chain '6' and resid 188 through 203 removed outlier: 3.893A pdb=" N HIS 6 192 " --> pdb=" O ASN 6 188 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS 6 201 " --> pdb=" O LYS 6 197 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN 6 202 " --> pdb=" O SER 6 198 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLU 6 203 " --> pdb=" O ILE 6 199 " (cutoff:3.500A) Processing helix chain '6' and resid 209 through 223 Proline residue: 6 223 - end of helix Processing helix chain '6' and resid 246 through 258 removed outlier: 3.989A pdb=" N THR 6 250 " --> pdb=" O ASP 6 246 " (cutoff:3.500A) Processing helix chain '6' and resid 270 through 282 removed outlier: 3.575A pdb=" N TYR 6 282 " --> pdb=" O LYS 6 278 " (cutoff:3.500A) Processing helix chain '6' and resid 293 through 306 removed outlier: 3.527A pdb=" N ALA 6 304 " --> pdb=" O LEU 6 300 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL 6 305 " --> pdb=" O PHE 6 301 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR 6 306 " --> pdb=" O ASN 6 302 " (cutoff:3.500A) Processing helix chain '6' and resid 372 through 385 removed outlier: 4.611A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) Proline residue: 6 385 - end of helix Processing helix chain '6' and resid 437 through 446 removed outlier: 3.685A pdb=" N HIS 6 445 " --> pdb=" O ASP 6 441 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU 6 446 " --> pdb=" O VAL 6 442 " (cutoff:3.500A) Processing helix chain '6' and resid 451 through 458 Proline residue: 6 458 - end of helix Processing helix chain '6' and resid 284 through 289 removed outlier: 4.330A pdb=" N PHE 6 287 " --> pdb=" O ASP 6 284 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR 6 288 " --> pdb=" O GLU 6 285 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LYS 6 289 " --> pdb=" O SER 6 286 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 284 through 289' Processing helix chain '7' and resid 126 through 131 removed outlier: 3.909A pdb=" N ARG 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) Proline residue: 7 131 - end of helix No H-bonds generated for 'chain '7' and resid 126 through 131' Processing helix chain '7' and resid 149 through 161 removed outlier: 3.576A pdb=" N ALA 7 153 " --> pdb=" O LEU 7 149 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) Processing helix chain '7' and resid 176 through 187 removed outlier: 3.839A pdb=" N GLY 7 187 " --> pdb=" O ALA 7 183 " (cutoff:3.500A) Processing helix chain '7' and resid 189 through 201 Processing helix chain '7' and resid 206 through 218 Processing helix chain '7' and resid 238 through 246 removed outlier: 4.399A pdb=" N LEU 7 242 " --> pdb=" O GLN 7 238 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN 7 243 " --> pdb=" O ALA 7 239 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU 7 245 " --> pdb=" O ILE 7 241 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU 7 246 " --> pdb=" O LEU 7 242 " (cutoff:3.500A) Processing helix chain '7' and resid 322 through 334 removed outlier: 4.509A pdb=" N ASP 7 334 " --> pdb=" O CYS 7 330 " (cutoff:3.500A) Processing helix chain '7' and resid 342 through 347 removed outlier: 5.606A pdb=" N HIS 7 347 " --> pdb=" O PHE 7 343 " (cutoff:3.500A) Processing helix chain '7' and resid 363 through 375 Processing helix chain '7' and resid 391 through 404 Processing helix chain '7' and resid 413 through 427 Processing helix chain '7' and resid 431 through 436 removed outlier: 5.078A pdb=" N ALA 7 436 " --> pdb=" O PRO 7 432 " (cutoff:3.500A) Processing helix chain '7' and resid 456 through 462 Processing helix chain '7' and resid 467 through 481 removed outlier: 5.358A pdb=" N GLU 7 481 " --> pdb=" O LEU 7 477 " (cutoff:3.500A) Processing helix chain '7' and resid 489 through 494 removed outlier: 4.395A pdb=" N VAL 7 493 " --> pdb=" O GLU 7 489 " (cutoff:3.500A) Proline residue: 7 494 - end of helix No H-bonds generated for 'chain '7' and resid 489 through 494' Processing helix chain '7' and resid 496 through 504 removed outlier: 4.893A pdb=" N ARG 7 500 " --> pdb=" O ALA 7 496 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL 7 501 " --> pdb=" O MET 7 497 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VAL 7 502 " --> pdb=" O PHE 7 498 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER 7 503 " --> pdb=" O ARG 7 499 " (cutoff:3.500A) Processing helix chain '7' and resid 522 through 531 removed outlier: 4.587A pdb=" N ASP 7 526 " --> pdb=" O ASP 7 522 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU 7 527 " --> pdb=" O LYS 7 523 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASN 7 528 " --> pdb=" O ILE 7 524 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N PHE 7 529 " --> pdb=" O GLY 7 525 " (cutoff:3.500A) Processing helix chain '7' and resid 539 through 547 Processing helix chain '7' and resid 562 through 572 removed outlier: 3.821A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU 7 572 " --> pdb=" O GLU 7 568 " (cutoff:3.500A) Processing helix chain '7' and resid 573 through 584 removed outlier: 3.739A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN 7 584 " --> pdb=" O LEU 7 580 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 602 Processing helix chain '7' and resid 611 through 623 Processing helix chain '7' and resid 632 through 646 Processing helix chain '7' and resid 655 through 661 removed outlier: 4.109A pdb=" N ASP 7 659 " --> pdb=" O SER 7 655 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR 7 660 " --> pdb=" O LYS 7 656 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER 7 661 " --> pdb=" O VAL 7 657 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 655 through 661' Processing helix chain '7' and resid 679 through 692 removed outlier: 3.690A pdb=" N ARG 7 689 " --> pdb=" O GLN 7 685 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE 7 690 " --> pdb=" O ARG 7 686 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG 7 692 " --> pdb=" O GLY 7 688 " (cutoff:3.500A) Processing helix chain '7' and resid 713 through 727 removed outlier: 4.118A pdb=" N TYR 7 717 " --> pdb=" O THR 7 713 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE 7 725 " --> pdb=" O LYS 7 721 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU 7 726 " --> pdb=" O ARG 7 722 " (cutoff:3.500A) Processing helix chain '7' and resid 752 through 767 removed outlier: 3.827A pdb=" N ASN 7 767 " --> pdb=" O VAL 7 763 " (cutoff:3.500A) Processing helix chain '7' and resid 830 through 835 removed outlier: 4.358A pdb=" N ARG 7 834 " --> pdb=" O HIS 7 830 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS 7 835 " --> pdb=" O PRO 7 831 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 830 through 835' Processing helix chain '7' and resid 693 through 698 removed outlier: 3.602A pdb=" N ARG 7 696 " --> pdb=" O ALA 7 693 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN 7 697 " --> pdb=" O LYS 7 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 107 removed outlier: 4.649A pdb=" N CYS A 107 " --> pdb=" O CYS A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 removed outlier: 4.248A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 146 removed outlier: 5.034A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N MET A 146 " --> pdb=" O CYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 6.036A pdb=" N SER A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.074A pdb=" N MET A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 235' Processing helix chain 'A' and resid 243 through 248 Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 367 through 375 removed outlier: 5.215A pdb=" N THR A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.138A pdb=" N SER A 418 " --> pdb=" O ASP A 414 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ARG A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.109A pdb=" N MET A 455 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 456' Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.928A pdb=" N THR A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Proline residue: A 477 - end of helix No H-bonds generated for 'chain 'A' and resid 471 through 479' Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.668A pdb=" N ILE A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL A 512 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 536 removed outlier: 3.558A pdb=" N LEU A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Proline residue: A 554 - end of helix Processing helix chain 'A' and resid 573 through 583 removed outlier: 3.706A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Proline residue: A 583 - end of helix Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 671 removed outlier: 4.139A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ALA A 671 " --> pdb=" O GLY A 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 671' Processing helix chain 'A' and resid 672 through 700 Processing helix chain 'A' and resid 709 through 738 removed outlier: 5.661A pdb=" N LYS A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 762 Processing helix chain 'A' and resid 793 through 798 Processing helix chain 'A' and resid 809 through 846 Processing helix chain 'A' and resid 874 through 879 removed outlier: 3.862A pdb=" N ILE A 878 " --> pdb=" O ASP A 874 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLU A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 874 through 879' Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.116A pdb=" N GLY A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLY A 888 " --> pdb=" O ASP A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 888' Processing helix chain 'A' and resid 889 through 897 Processing helix chain 'A' and resid 909 through 914 removed outlier: 4.607A pdb=" N LEU A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLU A 914 " --> pdb=" O PRO A 910 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 909 through 914' Processing helix chain 'A' and resid 915 through 920 removed outlier: 4.342A pdb=" N ILE A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 922 through 948 removed outlier: 4.186A pdb=" N GLN A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 948 " --> pdb=" O ARG A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 998 removed outlier: 3.751A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU A 998 " --> pdb=" O GLN A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1027 removed outlier: 5.050A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A1027 " --> pdb=" O ARG A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix removed outlier: 4.132A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A1079 " --> pdb=" O PRO A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1107 removed outlier: 4.456A pdb=" N VAL A1107 " --> pdb=" O GLU A1103 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1147 removed outlier: 3.833A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1177 removed outlier: 3.982A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A1173 " --> pdb=" O ILE A1169 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 removed outlier: 4.746A pdb=" N ASP A1206 " --> pdb=" O MET A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1249 through 1270 removed outlier: 4.273A pdb=" N GLU A1253 " --> pdb=" O ASP A1249 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ALA A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP A1257 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N HIS A1258 " --> pdb=" O ALA A1254 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A1269 " --> pdb=" O ASN A1265 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A1270 " --> pdb=" O THR A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1319 removed outlier: 4.056A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 removed outlier: 3.526A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1360 removed outlier: 4.757A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY A1360 " --> pdb=" O ILE A1356 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.981A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 removed outlier: 3.838A pdb=" N SER A1392 " --> pdb=" O GLY A1388 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASN A1393 " --> pdb=" O PHE A1389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1388 through 1393' Processing helix chain 'A' and resid 1395 through 1403 removed outlier: 3.854A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.604A pdb=" N ASN A1427 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1454 removed outlier: 4.292A pdb=" N MET A1454 " --> pdb=" O LEU A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1593 removed outlier: 5.731A pdb=" N TYR A1591 " --> pdb=" O SER A1588 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER A1592 " --> pdb=" O PRO A1589 " (cutoff:3.500A) Proline residue: A1593 - end of helix No H-bonds generated for 'chain 'A' and resid 1588 through 1593' Processing helix chain 'A' and resid 334 through 342 removed outlier: 3.588A pdb=" N GLY A 342 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 41 removed outlier: 3.676A pdb=" N SER B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 67 removed outlier: 4.567A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.818A pdb=" N GLU B 183 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N THR B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 185' Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.763A pdb=" N ARG B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 370 through 391 Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.714A pdb=" N LYS B 404 " --> pdb=" O HIS B 400 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG B 405 " --> pdb=" O PHE B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 405' Processing helix chain 'B' and resid 410 through 439 Processing helix chain 'B' and resid 443 through 464 removed outlier: 3.510A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASN B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N LYS B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 551 through 562 removed outlier: 3.623A pdb=" N GLY B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 Proline residue: B 575 - end of helix Processing helix chain 'B' and resid 592 through 607 removed outlier: 3.686A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 669 Processing helix chain 'B' and resid 680 through 688 removed outlier: 3.513A pdb=" N LEU B 684 " --> pdb=" O THR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 702 removed outlier: 3.713A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE B 701 " --> pdb=" O GLU B 697 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LEU B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 4.585A pdb=" N ILE B 748 " --> pdb=" O HIS B 744 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 744 through 749' Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.725A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 763 removed outlier: 3.903A pdb=" N ASN B 762 " --> pdb=" O PHE B 758 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLN B 763 " --> pdb=" O PRO B 759 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 758 through 763' Processing helix chain 'B' and resid 764 through 777 removed outlier: 4.507A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 777 " --> pdb=" O MET B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 789 removed outlier: 5.072A pdb=" N MET B 789 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 813 removed outlier: 4.295A pdb=" N GLU B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 849 Processing helix chain 'B' and resid 995 through 1000 Proline residue: B1000 - end of helix Processing helix chain 'B' and resid 1013 through 1021 removed outlier: 4.371A pdb=" N ILE B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.853A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1063 removed outlier: 3.637A pdb=" N GLY B1063 " --> pdb=" O LEU B1059 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.528A pdb=" N LYS B1102 " --> pdb=" O MET B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1211 Processing helix chain 'C' and resid 26 through 39 Processing helix chain 'C' and resid 59 through 71 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 76 through 81 removed outlier: 5.128A pdb=" N GLU C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 removed outlier: 5.462A pdb=" N PHE C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 removed outlier: 4.469A pdb=" N GLY C 171 " --> pdb=" O HIS C 167 " (cutoff:3.500A) Proline residue: C 172 - end of helix No H-bonds generated for 'chain 'C' and resid 167 through 172' Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 211 removed outlier: 4.116A pdb=" N GLU C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP C 211 " --> pdb=" O CYS C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 211' Processing helix chain 'C' and resid 239 through 268 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.728A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.524A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 196 Proline residue: D 196 - end of helix Processing helix chain 'D' and resid 203 through 219 removed outlier: 5.854A pdb=" N THR D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 27 removed outlier: 3.601A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 37 removed outlier: 3.569A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 4.128A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 125 removed outlier: 3.917A pdb=" N MET E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS E 122 " --> pdb=" O PRO E 118 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 136 through 141 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 25 through 33 removed outlier: 3.647A pdb=" N LYS F 32 " --> pdb=" O THR F 28 " (cutoff:3.500A) Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'F' and resid 147 through 152 removed outlier: 5.585A pdb=" N ILE F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 74 removed outlier: 3.707A pdb=" N LYS F 72 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA F 73 " --> pdb=" O LYS F 70 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE F 74 " --> pdb=" O GLU F 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 69 through 74' Processing helix chain 'G' and resid 14 through 19 removed outlier: 4.281A pdb=" N PHE G 18 " --> pdb=" O HIS G 14 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLY G 19 " --> pdb=" O PRO G 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 14 through 19' Processing helix chain 'G' and resid 21 through 37 removed outlier: 3.706A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLY G 36 " --> pdb=" O GLU G 32 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER G 37 " --> pdb=" O GLU G 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 94 removed outlier: 4.670A pdb=" N ASP H 92 " --> pdb=" O SER H 88 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASP H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 88 through 94' Processing helix chain 'H' and resid 128 through 133 removed outlier: 3.527A pdb=" N LEU H 132 " --> pdb=" O ASN H 128 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN H 133 " --> pdb=" O TYR H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 128 through 133' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.531A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.767A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 63 removed outlier: 4.440A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 11 removed outlier: 4.859A pdb=" N PHE K 10 " --> pdb=" O ARG K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.783A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 5.332A pdb=" N THR K 113 " --> pdb=" O TRP K 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 141 removed outlier: 5.500A pdb=" N ASP M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 158 Processing helix chain 'M' and resid 167 through 184 removed outlier: 3.794A pdb=" N GLU M 184 " --> pdb=" O CYS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 196 removed outlier: 3.588A pdb=" N ILE M 192 " --> pdb=" O THR M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 221 Processing helix chain 'M' and resid 234 through 247 removed outlier: 3.848A pdb=" N TYR M 238 " --> pdb=" O GLN M 234 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE M 239 " --> pdb=" O ASN M 235 " (cutoff:3.500A) Proline residue: M 240 - end of helix Processing helix chain 'M' and resid 249 through 267 removed outlier: 3.894A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE M 266 " --> pdb=" O LYS M 262 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LYS M 267 " --> pdb=" O CYS M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 290 Processing helix chain 'M' and resid 294 through 303 Processing helix chain 'M' and resid 305 through 320 removed outlier: 4.245A pdb=" N GLU M 318 " --> pdb=" O LYS M 314 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N HIS M 319 " --> pdb=" O ILE M 315 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG M 320 " --> pdb=" O LEU M 316 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 332 removed outlier: 3.507A pdb=" N ILE M 329 " --> pdb=" O ASP M 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 147 Processing helix chain 'O' and resid 171 through 180 Processing helix chain 'O' and resid 219 through 235 removed outlier: 3.844A pdb=" N ILE O 223 " --> pdb=" O GLN O 219 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLN O 225 " --> pdb=" O GLU O 221 " (cutoff:3.500A) Proline residue: O 232 - end of helix Processing helix chain 'Q' and resid 23 through 35 removed outlier: 4.973A pdb=" N MET Q 27 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 112 removed outlier: 3.838A pdb=" N LEU Q 111 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 107 through 112' Processing helix chain 'Q' and resid 152 through 168 Processing helix chain 'Q' and resid 336 through 347 Processing helix chain 'Q' and resid 405 through 414 removed outlier: 3.760A pdb=" N ASP Q 414 " --> pdb=" O GLU Q 410 " (cutoff:3.500A) Processing helix chain 'Q' and resid 423 through 432 Processing helix chain 'Q' and resid 436 through 451 removed outlier: 3.835A pdb=" N GLN Q 451 " --> pdb=" O ALA Q 447 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 removed outlier: 4.014A pdb=" N PHE Q 133 " --> pdb=" O ASN Q 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 128 through 133' Processing helix chain 'R' and resid 47 through 53 removed outlier: 4.336A pdb=" N LYS R 51 " --> pdb=" O ASN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 83 removed outlier: 3.918A pdb=" N ASP R 83 " --> pdb=" O GLU R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 246 removed outlier: 3.848A pdb=" N VAL R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 267 removed outlier: 3.549A pdb=" N THR R 262 " --> pdb=" O THR R 258 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR R 266 " --> pdb=" O THR R 262 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY R 267 " --> pdb=" O MET R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 287 removed outlier: 3.660A pdb=" N LYS R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER R 287 " --> pdb=" O GLU R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 311 removed outlier: 3.730A pdb=" N ASP R 311 " --> pdb=" O PHE R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 323 Processing helix chain 'R' and resid 325 through 337 removed outlier: 4.252A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 352 through 358 removed outlier: 4.114A pdb=" N LYS R 357 " --> pdb=" O PRO R 353 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU R 358 " --> pdb=" O GLU R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 66 removed outlier: 4.587A pdb=" N ASN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 29 removed outlier: 3.976A pdb=" N ARG U 22 " --> pdb=" O VAL U 18 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 50 removed outlier: 4.893A pdb=" N LEU U 35 " --> pdb=" O ASP U 31 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN U 36 " --> pdb=" O GLU U 32 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP U 37 " --> pdb=" O GLN U 33 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU U 38 " --> pdb=" O THR U 34 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS U 50 " --> pdb=" O LEU U 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 14 removed outlier: 4.546A pdb=" N SER V 13 " --> pdb=" O LEU V 9 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N THR V 14 " --> pdb=" O TYR V 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 9 through 14' Processing helix chain 'V' and resid 15 through 30 removed outlier: 4.059A pdb=" N THR V 25 " --> pdb=" O ASP V 21 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU V 26 " --> pdb=" O ALA V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 55 removed outlier: 3.725A pdb=" N LEU V 52 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYS V 53 " --> pdb=" O ALA V 49 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP V 54 " --> pdb=" O GLU V 50 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN V 55 " --> pdb=" O THR V 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 3 through 20 Processing helix chain 'W' and resid 22 through 36 removed outlier: 3.631A pdb=" N SER W 36 " --> pdb=" O ILE W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 48 Processing helix chain 'W' and resid 52 through 65 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 90 through 119 Proline residue: W 119 - end of helix Processing helix chain 'W' and resid 132 through 140 removed outlier: 3.803A pdb=" N VAL W 137 " --> pdb=" O GLN W 133 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 162 through 180 removed outlier: 4.501A pdb=" N LYS W 166 " --> pdb=" O GLY W 162 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU W 167 " --> pdb=" O LYS W 163 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 181 through 193 removed outlier: 3.583A pdb=" N SER W 192 " --> pdb=" O LYS W 188 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ARG W 193 " --> pdb=" O ILE W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 206 removed outlier: 3.859A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG W 205 " --> pdb=" O ILE W 201 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU W 206 " --> pdb=" O ALA W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 289 removed outlier: 5.053A pdb=" N VAL W 271 " --> pdb=" O ALA W 267 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA W 272 " --> pdb=" O SER W 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 291 through 296 removed outlier: 3.751A pdb=" N GLN W 296 " --> pdb=" O GLU W 292 " (cutoff:3.500A) Processing helix chain 'W' and resid 349 through 369 Processing helix chain 'X' and resid 106 through 116 removed outlier: 4.364A pdb=" N GLN X 116 " --> pdb=" O LEU X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 139 removed outlier: 4.255A pdb=" N LYS X 127 " --> pdb=" O HIS X 123 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLY X 139 " --> pdb=" O ILE X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 152 removed outlier: 3.677A pdb=" N LEU X 151 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 167 removed outlier: 4.078A pdb=" N GLU X 161 " --> pdb=" O ASP X 157 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP X 167 " --> pdb=" O LEU X 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 199 Processing helix chain 'X' and resid 206 through 214 removed outlier: 4.026A pdb=" N LEU X 210 " --> pdb=" O SER X 206 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS X 211 " --> pdb=" O CYS X 207 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP X 212 " --> pdb=" O LYS X 208 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLY X 213 " --> pdb=" O ASP X 209 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TRP X 214 " --> pdb=" O LEU X 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 206 through 214' Processing helix chain 'X' and resid 217 through 228 Processing helix chain 'X' and resid 256 through 266 removed outlier: 3.636A pdb=" N ASN X 265 " --> pdb=" O LYS X 261 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL X 266 " --> pdb=" O MET X 262 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 282 removed outlier: 3.990A pdb=" N LEU X 274 " --> pdb=" O GLN X 270 " (cutoff:3.500A) Proline residue: X 275 - end of helix removed outlier: 5.240A pdb=" N GLN X 279 " --> pdb=" O PRO X 275 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP X 280 " --> pdb=" O ARG X 276 " (cutoff:3.500A) Processing helix chain 'X' and resid 290 through 295 removed outlier: 4.589A pdb=" N LYS X 294 " --> pdb=" O PRO X 290 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ARG X 295 " --> pdb=" O ALA X 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 290 through 295' Processing helix chain 'a' and resid 13 through 20 Processing helix chain 'a' and resid 26 through 35 removed outlier: 3.601A pdb=" N TYR a 30 " --> pdb=" O ASN a 26 " (cutoff:3.500A) Proline residue: a 35 - end of helix Processing helix chain 'a' and resid 41 through 52 Processing helix chain 'a' and resid 87 through 97 removed outlier: 3.663A pdb=" N ILE a 93 " --> pdb=" O ALA a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 98 through 111 removed outlier: 4.284A pdb=" N LYS a 109 " --> pdb=" O GLU a 105 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP a 111 " --> pdb=" O LEU a 107 " (cutoff:3.500A) Processing helix chain 'a' and resid 165 through 193 removed outlier: 3.678A pdb=" N ILE a 169 " --> pdb=" O THR a 165 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP a 190 " --> pdb=" O GLU a 186 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU a 191 " --> pdb=" O SER a 187 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE a 192 " --> pdb=" O LEU a 188 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N GLU a 193 " --> pdb=" O TYR a 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 288 removed outlier: 3.585A pdb=" N ILE a 288 " --> pdb=" O MET a 284 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 56 removed outlier: 3.774A pdb=" N ASP b 34 " --> pdb=" O GLY b 30 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LYS b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 87 removed outlier: 3.682A pdb=" N LEU b 65 " --> pdb=" O GLN b 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 94 removed outlier: 6.496A pdb=" N SER b 92 " --> pdb=" O GLU b 88 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR b 93 " --> pdb=" O THR b 89 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL b 94 " --> pdb=" O LEU b 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 88 through 94' Processing helix chain 'b' and resid 106 through 115 removed outlier: 3.506A pdb=" N VAL b 110 " --> pdb=" O HIS b 106 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR b 112 " --> pdb=" O SER b 108 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU b 113 " --> pdb=" O LEU b 109 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG b 115 " --> pdb=" O THR b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 119 through 134 removed outlier: 3.826A pdb=" N ASP b 123 " --> pdb=" O ILE b 119 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY b 134 " --> pdb=" O ARG b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 171 removed outlier: 3.981A pdb=" N HIS b 170 " --> pdb=" O GLU b 166 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASP b 171 " --> pdb=" O TYR b 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 197 through 207 Processing helix chain 'c' and resid 3 through 40 removed outlier: 4.052A pdb=" N LEU c 24 " --> pdb=" O LEU c 20 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN c 25 " --> pdb=" O CYS c 21 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY c 40 " --> pdb=" O GLU c 36 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 77 removed outlier: 3.886A pdb=" N VAL c 77 " --> pdb=" O LEU c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 92 through 110 Processing helix chain 'd' and resid 89 through 95 removed outlier: 3.992A pdb=" N ILE d 93 " --> pdb=" O ASN d 89 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR d 94 " --> pdb=" O PRO d 90 " (cutoff:3.500A) Processing helix chain 'd' and resid 99 through 111 Proline residue: d 104 - end of helix removed outlier: 3.943A pdb=" N GLY d 111 " --> pdb=" O LEU d 107 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 130 removed outlier: 3.822A pdb=" N LEU d 124 " --> pdb=" O ASN d 120 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS d 129 " --> pdb=" O GLN d 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN d 130 " --> pdb=" O ASN d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 231 removed outlier: 3.836A pdb=" N SER d 231 " --> pdb=" O LEU d 227 " (cutoff:3.500A) Processing helix chain 'd' and resid 233 through 242 removed outlier: 6.769A pdb=" N GLY d 237 " --> pdb=" O LYS d 233 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N MET d 238 " --> pdb=" O GLU d 234 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER d 239 " --> pdb=" O SER d 235 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N SER d 240 " --> pdb=" O THR d 236 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET d 241 " --> pdb=" O GLY d 237 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER d 242 " --> pdb=" O MET d 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 233 through 242' Processing helix chain 'd' and resid 243 through 249 Processing helix chain 'd' and resid 265 through 316 Processing helix chain 'd' and resid 424 through 453 removed outlier: 3.906A pdb=" N ALA d 450 " --> pdb=" O LYS d 446 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU d 451 " --> pdb=" O LYS d 447 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU d 452 " --> pdb=" O GLU d 448 " (cutoff:3.500A) Processing helix chain 'd' and resid 497 through 526 Processing helix chain 'd' and resid 541 through 570 removed outlier: 4.172A pdb=" N ILE d 545 " --> pdb=" O ILE d 541 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL d 549 " --> pdb=" O ILE d 545 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP d 568 " --> pdb=" O ASP d 564 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ILE d 569 " --> pdb=" O TYR d 565 " (cutoff:3.500A) Processing helix chain 'd' and resid 593 through 611 removed outlier: 3.810A pdb=" N PHE d 606 " --> pdb=" O GLU d 602 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS d 608 " --> pdb=" O ARG d 604 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU d 609 " --> pdb=" O ALA d 605 " (cutoff:3.500A) Processing helix chain 'd' and resid 666 through 681 removed outlier: 4.321A pdb=" N VAL d 670 " --> pdb=" O ASP d 666 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA d 679 " --> pdb=" O HIS d 675 " (cutoff:3.500A) Processing helix chain 'd' and resid 534 through 539 removed outlier: 3.816A pdb=" N ILE d 539 " --> pdb=" O ASN d 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 534 through 539' Processing helix chain 'e' and resid 12 through 28 removed outlier: 3.824A pdb=" N TYR e 16 " --> pdb=" O GLY e 12 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP e 17 " --> pdb=" O ASP e 13 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU e 18 " --> pdb=" O ASP e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 71 through 77 removed outlier: 4.142A pdb=" N LEU e 75 " --> pdb=" O PRO e 71 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASP e 77 " --> pdb=" O SER e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 87 through 94 removed outlier: 4.567A pdb=" N LYS e 91 " --> pdb=" O PHE e 87 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER e 92 " --> pdb=" O ARG e 88 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE e 93 " --> pdb=" O ILE e 89 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR e 94 " --> pdb=" O LEU e 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 87 through 94' Processing helix chain 'e' and resid 101 through 111 Processing helix chain 'e' and resid 199 through 208 removed outlier: 3.665A pdb=" N GLY e 208 " --> pdb=" O MET e 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 264 through 283 Processing helix chain 'e' and resid 292 through 297 removed outlier: 3.601A pdb=" N MET e 296 " --> pdb=" O ASP e 292 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 25 removed outlier: 3.680A pdb=" N SER f 25 " --> pdb=" O LYS f 21 " (cutoff:3.500A) Processing helix chain 'f' and resid 88 through 95 removed outlier: 4.004A pdb=" N GLY f 95 " --> pdb=" O LEU f 91 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 111 Processing helix chain 'f' and resid 162 through 178 removed outlier: 4.982A pdb=" N LYS f 166 " --> pdb=" O GLU f 162 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG f 178 " --> pdb=" O LEU f 174 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 210 removed outlier: 5.401A pdb=" N LEU f 210 " --> pdb=" O ARG f 206 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 29 removed outlier: 4.004A pdb=" N TYR g 7 " --> pdb=" O ASN g 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU g 8 " --> pdb=" O GLN g 4 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL g 19 " --> pdb=" O THR g 15 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU g 21 " --> pdb=" O LEU g 17 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA g 22 " --> pdb=" O SER g 18 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR g 28 " --> pdb=" O LEU g 24 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N THR g 29 " --> pdb=" O ILE g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 86 removed outlier: 3.780A pdb=" N VAL g 50 " --> pdb=" O SER g 46 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL g 58 " --> pdb=" O SER g 54 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR g 62 " --> pdb=" O VAL g 58 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET g 63 " --> pdb=" O ASN g 59 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN g 64 " --> pdb=" O ASN g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 117 Processing helix chain 'h' and resid 40 through 63 removed outlier: 4.012A pdb=" N GLU h 44 " --> pdb=" O VAL h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 66 through 75 removed outlier: 4.285A pdb=" N ALA h 70 " --> pdb=" O ASN h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 127 removed outlier: 3.720A pdb=" N ALA h 127 " --> pdb=" O ASP h 123 " (cutoff:3.500A) Processing helix chain 'h' and resid 130 through 148 removed outlier: 3.750A pdb=" N VAL h 134 " --> pdb=" O MET h 130 " (cutoff:3.500A) Processing helix chain 'h' and resid 149 through 162 removed outlier: 4.902A pdb=" N LYS h 162 " --> pdb=" O THR h 158 " (cutoff:3.500A) Processing helix chain 'h' and resid 184 through 191 Processing helix chain 'h' and resid 192 through 200 Processing helix chain 'h' and resid 201 through 206 removed outlier: 5.761A pdb=" N ILE h 206 " --> pdb=" O GLU h 202 " (cutoff:3.500A) Processing helix chain 'i' and resid 17 through 24 removed outlier: 5.065A pdb=" N LYS i 21 " --> pdb=" O PRO i 17 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE i 22 " --> pdb=" O PRO i 18 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE i 23 " --> pdb=" O TYR i 19 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR i 24 " --> pdb=" O VAL i 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 17 through 24' Processing helix chain 'i' and resid 25 through 35 Proline residue: i 32 - end of helix Processing helix chain 'i' and resid 60 through 67 removed outlier: 4.721A pdb=" N TYR i 64 " --> pdb=" O CYS i 60 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU i 65 " --> pdb=" O ALA i 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE i 66 " --> pdb=" O LEU i 62 " (cutoff:3.500A) Proline residue: i 67 - end of helix No H-bonds generated for 'chain 'i' and resid 60 through 67' Processing helix chain 'i' and resid 91 through 96 Processing helix chain 'i' and resid 111 through 140 removed outlier: 4.743A pdb=" N LYS i 115 " --> pdb=" O ASN i 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 164 through 213 removed outlier: 4.608A pdb=" N HIS i 168 " --> pdb=" O GLU i 164 " (cutoff:3.500A) Processing helix chain 'i' and resid 141 through 146 removed outlier: 5.703A pdb=" N TYR i 144 " --> pdb=" O PRO i 141 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU i 145 " --> pdb=" O ASP i 142 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG i 146 " --> pdb=" O MET i 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 141 through 146' Processing helix chain 'j' and resid 5 through 16 removed outlier: 3.661A pdb=" N ASN j 9 " --> pdb=" O ASN j 5 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 80 removed outlier: 6.587A pdb=" N HIS j 68 " --> pdb=" O GLU j 64 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE j 69 " --> pdb=" O PHE j 65 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG j 77 " --> pdb=" O LEU j 73 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS j 78 " --> pdb=" O HIS j 74 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP j 79 " --> pdb=" O GLN j 75 " (cutoff:3.500A) Proline residue: j 80 - end of helix Processing helix chain 'j' and resid 86 through 109 removed outlier: 4.467A pdb=" N LEU j 90 " --> pdb=" O GLN j 86 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER j 93 " --> pdb=" O THR j 89 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE j 94 " --> pdb=" O LEU j 90 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN j 108 " --> pdb=" O LEU j 104 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLU j 109 " --> pdb=" O ILE j 105 " (cutoff:3.500A) Processing helix chain 'j' and resid 110 through 117 removed outlier: 3.952A pdb=" N SER j 116 " --> pdb=" O LYS j 112 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS j 117 " --> pdb=" O ASP j 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 118 through 148 removed outlier: 4.000A pdb=" N GLN j 131 " --> pdb=" O HIS j 127 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU j 132 " --> pdb=" O GLN j 128 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU j 133 " --> pdb=" O ARG j 129 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU j 143 " --> pdb=" O VAL j 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN j 148 " --> pdb=" O TYR j 144 " (cutoff:3.500A) Processing helix chain 'k' and resid 1 through 39 Processing helix chain 'k' and resid 42 through 69 removed outlier: 3.612A pdb=" N SER k 67 " --> pdb=" O LEU k 63 " (cutoff:3.500A) Processing helix chain 'k' and resid 72 through 78 removed outlier: 4.833A pdb=" N LYS k 76 " --> pdb=" O SER k 72 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP k 78 " --> pdb=" O LEU k 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 80 through 90 removed outlier: 3.965A pdb=" N VAL k 84 " --> pdb=" O PRO k 80 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY k 90 " --> pdb=" O TYR k 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 133 removed outlier: 4.009A pdb=" N TYR k 96 " --> pdb=" O ASN k 92 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR k 97 " --> pdb=" O PRO k 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 134 through 149 removed outlier: 5.186A pdb=" N GLU k 138 " --> pdb=" O PRO k 134 " (cutoff:3.500A) Proline residue: k 139 - end of helix Proline residue: k 149 - end of helix Processing helix chain 'k' and resid 151 through 156 removed outlier: 4.686A pdb=" N ASN k 155 " --> pdb=" O ASP k 151 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N THR k 156 " --> pdb=" O ASN k 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 151 through 156' Processing helix chain 'l' and resid 91 through 116 removed outlier: 3.824A pdb=" N VAL l 115 " --> pdb=" O MET l 111 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N HIS l 116 " --> pdb=" O LYS l 112 " (cutoff:3.500A) Processing helix chain 'l' and resid 122 through 155 removed outlier: 3.647A pdb=" N ILE l 154 " --> pdb=" O TRP l 150 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS l 155 " --> pdb=" O THR l 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 158 through 194 removed outlier: 3.528A pdb=" N LEU l 162 " --> pdb=" O ASN l 158 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET l 174 " --> pdb=" O ARG l 170 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL l 176 " --> pdb=" O THR l 172 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN l 177 " --> pdb=" O ASN l 173 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE l 180 " --> pdb=" O VAL l 176 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN l 192 " --> pdb=" O ASN l 188 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ALA l 193 " --> pdb=" O SER l 189 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS l 194 " --> pdb=" O MET l 190 " (cutoff:3.500A) Processing helix chain 'l' and resid 199 through 209 removed outlier: 3.763A pdb=" N ALA l 203 " --> pdb=" O ASP l 199 " (cutoff:3.500A) Processing helix chain 'l' and resid 238 through 261 removed outlier: 3.675A pdb=" N ILE l 257 " --> pdb=" O VAL l 253 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA l 258 " --> pdb=" O SER l 254 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU l 259 " --> pdb=" O ILE l 255 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET l 260 " --> pdb=" O LYS l 256 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN l 261 " --> pdb=" O ILE l 257 " (cutoff:3.500A) Processing helix chain 'l' and resid 344 through 359 removed outlier: 3.839A pdb=" N LEU l 357 " --> pdb=" O ASN l 353 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER l 359 " --> pdb=" O ILE l 355 " (cutoff:3.500A) Processing helix chain 'l' and resid 361 through 390 removed outlier: 3.837A pdb=" N SER l 365 " --> pdb=" O ASP l 361 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA l 390 " --> pdb=" O PHE l 386 " (cutoff:3.500A) Processing helix chain 'l' and resid 396 through 401 removed outlier: 3.725A pdb=" N LEU l 400 " --> pdb=" O SER l 396 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE l 401 " --> pdb=" O LYS l 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 396 through 401' Processing helix chain 'l' and resid 444 through 450 Processing helix chain 'l' and resid 463 through 487 Processing helix chain 'l' and resid 530 through 543 removed outlier: 7.239A pdb=" N ASN l 535 " --> pdb=" O PRO l 531 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR l 536 " --> pdb=" O LEU l 532 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA l 543 " --> pdb=" O LYS l 539 " (cutoff:3.500A) Processing helix chain 'l' and resid 545 through 573 Processing helix chain 'l' and resid 684 through 703 removed outlier: 4.192A pdb=" N LEU l 696 " --> pdb=" O GLN l 692 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN l 697 " --> pdb=" O ARG l 693 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET l 703 " --> pdb=" O ILE l 699 " (cutoff:3.500A) Processing helix chain 'l' and resid 264 through 269 removed outlier: 3.640A pdb=" N ASN l 267 " --> pdb=" O LYS l 264 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER l 268 " --> pdb=" O PRO l 265 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR l 269 " --> pdb=" O LEU l 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 264 through 269' Processing helix chain 'm' and resid 33 through 39 removed outlier: 3.579A pdb=" N TYR m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 40 through 48 removed outlier: 3.568A pdb=" N GLN m 46 " --> pdb=" O ASP m 42 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL m 47 " --> pdb=" O ILE m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 64 through 70 removed outlier: 4.908A pdb=" N ASP m 70 " --> pdb=" O ASN m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 88 through 95 removed outlier: 4.474A pdb=" N ILE m 92 " --> pdb=" O GLN m 88 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN m 95 " --> pdb=" O HIS m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 129 removed outlier: 4.985A pdb=" N LEU m 127 " --> pdb=" O ARG m 123 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE m 128 " --> pdb=" O ASP m 124 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN m 129 " --> pdb=" O ILE m 125 " (cutoff:3.500A) Processing helix chain 'm' and resid 134 through 145 removed outlier: 4.362A pdb=" N PHE m 145 " --> pdb=" O VAL m 141 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 29 Processing helix chain 'n' and resid 51 through 80 Processing helix chain 'n' and resid 86 through 138 removed outlier: 4.094A pdb=" N MET n 96 " --> pdb=" O ARG n 92 " (cutoff:3.500A) Processing helix chain 'o' and resid 21 through 34 removed outlier: 3.960A pdb=" N LEU o 33 " --> pdb=" O PHE o 29 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA o 34 " --> pdb=" O ILE o 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 45 removed outlier: 3.799A pdb=" N VAL o 39 " --> pdb=" O ASN o 35 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR o 44 " --> pdb=" O THR o 40 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN o 45 " --> pdb=" O TYR o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 51 Processing helix chain 'o' and resid 52 through 67 removed outlier: 4.532A pdb=" N GLU o 62 " --> pdb=" O LEU o 58 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR o 63 " --> pdb=" O LYS o 59 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TRP o 64 " --> pdb=" O TYR o 60 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N CYS o 65 " --> pdb=" O LEU o 61 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN o 66 " --> pdb=" O GLU o 62 " (cutoff:3.500A) Proline residue: o 67 - end of helix Processing helix chain 'o' and resid 68 through 73 removed outlier: 4.415A pdb=" N CYS o 72 " --> pdb=" O PRO o 68 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE o 73 " --> pdb=" O TYR o 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 68 through 73' Processing helix chain 'o' and resid 75 through 93 removed outlier: 4.488A pdb=" N LEU o 79 " --> pdb=" O TYR o 75 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN o 86 " --> pdb=" O LEU o 82 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY o 87 " --> pdb=" O LYS o 83 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE o 88 " --> pdb=" O LEU o 84 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET o 89 " --> pdb=" O LEU o 85 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU o 90 " --> pdb=" O ASN o 86 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER o 91 " --> pdb=" O GLY o 87 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA o 92 " --> pdb=" O PHE o 88 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE o 93 " --> pdb=" O MET o 89 " (cutoff:3.500A) Processing helix chain 'o' and resid 102 through 114 removed outlier: 4.470A pdb=" N LEU o 106 " --> pdb=" O GLY o 102 " (cutoff:3.500A) Proline residue: o 107 - end of helix Processing helix chain 'o' and resid 115 through 126 Processing helix chain 'p' and resid 6 through 22 removed outlier: 4.002A pdb=" N THR p 10 " --> pdb=" O SER p 6 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS p 22 " --> pdb=" O PHE p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 27 through 39 removed outlier: 4.437A pdb=" N LEU p 38 " --> pdb=" O LEU p 34 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY p 39 " --> pdb=" O CYS p 35 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 110 removed outlier: 3.557A pdb=" N ASN p 106 " --> pdb=" O ASN p 102 " (cutoff:3.500A) Processing helix chain 'p' and resid 114 through 131 removed outlier: 3.665A pdb=" N TYR p 130 " --> pdb=" O LEU p 126 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER p 131 " --> pdb=" O LEU p 127 " (cutoff:3.500A) Processing helix chain 'p' and resid 164 through 183 removed outlier: 4.092A pdb=" N SER p 172 " --> pdb=" O PHE p 168 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS p 173 " --> pdb=" O THR p 169 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 58 removed outlier: 4.744A pdb=" N VAL r 46 " --> pdb=" O ARG r 42 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA r 47 " --> pdb=" O PRO r 43 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU r 48 " --> pdb=" O GLY r 44 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR r 58 " --> pdb=" O TYR r 54 " (cutoff:3.500A) Processing helix chain 'r' and resid 63 through 79 removed outlier: 3.511A pdb=" N PHE r 67 " --> pdb=" O ARG r 63 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP r 77 " --> pdb=" O GLU r 73 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE r 78 " --> pdb=" O ILE r 74 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 115 removed outlier: 3.526A pdb=" N LYS r 115 " --> pdb=" O ALA r 111 " (cutoff:3.500A) Processing helix chain 'r' and resid 120 through 132 Processing helix chain 's' and resid 25 through 31 removed outlier: 3.929A pdb=" N ILE s 29 " --> pdb=" O ASN s 25 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N THR s 30 " --> pdb=" O ILE s 26 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N LYS s 31 " --> pdb=" O GLN s 27 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 25 through 31' Processing helix chain 's' and resid 32 through 42 Processing helix chain 's' and resid 49 through 77 removed outlier: 4.287A pdb=" N GLU s 53 " --> pdb=" O LEU s 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA s 76 " --> pdb=" O TYR s 72 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS s 77 " --> pdb=" O THR s 73 " (cutoff:3.500A) Processing helix chain 's' and resid 82 through 94 removed outlier: 3.749A pdb=" N GLN s 93 " --> pdb=" O ALA s 89 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY s 94 " --> pdb=" O LEU s 90 " (cutoff:3.500A) Processing helix chain 't' and resid 16 through 22 removed outlier: 3.507A pdb=" N ARG t 20 " --> pdb=" O THR t 16 " (cutoff:3.500A) Processing helix chain 't' and resid 26 through 38 Processing helix chain 't' and resid 44 through 74 Proline residue: t 48 - end of helix Processing helix chain 't' and resid 79 through 91 removed outlier: 3.817A pdb=" N ASP t 90 " --> pdb=" O ALA t 86 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU t 91 " --> pdb=" O VAL t 87 " (cutoff:3.500A) Processing helix chain 't' and resid 92 through 98 Processing helix chain 'u' and resid 34 through 46 Processing helix chain 'u' and resid 52 through 82 removed outlier: 3.893A pdb=" N ASN u 81 " --> pdb=" O LEU u 77 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS u 82 " --> pdb=" O ALA u 78 " (cutoff:3.500A) Processing helix chain 'u' and resid 87 through 99 removed outlier: 3.636A pdb=" N ILE u 91 " --> pdb=" O THR u 87 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 122 removed outlier: 3.907A pdb=" N LYS u 122 " --> pdb=" O TYR u 118 " (cutoff:3.500A) Processing helix chain 'v' and resid 42 through 58 removed outlier: 4.484A pdb=" N VAL v 46 " --> pdb=" O ARG v 42 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA v 47 " --> pdb=" O PRO v 43 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU v 48 " --> pdb=" O GLY v 44 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N THR v 58 " --> pdb=" O TYR v 54 " (cutoff:3.500A) Processing helix chain 'v' and resid 63 through 79 removed outlier: 3.501A pdb=" N PHE v 67 " --> pdb=" O ARG v 63 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP v 77 " --> pdb=" O GLU v 73 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE v 78 " --> pdb=" O ILE v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 85 through 115 removed outlier: 3.916A pdb=" N LYS v 115 " --> pdb=" O ALA v 111 " (cutoff:3.500A) Processing helix chain 'v' and resid 120 through 132 removed outlier: 3.513A pdb=" N ILE v 124 " --> pdb=" O MET v 120 " (cutoff:3.500A) Processing helix chain 'w' and resid 24 through 29 removed outlier: 3.873A pdb=" N GLY w 28 " --> pdb=" O ASP w 24 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE w 29 " --> pdb=" O ASN w 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 24 through 29' Processing helix chain 'w' and resid 30 through 42 Processing helix chain 'w' and resid 49 through 77 removed outlier: 4.023A pdb=" N GLU w 53 " --> pdb=" O LEU w 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA w 76 " --> pdb=" O TYR w 72 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS w 77 " --> pdb=" O THR w 73 " (cutoff:3.500A) Processing helix chain 'w' and resid 82 through 94 removed outlier: 3.668A pdb=" N GLN w 93 " --> pdb=" O ALA w 89 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY w 94 " --> pdb=" O LEU w 90 " (cutoff:3.500A) Processing helix chain 'x' and resid 16 through 22 Processing helix chain 'x' and resid 26 through 38 removed outlier: 4.158A pdb=" N VAL x 30 " --> pdb=" O PRO x 26 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN x 38 " --> pdb=" O LEU x 34 " (cutoff:3.500A) Processing helix chain 'x' and resid 44 through 74 Proline residue: x 48 - end of helix Processing helix chain 'x' and resid 79 through 91 removed outlier: 3.658A pdb=" N ASP x 90 " --> pdb=" O ALA x 86 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLU x 91 " --> pdb=" O VAL x 87 " (cutoff:3.500A) Processing helix chain 'x' and resid 92 through 98 removed outlier: 4.242A pdb=" N LEU x 96 " --> pdb=" O GLU x 92 " (cutoff:3.500A) Processing helix chain 'x' and resid 112 through 117 Proline residue: x 117 - end of helix Processing helix chain 'y' and resid 34 through 46 Processing helix chain 'y' and resid 52 through 82 removed outlier: 4.153A pdb=" N ASN y 81 " --> pdb=" O LEU y 77 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS y 82 " --> pdb=" O ALA y 78 " (cutoff:3.500A) Processing helix chain 'y' and resid 87 through 99 removed outlier: 3.719A pdb=" N ILE y 91 " --> pdb=" O THR y 87 " (cutoff:3.500A) Processing helix chain 'y' and resid 101 through 122 Processing sheet with id= 1, first strand: chain '0' and resid 1 through 4 Processing sheet with id= 2, first strand: chain '0' and resid 104 through 108 removed outlier: 5.324A pdb=" N SER 0 455 " --> pdb=" O SER 0 230 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL 0 456 " --> pdb=" O GLY 0 36 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER 0 460 " --> pdb=" O LEU 0 40 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N MET 0 42 " --> pdb=" O SER 0 460 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU 0 479 " --> pdb=" O ASN 0 37 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE 0 39 " --> pdb=" O LEU 0 479 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '0' and resid 350 through 354 removed outlier: 7.366A pdb=" N HIS 0 350 " --> pdb=" O PRO 0 422 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '0' and resid 491 through 498 removed outlier: 3.751A pdb=" N GLY 0 677 " --> pdb=" O SER 0 491 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU 0 493 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG 0 618 " --> pdb=" O TYR 0 676 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR 0 619 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA 0 596 " --> pdb=" O ASP 0 535 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL 0 601 " --> pdb=" O GLU 0 572 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '1' and resid 3 through 7 removed outlier: 6.833A pdb=" N HIS 1 3 " --> pdb=" O ILE 1 18 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU 1 27 " --> pdb=" O VAL 1 40 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS 1 36 " --> pdb=" O SER 1 31 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '1' and resid 46 through 50 removed outlier: 5.266A pdb=" N MET 1 58 " --> pdb=" O PHE 1 91 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN 1 85 " --> pdb=" O GLY 1 64 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '2' and resid 87 through 91 Processing sheet with id= 8, first strand: chain '2' and resid 173 through 177 removed outlier: 3.635A pdb=" N VAL 2 176 " --> pdb=" O GLU 2 181 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU 2 181 " --> pdb=" O VAL 2 176 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '2' and resid 236 through 239 removed outlier: 8.073A pdb=" N SER 2 267 " --> pdb=" O ILE 2 239 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '2' and resid 337 through 342 removed outlier: 4.024A pdb=" N SER 2 338 " --> pdb=" O TYR 2 350 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS 2 346 " --> pdb=" O GLU 2 342 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHE 2 345 " --> pdb=" O ILE 2 378 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER 2 349 " --> pdb=" O VAL 2 374 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL 2 374 " --> pdb=" O SER 2 349 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '2' and resid 482 through 486 removed outlier: 3.702A pdb=" N TRP 2 483 " --> pdb=" O PHE 2 492 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '4' and resid 83 through 86 removed outlier: 6.494A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER 4 24 " --> pdb=" O ALA 4 70 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N CYS 4 181 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL 4 234 " --> pdb=" O ILE 4 210 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '4' and resid 287 through 290 removed outlier: 4.479A pdb=" N CYS 4 294 " --> pdb=" O CYS 4 289 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '4' and resid 303 through 306 removed outlier: 6.299A pdb=" N ASN 4 303 " --> pdb=" O PHE 4 312 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER 4 310 " --> pdb=" O CYS 4 305 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '5' and resid 7 through 12 No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain '6' and resid 179 through 182 removed outlier: 6.807A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG 6 124 " --> pdb=" O ILE 6 166 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '6' and resid 325 through 329 removed outlier: 3.739A pdb=" N THR 6 326 " --> pdb=" O PHE 6 348 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY 6 346 " --> pdb=" O ILE 6 328 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER 6 354 " --> pdb=" O CYS 6 349 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '6' and resid 333 through 337 removed outlier: 4.362A pdb=" N LYS 6 341 " --> pdb=" O CYS 6 336 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '6' and resid 389 through 392 removed outlier: 6.597A pdb=" N ARG 6 426 " --> pdb=" O VAL 6 392 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN 6 434 " --> pdb=" O CYS 6 429 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '6' and resid 401 through 404 removed outlier: 7.143A pdb=" N GLU 6 401 " --> pdb=" O PHE 6 410 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N SER 6 408 " --> pdb=" O CYS 6 403 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '7' and resid 132 through 136 removed outlier: 3.800A pdb=" N ARG 7 140 " --> pdb=" O SER 7 135 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLY 7 139 " --> pdb=" O ILE 7 175 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '7' and resid 223 through 227 removed outlier: 4.556A pdb=" N TYR 7 232 " --> pdb=" O ILE 7 318 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS 7 314 " --> pdb=" O THR 7 236 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '7' and resid 451 through 455 removed outlier: 3.570A pdb=" N ALA 7 509 " --> pdb=" O GLY 7 483 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '7' and resid 650 through 654 Processing sheet with id= 25, first strand: chain 'A' and resid 16 through 19 removed outlier: 4.721A pdb=" N GLU A1417 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'A' and resid 81 through 86 removed outlier: 6.671A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'A' and resid 150 through 153 removed outlier: 5.744A pdb=" N THR A 150 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.909A pdb=" N LYS A 180 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'A' and resid 362 through 366 Processing sheet with id= 30, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.725A pdb=" N TRP A 430 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'A' and resid 442 through 446 removed outlier: 3.652A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE A 347 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'A' and resid 588 through 591 Processing sheet with id= 33, first strand: chain 'A' and resid 1148 through 1155 removed outlier: 6.709A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE A1237 " --> pdb=" O SER A1229 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASP A1223 " --> pdb=" O VAL A1243 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'A' and resid 1281 through 1293 removed outlier: 3.891A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A1297 " --> pdb=" O SER A1293 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER A1115 " --> pdb=" O ASN A1330 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 93 through 99 removed outlier: 4.601A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 100 through 103 Processing sheet with id= 37, first strand: chain 'B' and resid 209 through 213 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'B' and resid 221 through 228 removed outlier: 5.321A pdb=" N ILE B 222 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 241 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 235 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 543 through 546 removed outlier: 4.480A pdb=" N ARG B 632 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 587 through 591 removed outlier: 3.759A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS B 622 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 792 through 797 removed outlier: 8.107A pdb=" N ARG B 852 " --> pdb=" O TYR B 797 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 821 through 827 removed outlier: 4.247A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP B 978 " --> pdb=" O ILE B 990 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 982 " --> pdb=" O GLN B 986 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN B 986 " --> pdb=" O SER B 982 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'B' and resid 872 through 875 removed outlier: 4.492A pdb=" N GLY B 913 " --> pdb=" O GLU B 875 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS B 914 " --> pdb=" O ALA B 937 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER B 933 " --> pdb=" O ILE B 918 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'B' and resid 904 through 907 removed outlier: 7.369A pdb=" N GLU B 945 " --> pdb=" O GLY B 907 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B' and resid 1158 through 1164 removed outlier: 8.543A pdb=" N ASP B1190 " --> pdb=" O GLY B1164 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'B' and resid 1171 through 1175 Processing sheet with id= 47, first strand: chain 'B' and resid 124 through 128 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'B' and resid 1068 through 1071 removed outlier: 6.004A pdb=" N GLY B1068 " --> pdb=" O PHE B1087 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 7 through 11 removed outlier: 6.542A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 47 through 52 removed outlier: 6.427A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN C 151 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 98 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= 52, first strand: chain 'D' and resid 35 through 38 removed outlier: 7.169A pdb=" N LEU D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.628A pdb=" N VAL E 80 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR E 107 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'E' and resid 151 through 156 removed outlier: 4.960A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU E 194 " --> pdb=" O CYS E 214 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'F' and resid 134 through 138 removed outlier: 3.946A pdb=" N SER F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'G' and resid 6 through 13 Processing sheet with id= 57, first strand: chain 'G' and resid 85 through 89 Processing sheet with id= 58, first strand: chain 'G' and resid 98 through 102 Processing sheet with id= 59, first strand: chain 'G' and resid 120 through 123 removed outlier: 3.516A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'G' and resid 149 through 152 removed outlier: 3.627A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'H' and resid 5 through 11 Processing sheet with id= 62, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.207A pdb=" N CYS H 36 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'I' and resid 5 through 8 removed outlier: 5.475A pdb=" N ARG I 5 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASN I 12 " --> pdb=" O CYS I 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU I 26 " --> pdb=" O ARG I 17 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'I' and resid 83 through 87 removed outlier: 5.965A pdb=" N LEU I 99 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS I 108 " --> pdb=" O CYS I 103 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.801A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'L' and resid 37 through 41 removed outlier: 3.681A pdb=" N LEU L 27 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LYS L 28 " --> pdb=" O ALA L 59 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ILE L 55 " --> pdb=" O ALA L 32 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'M' and resid 33 through 38 removed outlier: 7.815A pdb=" N LYS M 33 " --> pdb=" O ALA M 46 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU M 50 " --> pdb=" O CYS M 45 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'O' and resid 101 through 105 removed outlier: 3.642A pdb=" N VAL O 122 " --> pdb=" O LEU O 114 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE O 116 " --> pdb=" O LYS O 120 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS O 120 " --> pdb=" O PHE O 116 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL O 71 " --> pdb=" O GLN O 158 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'O' and resid 161 through 165 removed outlier: 4.524A pdb=" N LYS O 211 " --> pdb=" O PHE O 207 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE O 202 " --> pdb=" O MET O 197 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N PHE O 182 " --> pdb=" O ARG O 196 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Q' and resid 102 through 105 removed outlier: 4.501A pdb=" N SER Q 383 " --> pdb=" O GLU Q 379 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR Q 373 " --> pdb=" O ALA Q 389 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Q' and resid 117 through 122 removed outlier: 4.848A pdb=" N ALA Q 397 " --> pdb=" O GLN Q 122 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL Q 392 " --> pdb=" O GLU Q 366 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN Q 359 " --> pdb=" O ASP Q 354 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'R' and resid 69 through 73 removed outlier: 6.816A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU R 124 " --> pdb=" O SER R 102 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N SER R 102 " --> pdb=" O LEU R 124 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'R' and resid 134 through 139 removed outlier: 6.742A pdb=" N VAL R 134 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA R 213 " --> pdb=" O THR R 136 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'R' and resid 338 through 341 removed outlier: 3.938A pdb=" N LYS R 348 " --> pdb=" O VAL R 340 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'U' and resid 242 through 247 removed outlier: 4.623A pdb=" N LEU U 243 " --> pdb=" O THR U 268 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU U 247 " --> pdb=" O ASP U 264 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASP U 264 " --> pdb=" O LEU U 247 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY U 265 " --> pdb=" O PHE U 276 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE U 276 " --> pdb=" O GLY U 265 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'U' and resid 250 through 254 removed outlier: 3.681A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG U 257 " --> pdb=" O THR U 254 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ALA U 256 " --> pdb=" O TRP U 285 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA U 283 " --> pdb=" O TRP U 258 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'V' and resid 59 through 64 removed outlier: 5.476A pdb=" N LYS V 59 " --> pdb=" O GLU V 88 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER V 104 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'V' and resid 68 through 71 Processing sheet with id= 79, first strand: chain 'W' and resid 67 through 73 removed outlier: 3.860A pdb=" N GLN W 72 " --> pdb=" O ARG W 84 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG W 84 " --> pdb=" O GLN W 72 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'W' and resid 122 through 125 removed outlier: 3.633A pdb=" N THR W 129 " --> pdb=" O CYS W 124 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'X' and resid 168 through 173 removed outlier: 5.257A pdb=" N ARG X 168 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR X 177 " --> pdb=" O ASP X 172 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'a' and resid 112 through 115 removed outlier: 3.516A pdb=" N GLY a 112 " --> pdb=" O ARG a 133 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS a 130 " --> pdb=" O LEU a 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG a 132 " --> pdb=" O ILE a 148 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE a 148 " --> pdb=" O ARG a 132 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'a' and resid 160 through 163 removed outlier: 5.342A pdb=" N ASP a 152 " --> pdb=" O SER a 163 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'a' and resid 126 through 130 removed outlier: 4.362A pdb=" N GLN a 151 " --> pdb=" O LYS a 130 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'd' and resid 321 through 327 removed outlier: 5.057A pdb=" N VAL d 321 " --> pdb=" O LYS d 338 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP d 327 " --> pdb=" O GLN d 332 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N GLN d 332 " --> pdb=" O ASP d 327 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'd' and resid 354 through 361 removed outlier: 7.129A pdb=" N ILE d 354 " --> pdb=" O HIS d 371 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'd' and resid 403 through 406 removed outlier: 6.710A pdb=" N ILE d 393 " --> pdb=" O SER d 406 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASN d 463 " --> pdb=" O LEU d 478 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS d 464 " --> pdb=" O GLU d 460 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLY d 456 " --> pdb=" O GLU d 468 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'd' and resid 573 through 579 removed outlier: 4.395A pdb=" N SER d 574 " --> pdb=" O ASN d 620 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU d 631 " --> pdb=" O ILE d 619 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU d 621 " --> pdb=" O PRO d 629 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N SER d 628 " --> pdb=" O GLY d 652 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY d 652 " --> pdb=" O SER d 628 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL d 658 " --> pdb=" O ALA d 651 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'e' and resid 243 through 246 removed outlier: 6.774A pdb=" N ILE e 235 " --> pdb=" O ILE e 246 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLN e 214 " --> pdb=" O ILE e 238 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG e 63 " --> pdb=" O SER e 169 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER e 169 " --> pdb=" O ARG e 63 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLU e 69 " --> pdb=" O PRO e 163 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'e' and resid 228 through 234 Processing sheet with id= 91, first strand: chain 'f' and resid 76 through 81 removed outlier: 3.696A pdb=" N ASP f 38 " --> pdb=" O THR f 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER f 36 " --> pdb=" O HIS f 63 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR f 41 " --> pdb=" O ARG f 119 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE f 115 " --> pdb=" O SER f 45 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'f' and resid 127 through 132 removed outlier: 3.559A pdb=" N LEU f 135 " --> pdb=" O LEU f 132 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY f 150 " --> pdb=" O LEU f 142 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS f 3 " --> pdb=" O ALA f 157 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'f' and resid 36 through 41 removed outlier: 3.697A pdb=" N GLN f 120 " --> pdb=" O THR f 41 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'i' and resid 74 through 77 removed outlier: 9.500A pdb=" N GLN i 74 " --> pdb=" O VAL i 85 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL i 85 " --> pdb=" O GLN i 74 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'l' and resid 275 through 280 removed outlier: 3.518A pdb=" N ASP l 301 " --> pdb=" O GLN l 287 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'l' and resid 402 through 405 removed outlier: 3.604A pdb=" N THR l 412 " --> pdb=" O ASN l 403 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS l 426 " --> pdb=" O ASP l 443 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL l 455 " --> pdb=" O TRP l 442 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'l' and resid 498 through 501 removed outlier: 6.598A pdb=" N PHE l 501 " --> pdb=" O ILE l 513 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE l 513 " --> pdb=" O PHE l 501 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N GLN l 514 " --> pdb=" O ARG l 527 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN l 523 " --> pdb=" O ASP l 518 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'l' and resid 574 through 577 removed outlier: 4.897A pdb=" N PHE l 626 " --> pdb=" O SER l 577 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'p' and resid 42 through 47 removed outlier: 6.524A pdb=" N LEU p 51 " --> pdb=" O LEU p 47 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLU p 50 " --> pdb=" O LYS p 69 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR p 67 " --> pdb=" O SER p 52 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP p 66 " --> pdb=" O GLN p 75 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG p 73 " --> pdb=" O ASN p 68 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'p' and resid 186 through 190 Processing sheet with id=101, first strand: chain 'p' and resid 61 through 66 removed outlier: 4.539A pdb=" N ASP p 76 " --> pdb=" O ASP p 66 " (cutoff:3.500A) 5131 hydrogen bonds defined for protein. 15252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 477 hydrogen bonds 942 hydrogen bond angles 0 basepair planarities 193 basepair parallelities 368 stacking parallelities Total time for adding SS restraints: 56.28 Time building geometry restraints manager: 36.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 48131 1.42 - 1.63: 67504 1.63 - 1.85: 824 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 116471 Sorted by residual: bond pdb=" CG PRO l 346 " pdb=" CD PRO l 346 " ideal model delta sigma weight residual 1.503 1.376 0.127 3.40e-02 8.65e+02 1.40e+01 bond pdb=" CB PRO l 346 " pdb=" CG PRO l 346 " ideal model delta sigma weight residual 1.492 1.638 -0.146 5.00e-02 4.00e+02 8.47e+00 bond pdb=" C ARG d 543 " pdb=" N PRO d 544 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.20e-02 6.94e+03 7.66e+00 bond pdb=" N PRO l 346 " pdb=" CD PRO l 346 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.38e+00 bond pdb=" C TRP l 632 " pdb=" N PRO l 633 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.42e+00 ... (remaining 116466 not shown) Histogram of bond angle deviations from ideal: 73.65 - 86.20: 12 86.20 - 98.74: 25 98.74 - 111.28: 50545 111.28 - 123.83: 104481 123.83 - 136.37: 4002 Bond angle restraints: 159065 Sorted by residual: angle pdb=" CA PRO l 346 " pdb=" N PRO l 346 " pdb=" CD PRO l 346 " ideal model delta sigma weight residual 112.00 95.84 16.16 1.40e+00 5.10e-01 1.33e+02 angle pdb=" N PRO l 346 " pdb=" CA PRO l 346 " pdb=" C PRO l 346 " ideal model delta sigma weight residual 114.18 122.98 -8.80 1.39e+00 5.18e-01 4.01e+01 angle pdb=" CA ARG e 55 " pdb=" CB ARG e 55 " pdb=" CG ARG e 55 " ideal model delta sigma weight residual 114.10 126.69 -12.59 2.00e+00 2.50e-01 3.96e+01 angle pdb=" N PRO l 346 " pdb=" CD PRO l 346 " pdb=" CG PRO l 346 " ideal model delta sigma weight residual 103.20 95.11 8.09 1.50e+00 4.44e-01 2.91e+01 angle pdb=" CB ARG i 190 " pdb=" CG ARG i 190 " pdb=" CD ARG i 190 " ideal model delta sigma weight residual 111.30 123.27 -11.97 2.30e+00 1.89e-01 2.71e+01 ... (remaining 159060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 67774 35.49 - 70.98: 2553 70.98 - 106.47: 122 106.47 - 141.97: 0 141.97 - 177.46: 2 Dihedral angle restraints: 70451 sinusoidal: 32086 harmonic: 38365 Sorted by residual: dihedral pdb=" CA MET R 294 " pdb=" C MET R 294 " pdb=" N PRO R 295 " pdb=" CA PRO R 295 " ideal model delta harmonic sigma weight residual -180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA LEU V 9 " pdb=" C LEU V 9 " pdb=" N TYR V 10 " pdb=" CA TYR V 10 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA LEU A 415 " pdb=" C LEU A 415 " pdb=" N ARG A 416 " pdb=" CA ARG A 416 " ideal model delta harmonic sigma weight residual 180.00 153.46 26.54 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 70448 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 17108 0.100 - 0.200: 908 0.200 - 0.300: 31 0.300 - 0.401: 3 0.401 - 0.501: 2 Chirality restraints: 18052 Sorted by residual: chirality pdb=" CB ILE B 870 " pdb=" CA ILE B 870 " pdb=" CG1 ILE B 870 " pdb=" CG2 ILE B 870 " both_signs ideal model delta sigma weight residual False 2.64 2.14 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA PRO l 346 " pdb=" N PRO l 346 " pdb=" C PRO l 346 " pdb=" CB PRO l 346 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CB ILE d 425 " pdb=" CA ILE d 425 " pdb=" CG1 ILE d 425 " pdb=" CG2 ILE d 425 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 18049 not shown) Planarity restraints: 18892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 797 " -0.045 2.00e-02 2.50e+03 3.47e-02 2.40e+01 pdb=" CG TYR B 797 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR B 797 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR B 797 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 797 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 797 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 797 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 797 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 127 " -0.076 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO E 128 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS l 345 " -0.077 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO l 346 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO l 346 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO l 346 " -0.059 5.00e-02 4.00e+02 ... (remaining 18889 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 1927 2.65 - 3.21: 101874 3.21 - 3.78: 193924 3.78 - 4.34: 258557 4.34 - 4.90: 410159 Nonbonded interactions: 966441 Sorted by model distance: nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.091 2.170 nonbonded pdb=" OG1 THR i 24 " pdb=" ND2 ASN i 27 " model vdw 2.198 2.520 nonbonded pdb=" O HIS A 451 " pdb=" OG SER A 454 " model vdw 2.216 2.440 nonbonded pdb=" OG1 THR A 596 " pdb=" O LEU A 598 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR l 110 " pdb=" O LYS l 126 " model vdw 2.236 2.440 ... (remaining 966436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'r' selection = (chain 'v' and resid 38 through 134) } ncs_group { reference = (chain 's' and resid 23 through 102) selection = chain 'w' } ncs_group { reference = (chain 't' and resid 13 through 118) selection = chain 'x' } ncs_group { reference = (chain 'u' and resid 28 through 122) selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 16.380 Check model and map are aligned: 1.180 Set scattering table: 0.760 Process input model: 315.440 Find NCS groups from input model: 3.300 Set up NCS constraints: 0.470 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: 0.020 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 343.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5371 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 116471 Z= 0.266 Angle : 0.748 16.164 159065 Z= 0.389 Chirality : 0.048 0.501 18052 Planarity : 0.006 0.113 18892 Dihedral : 16.416 177.457 45497 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.09 % 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: -0.68 (0.07), residues: 12842 helix: -0.19 (0.06), residues: 5846 sheet: -0.29 (0.13), residues: 1673 loop : -0.61 (0.08), residues: 5323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP 2 483 HIS 0.018 0.001 HIS i 200 PHE 0.049 0.002 PHE j 70 TYR 0.083 0.002 TYR B 797 ARG 0.022 0.001 ARG i 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1264 time to evaluate : 9.173 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: 0 25 MET cc_start: -0.0013 (mpp) cc_final: -0.1108 (mmp) REVERT: 0 61 MET cc_start: 0.1624 (mmm) cc_final: -0.0160 (mtt) REVERT: 1 328 MET cc_start: 0.6778 (pmm) cc_final: 0.5912 (ppp) REVERT: 1 385 MET cc_start: 0.2345 (mtt) cc_final: 0.1338 (mmt) REVERT: 2 227 MET cc_start: -0.6744 (tmm) cc_final: -0.7008 (mtt) REVERT: 3 12 MET cc_start: 0.8268 (tmm) cc_final: 0.8030 (tmm) REVERT: 4 206 MET cc_start: -0.2619 (mtp) cc_final: -0.3335 (ptp) REVERT: 4 252 MET cc_start: -0.2697 (mmp) cc_final: -0.3818 (mmt) REVERT: 6 322 MET cc_start: 0.4631 (ptp) cc_final: 0.3758 (ppp) REVERT: 6 384 MET cc_start: 0.2485 (pmm) cc_final: 0.1840 (ppp) REVERT: 7 112 MET cc_start: -0.1617 (pmm) cc_final: -0.1959 (ttt) REVERT: 7 445 MET cc_start: -0.0094 (mmm) cc_final: -0.0384 (mmp) REVERT: 7 541 MET cc_start: 0.5424 (mmt) cc_final: 0.4428 (mpp) REVERT: 7 561 MET cc_start: -0.1067 (mtp) cc_final: -0.1860 (mmm) REVERT: A 88 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8906 (mmtp) REVERT: A 368 LYS cc_start: 0.8321 (tttt) cc_final: 0.7655 (tttt) REVERT: A 780 VAL cc_start: 0.8720 (t) cc_final: 0.7993 (p) REVERT: A 873 MET cc_start: 0.8832 (mmp) cc_final: 0.8351 (mmm) REVERT: A 1112 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7919 (tttt) REVERT: A 1306 LEU cc_start: 0.8471 (mp) cc_final: 0.8166 (mp) REVERT: A 1398 MET cc_start: 0.7826 (ttt) cc_final: 0.7584 (mtp) REVERT: A 1403 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 115 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7774 (tp40) REVERT: B 135 ARG cc_start: 0.8286 (mmt90) cc_final: 0.7746 (mpt-90) REVERT: B 272 THR cc_start: 0.9339 (m) cc_final: 0.9099 (p) REVERT: B 302 CYS cc_start: 0.8499 (t) cc_final: 0.8287 (t) REVERT: B 388 CYS cc_start: 0.8721 (t) cc_final: 0.8399 (t) REVERT: B 513 GLN cc_start: 0.7964 (mt0) cc_final: 0.7738 (mt0) REVERT: B 662 MET cc_start: 0.8805 (mtt) cc_final: 0.8586 (mtt) REVERT: B 836 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7581 (mt-10) REVERT: B 1124 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.7171 (tpm170) REVERT: C 187 LYS cc_start: 0.8836 (mttm) cc_final: 0.8557 (mttp) REVERT: F 32 LYS cc_start: 0.1329 (mttp) cc_final: 0.1068 (mptt) REVERT: H 137 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7502 (pp30) REVERT: I 113 ASP cc_start: 0.7793 (t0) cc_final: 0.7546 (t0) REVERT: J 67 GLU cc_start: 0.5669 (tm-30) cc_final: 0.4948 (tt0) REVERT: J 69 ARG cc_start: 0.4750 (ttp-170) cc_final: 0.4291 (mmm160) REVERT: M 81 GLU cc_start: 0.6682 (tp30) cc_final: 0.6271 (tp30) REVERT: M 104 MET cc_start: 0.8418 (pmm) cc_final: 0.8074 (tpp) REVERT: M 172 MET cc_start: 0.8651 (mmm) cc_final: 0.8221 (mtm) REVERT: M 182 ARG cc_start: 0.8612 (mmt180) cc_final: 0.8209 (mmt180) REVERT: Q 27 MET cc_start: 0.4719 (ppp) cc_final: 0.3279 (mmm) REVERT: Q 34 MET cc_start: 0.4136 (mpp) cc_final: 0.3373 (ppp) REVERT: Q 413 MET cc_start: 0.7850 (mmm) cc_final: 0.7103 (ppp) REVERT: U 252 THR cc_start: 0.7173 (p) cc_final: 0.6537 (p) REVERT: W 111 ASP cc_start: 0.8178 (m-30) cc_final: 0.7704 (t0) REVERT: W 123 MET cc_start: 0.7265 (tmm) cc_final: 0.6917 (tmm) REVERT: a 281 ASP cc_start: 0.8601 (p0) cc_final: 0.8043 (m-30) REVERT: c 1 MET cc_start: 0.4871 (tpt) cc_final: 0.4235 (tmm) REVERT: d 411 MET cc_start: 0.0563 (tpt) cc_final: -0.0004 (mmm) REVERT: e 52 VAL cc_start: 0.8015 (m) cc_final: 0.7444 (t) REVERT: f 14 PRO cc_start: 0.7932 (Cg_exo) cc_final: 0.7698 (Cg_endo) REVERT: h 51 ASP cc_start: 0.8727 (m-30) cc_final: 0.8482 (m-30) REVERT: h 62 ARG cc_start: 0.1974 (mmm160) cc_final: 0.1362 (mtt-85) REVERT: h 68 ASP cc_start: 0.8914 (m-30) cc_final: 0.8694 (t0) REVERT: h 92 ASN cc_start: 0.9570 (m-40) cc_final: 0.9346 (p0) REVERT: h 130 MET cc_start: 0.7434 (ppp) cc_final: 0.7151 (ppp) REVERT: i 70 MET cc_start: 0.2676 (mmp) cc_final: 0.0787 (tpt) REVERT: i 95 MET cc_start: -0.3203 (ttm) cc_final: -0.5115 (ptt) REVERT: j 138 ASP cc_start: 0.9346 (p0) cc_final: 0.9110 (p0) REVERT: k 1 MET cc_start: 0.0696 (tpt) cc_final: -0.0704 (tpt) REVERT: l 453 MET cc_start: 0.4160 (ttp) cc_final: 0.3141 (ttt) REVERT: l 676 MET cc_start: 0.5739 (ppp) cc_final: 0.5506 (pmm) REVERT: m 122 ASN cc_start: 0.8246 (m-40) cc_final: 0.7921 (m-40) REVERT: n 42 MET cc_start: -0.2005 (pmm) cc_final: -0.4228 (ptt) outliers start: 0 outliers final: 0 residues processed: 1264 average time/residue: 1.0346 time to fit residues: 2198.2821 Evaluate side-chains 723 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 723 time to evaluate : 9.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 1120 optimal weight: 30.0000 chunk 1005 optimal weight: 40.0000 chunk 558 optimal weight: 0.4980 chunk 343 optimal weight: 0.8980 chunk 678 optimal weight: 20.0000 chunk 537 optimal weight: 0.0970 chunk 1040 optimal weight: 4.9990 chunk 402 optimal weight: 4.9990 chunk 632 optimal weight: 5.9990 chunk 774 optimal weight: 110.0000 chunk 1205 optimal weight: 40.0000 overall best weight: 2.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 201 ASN 1 468 GLN 4 64 HIS 4 81 GLN 7 465 ASN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN A 877 HIS ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN B 862 GLN B 878 GLN B 887 HIS B1013 ASN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 ASN E 32 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 ASN I 89 GLN K 92 ASN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 364 GLN d 600 ASN e 57 GLN e 183 GLN f 48 ASN f 63 HIS ** f 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 163 ASN j 9 ASN k 52 ASN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 115 GLN n 7 GLN ** n 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 ASN ** w 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5447 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 116471 Z= 0.260 Angle : 0.601 11.234 159065 Z= 0.320 Chirality : 0.042 0.241 18052 Planarity : 0.004 0.072 18892 Dihedral : 17.311 175.506 18776 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.70 % Favored : 97.29 % Rotamer: Outliers : 0.76 % Allowed : 6.68 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.07), residues: 12842 helix: 0.72 (0.07), residues: 5935 sheet: -0.32 (0.13), residues: 1637 loop : -0.46 (0.08), residues: 5270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 2 483 HIS 0.009 0.001 HIS A 659 PHE 0.032 0.002 PHE j 70 TYR 0.039 0.001 TYR B 797 ARG 0.018 0.000 ARG a 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 757 time to evaluate : 9.188 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: 0 25 MET cc_start: -0.0086 (mpp) cc_final: -0.0451 (mmp) REVERT: 0 61 MET cc_start: 0.1907 (mmm) cc_final: 0.0249 (mtt) REVERT: 0 485 MET cc_start: -0.2722 (mtt) cc_final: -0.2937 (mtt) REVERT: 0 495 MET cc_start: 0.1357 (ptp) cc_final: 0.0167 (tmm) REVERT: 0 679 MET cc_start: 0.5968 (mpp) cc_final: 0.5175 (mpp) REVERT: 1 385 MET cc_start: 0.2390 (mtt) cc_final: 0.1285 (mmt) REVERT: 2 210 MET cc_start: 0.0994 (ptm) cc_final: 0.0526 (ptt) REVERT: 2 249 MET cc_start: 0.0401 (ppp) cc_final: -0.0895 (ptt) REVERT: 4 197 MET cc_start: 0.5608 (ptt) cc_final: 0.5265 (ptt) REVERT: 4 206 MET cc_start: -0.2516 (mtp) cc_final: -0.3241 (ptp) REVERT: 4 252 MET cc_start: -0.2544 (mmp) cc_final: -0.3764 (mmt) REVERT: 6 384 MET cc_start: 0.2497 (pmm) cc_final: 0.2125 (ppp) REVERT: 7 112 MET cc_start: -0.1945 (pmm) cc_final: -0.2196 (ttt) REVERT: 7 445 MET cc_start: 0.0196 (mmm) cc_final: -0.0742 (mpp) REVERT: 7 561 MET cc_start: -0.1040 (mtp) cc_final: -0.1732 (mmm) REVERT: A 177 ASP cc_start: 0.8704 (p0) cc_final: 0.8379 (p0) REVERT: A 368 LYS cc_start: 0.8345 (tttt) cc_final: 0.7663 (tttt) REVERT: A 538 ASP cc_start: 0.7787 (m-30) cc_final: 0.7540 (t0) REVERT: A 1033 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7159 (tm-30) REVERT: A 1112 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7911 (tttt) REVERT: B 115 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7921 (tp40) REVERT: B 302 CYS cc_start: 0.8613 (t) cc_final: 0.8374 (t) REVERT: B 384 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8387 (mmp80) REVERT: B 556 THR cc_start: 0.9109 (m) cc_final: 0.8805 (p) REVERT: B 620 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7589 (ttm-80) REVERT: B 1013 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8605 (t0) REVERT: C 50 GLU cc_start: 0.7595 (tt0) cc_final: 0.7351 (mt-10) REVERT: G 106 MET cc_start: 0.8499 (ptm) cc_final: 0.8095 (ptp) REVERT: H 137 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7385 (pp30) REVERT: J 69 ARG cc_start: 0.5003 (ttp-170) cc_final: 0.4491 (mmm160) REVERT: K 84 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8204 (mtpt) REVERT: M 104 MET cc_start: 0.8495 (pmm) cc_final: 0.8075 (tpp) REVERT: Q 27 MET cc_start: 0.5171 (ppp) cc_final: 0.3013 (mmm) REVERT: Q 34 MET cc_start: 0.4288 (mpp) cc_final: 0.3859 (ptm) REVERT: W 111 ASP cc_start: 0.8162 (m-30) cc_final: 0.7718 (t0) REVERT: X 262 MET cc_start: 0.8552 (ppp) cc_final: 0.8170 (ppp) REVERT: a 48 MET cc_start: 0.6234 (mmt) cc_final: 0.5938 (mmt) REVERT: a 99 MET cc_start: 0.3512 (pmm) cc_final: 0.2879 (ppp) REVERT: a 175 MET cc_start: 0.8907 (mmm) cc_final: 0.8599 (mmm) REVERT: a 281 ASP cc_start: 0.8666 (p0) cc_final: 0.8169 (m-30) REVERT: b 31 GLN cc_start: 0.9208 (pm20) cc_final: 0.8414 (pm20) REVERT: c 1 MET cc_start: 0.5179 (tpt) cc_final: 0.4261 (tmm) REVERT: c 23 MET cc_start: 0.8625 (mmm) cc_final: 0.8206 (mmt) REVERT: d 411 MET cc_start: 0.0959 (tpt) cc_final: 0.0220 (mmm) REVERT: f 14 PRO cc_start: 0.7947 (Cg_exo) cc_final: 0.7702 (Cg_endo) REVERT: f 78 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7596 (ttm) REVERT: h 62 ARG cc_start: 0.2240 (mmm160) cc_final: 0.1527 (mmt180) REVERT: h 68 ASP cc_start: 0.8835 (m-30) cc_final: 0.8620 (t0) REVERT: h 192 MET cc_start: 0.1429 (tmm) cc_final: 0.1223 (tmm) REVERT: i 70 MET cc_start: 0.2747 (mmp) cc_final: 0.0754 (tpt) REVERT: i 95 MET cc_start: -0.3706 (ttm) cc_final: -0.5499 (ptt) REVERT: k 1 MET cc_start: 0.0923 (tpt) cc_final: -0.0642 (tpt) REVERT: k 2 ASN cc_start: 0.8211 (t0) cc_final: 0.7650 (p0) REVERT: l 111 MET cc_start: -0.3151 (tpt) cc_final: -0.3439 (mtt) REVERT: l 357 LEU cc_start: 0.8353 (mp) cc_final: 0.7716 (pt) REVERT: l 453 MET cc_start: 0.4454 (ttp) cc_final: 0.3417 (ttt) REVERT: l 676 MET cc_start: 0.5665 (ppp) cc_final: 0.5418 (pmm) REVERT: n 42 MET cc_start: -0.2257 (pmm) cc_final: -0.4330 (ptt) REVERT: v 90 MET cc_start: 0.0657 (tpt) cc_final: 0.0274 (tpt) outliers start: 89 outliers final: 41 residues processed: 806 average time/residue: 0.9963 time to fit residues: 1373.9803 Evaluate side-chains 687 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 644 time to evaluate : 8.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 350 HIS Chi-restraints excluded: chain 1 residue 66 VAL Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain Q residue 371 ASP Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain b residue 128 TYR Chi-restraints excluded: chain c residue 36 GLU Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 57 GLN Chi-restraints excluded: chain e residue 179 SER Chi-restraints excluded: chain e residue 225 LYS Chi-restraints excluded: chain e residue 286 ILE Chi-restraints excluded: chain e residue 290 VAL Chi-restraints excluded: chain f residue 18 THR Chi-restraints excluded: chain f residue 78 MET Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain i residue 143 MET Chi-restraints excluded: chain p residue 43 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 669 optimal weight: 0.9990 chunk 373 optimal weight: 3.9990 chunk 1002 optimal weight: 8.9990 chunk 820 optimal weight: 30.0000 chunk 332 optimal weight: 1.9990 chunk 1207 optimal weight: 50.0000 chunk 1304 optimal weight: 10.0000 chunk 1075 optimal weight: 50.0000 chunk 1197 optimal weight: 20.0000 chunk 411 optimal weight: 0.9980 chunk 968 optimal weight: 50.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 645 ASN 1 92 ASN 1 575 GLN 2 8 HIS 6 202 GLN ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 650 GLN A 906 HIS A 953 ASN A1270 ASN ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 GLN ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1013 ASN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN W 72 GLN b 45 HIS ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 GLN c 7 GLN ** e 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 4 GLN ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** i 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 157 ASN j 75 GLN ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 29 ASN ** n 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 73 ASN w 25 ASN ** x 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5486 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 116471 Z= 0.324 Angle : 0.583 11.366 159065 Z= 0.309 Chirality : 0.042 0.206 18052 Planarity : 0.004 0.129 18892 Dihedral : 17.229 178.872 18776 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.09 % Allowed : 8.76 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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 (0.07), residues: 12842 helix: 1.07 (0.07), residues: 5928 sheet: -0.34 (0.13), residues: 1612 loop : -0.43 (0.08), residues: 5302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP l 632 HIS 0.010 0.001 HIS A 659 PHE 0.036 0.002 PHE A1220 TYR 0.023 0.001 TYR 7 581 ARG 0.034 0.000 ARG Q 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 678 time to evaluate : 9.333 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: 0 61 MET cc_start: 0.1966 (mmm) cc_final: 0.0451 (mtt) REVERT: 0 485 MET cc_start: -0.2713 (mtt) cc_final: -0.3309 (mtt) REVERT: 0 622 MET cc_start: 0.4389 (tpt) cc_final: 0.4144 (tpt) REVERT: 0 679 MET cc_start: 0.6031 (mpp) cc_final: 0.5346 (mpp) REVERT: 1 385 MET cc_start: 0.2215 (mtt) cc_final: 0.1321 (mmt) REVERT: 3 12 MET cc_start: 0.8577 (tmm) cc_final: 0.8155 (tmm) REVERT: 4 197 MET cc_start: 0.5520 (ptt) cc_final: 0.5259 (ptt) REVERT: 4 206 MET cc_start: -0.2322 (mtp) cc_final: -0.3623 (ptp) REVERT: 4 252 MET cc_start: -0.2592 (mmp) cc_final: -0.3800 (mmt) REVERT: 6 322 MET cc_start: 0.3036 (OUTLIER) cc_final: 0.2175 (ppp) REVERT: 7 445 MET cc_start: 0.0369 (mmm) cc_final: -0.0562 (mpp) REVERT: 7 561 MET cc_start: -0.1150 (mtp) cc_final: -0.1884 (mmm) REVERT: A 22 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.9076 (m-10) REVERT: A 238 CYS cc_start: 0.8300 (t) cc_final: 0.8069 (t) REVERT: A 368 LYS cc_start: 0.8374 (tttt) cc_final: 0.7681 (tttt) REVERT: A 538 ASP cc_start: 0.7945 (m-30) cc_final: 0.7551 (t0) REVERT: A 1033 GLN cc_start: 0.7323 (tm-30) cc_final: 0.6826 (tm-30) REVERT: A 1112 LYS cc_start: 0.8314 (mmmt) cc_final: 0.8043 (mttt) REVERT: B 115 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7951 (tp40) REVERT: B 384 ARG cc_start: 0.8749 (mtp85) cc_final: 0.8508 (mmp80) REVERT: B 556 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8774 (p) REVERT: B 591 ARG cc_start: 0.7749 (mmt180) cc_final: 0.7462 (mmt180) REVERT: B 595 ARG cc_start: 0.7762 (ptm-80) cc_final: 0.7542 (ptm-80) REVERT: C 50 GLU cc_start: 0.7662 (tt0) cc_final: 0.7434 (mt-10) REVERT: G 106 MET cc_start: 0.8570 (ptm) cc_final: 0.8351 (ptp) REVERT: H 137 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7383 (pp30) REVERT: J 69 ARG cc_start: 0.5245 (ttp-170) cc_final: 0.4603 (mmm160) REVERT: K 20 LYS cc_start: 0.8080 (tppt) cc_final: 0.7818 (tppt) REVERT: K 84 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8245 (tttt) REVERT: M 104 MET cc_start: 0.8509 (pmm) cc_final: 0.8065 (tpp) REVERT: M 191 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: Q 27 MET cc_start: 0.4596 (ppp) cc_final: 0.2955 (mmm) REVERT: W 111 ASP cc_start: 0.8190 (m-30) cc_final: 0.7678 (t0) REVERT: W 123 MET cc_start: 0.6677 (tmm) cc_final: 0.6093 (tmm) REVERT: a 175 MET cc_start: 0.9026 (mmm) cc_final: 0.8689 (mmm) REVERT: a 281 ASP cc_start: 0.8695 (p0) cc_final: 0.8193 (m-30) REVERT: b 31 GLN cc_start: 0.8860 (pm20) cc_final: 0.8584 (pm20) REVERT: c 1 MET cc_start: 0.5140 (tpt) cc_final: 0.4196 (tmm) REVERT: d 195 MET cc_start: 0.5706 (tmm) cc_final: 0.4718 (tpt) REVERT: d 313 MET cc_start: 0.2237 (OUTLIER) cc_final: 0.1957 (ttt) REVERT: d 575 ILE cc_start: 0.2382 (OUTLIER) cc_final: 0.1986 (pt) REVERT: e 256 TYR cc_start: 0.7347 (p90) cc_final: 0.6881 (p90) REVERT: f 14 PRO cc_start: 0.8149 (Cg_exo) cc_final: 0.7814 (Cg_endo) REVERT: g 27 MET cc_start: 0.6936 (ppp) cc_final: 0.6058 (ppp) REVERT: h 62 ARG cc_start: 0.2087 (mmm160) cc_final: 0.1600 (mmt180) REVERT: h 68 ASP cc_start: 0.8827 (m-30) cc_final: 0.8615 (t0) REVERT: i 70 MET cc_start: 0.2794 (mmp) cc_final: 0.0781 (tpt) REVERT: i 95 MET cc_start: -0.3715 (ttm) cc_final: -0.5525 (ptt) REVERT: k 1 MET cc_start: 0.0551 (tpt) cc_final: -0.0003 (tpt) REVERT: l 453 MET cc_start: 0.4543 (ttp) cc_final: 0.3652 (ttt) REVERT: l 676 MET cc_start: 0.5741 (ppp) cc_final: 0.5414 (pmm) REVERT: n 42 MET cc_start: -0.2388 (pmm) cc_final: -0.4397 (ptt) REVERT: p 9 GLU cc_start: 0.7348 (pp20) cc_final: 0.6647 (pm20) REVERT: s 84 MET cc_start: 0.1844 (tpp) cc_final: 0.1527 (tpt) REVERT: v 90 MET cc_start: 0.0639 (tpt) cc_final: 0.0175 (tpt) outliers start: 128 outliers final: 69 residues processed: 768 average time/residue: 1.0550 time to fit residues: 1405.2188 Evaluate side-chains 695 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 620 time to evaluate : 9.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 350 HIS Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 1 residue 66 VAL Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 2 residue 8 HIS Chi-restraints excluded: chain 6 residue 322 MET Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 191 GLU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain Q residue 371 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 288 VAL Chi-restraints excluded: chain b residue 42 GLN Chi-restraints excluded: chain b residue 56 LYS Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 199 ASP Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain d residue 313 MET Chi-restraints excluded: chain d residue 575 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 286 ILE Chi-restraints excluded: chain e residue 290 VAL Chi-restraints excluded: chain f residue 130 LEU Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain i residue 143 MET Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain p residue 43 PHE Chi-restraints excluded: chain y residue 59 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 1192 optimal weight: 9.9990 chunk 907 optimal weight: 50.0000 chunk 626 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 576 optimal weight: 0.8980 chunk 810 optimal weight: 7.9990 chunk 1211 optimal weight: 30.0000 chunk 1282 optimal weight: 20.0000 chunk 632 optimal weight: 2.9990 chunk 1148 optimal weight: 40.0000 chunk 345 optimal weight: 3.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 8 HIS 3 107 ASN 4 246 GLN 6 212 ASN 6 296 HIS ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1265 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B1013 ASN ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN ** W 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 ASN ** b 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 GLN ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 GLN ** e 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 197 ASN ** f 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 99 GLN i 111 ASN i 157 ASN i 198 GLN ** j 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 402 HIS ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 57 ASN t 73 ASN x 31 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5516 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 116471 Z= 0.390 Angle : 0.596 14.446 159065 Z= 0.314 Chirality : 0.042 0.230 18052 Planarity : 0.004 0.087 18892 Dihedral : 17.188 178.893 18776 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.32 % Allowed : 10.06 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.44 (0.07), residues: 12842 helix: 1.20 (0.07), residues: 5941 sheet: -0.43 (0.13), residues: 1635 loop : -0.42 (0.09), residues: 5266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP l 632 HIS 0.024 0.001 HIS 2 8 PHE 0.046 0.002 PHE 0 720 TYR 0.024 0.001 TYR A 465 ARG 0.009 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 654 time to evaluate : 9.352 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: 0.1860 (mmm) cc_final: 0.0400 (mtt) REVERT: 0 485 MET cc_start: -0.2682 (mtt) cc_final: -0.3271 (mtt) REVERT: 0 495 MET cc_start: 0.1884 (tmm) cc_final: 0.1604 (tmm) REVERT: 0 622 MET cc_start: 0.4598 (tpt) cc_final: 0.4112 (tpt) REVERT: 1 385 MET cc_start: 0.1989 (mtt) cc_final: 0.1107 (mmt) REVERT: 2 249 MET cc_start: 0.0353 (ppp) cc_final: -0.0474 (ptt) REVERT: 2 253 MET cc_start: -0.4724 (mmm) cc_final: -0.6004 (ptp) REVERT: 4 252 MET cc_start: -0.2276 (mmp) cc_final: -0.3500 (mmt) REVERT: 6 322 MET cc_start: 0.3233 (tmm) cc_final: 0.2957 (tmm) REVERT: 7 112 MET cc_start: -0.2527 (ttt) cc_final: -0.3194 (ppp) REVERT: 7 445 MET cc_start: 0.0336 (mmm) cc_final: -0.0597 (mpp) REVERT: 7 561 MET cc_start: -0.1283 (mtp) cc_final: -0.1974 (mmm) REVERT: A 22 PHE cc_start: 0.9373 (OUTLIER) cc_final: 0.9093 (m-10) REVERT: A 177 ASP cc_start: 0.8786 (p0) cc_final: 0.8582 (p0) REVERT: A 238 CYS cc_start: 0.8292 (t) cc_final: 0.8003 (t) REVERT: A 304 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8068 (mmt) REVERT: A 368 LYS cc_start: 0.8491 (tttt) cc_final: 0.7749 (tttt) REVERT: A 538 ASP cc_start: 0.8040 (m-30) cc_final: 0.7785 (m-30) REVERT: A 780 VAL cc_start: 0.8477 (t) cc_final: 0.8248 (p) REVERT: A 1112 LYS cc_start: 0.8378 (mmmt) cc_final: 0.8057 (mttt) REVERT: B 384 ARG cc_start: 0.8801 (mmp80) cc_final: 0.8590 (mmp80) REVERT: B 595 ARG cc_start: 0.7783 (ptm-80) cc_final: 0.7446 (ttp80) REVERT: C 227 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8934 (p) REVERT: G 106 MET cc_start: 0.8572 (ptm) cc_final: 0.8223 (ptm) REVERT: H 137 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7420 (pp30) REVERT: J 69 ARG cc_start: 0.5207 (ttp-170) cc_final: 0.4719 (mmm160) REVERT: K 20 LYS cc_start: 0.8100 (tppt) cc_final: 0.7865 (tppt) REVERT: K 84 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8371 (tttt) REVERT: M 104 MET cc_start: 0.8542 (pmm) cc_final: 0.8054 (tpp) REVERT: M 191 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: Q 27 MET cc_start: 0.4985 (ppp) cc_final: 0.3309 (mmm) REVERT: W 111 ASP cc_start: 0.8228 (m-30) cc_final: 0.7670 (t0) REVERT: X 262 MET cc_start: 0.8122 (ppp) cc_final: 0.7728 (ppp) REVERT: X 265 ASN cc_start: 0.8119 (m110) cc_final: 0.7898 (p0) REVERT: a 108 MET cc_start: 0.4279 (mmt) cc_final: 0.3963 (mmt) REVERT: a 175 MET cc_start: 0.9053 (mmm) cc_final: 0.8732 (mmm) REVERT: a 281 ASP cc_start: 0.8732 (p0) cc_final: 0.8281 (m-30) REVERT: b 31 GLN cc_start: 0.8901 (pm20) cc_final: 0.8620 (pm20) REVERT: c 1 MET cc_start: 0.5133 (tpt) cc_final: 0.4178 (tmm) REVERT: c 23 MET cc_start: 0.7701 (mmt) cc_final: 0.7426 (mmt) REVERT: d 195 MET cc_start: 0.5672 (tmm) cc_final: 0.4709 (tpt) REVERT: d 575 ILE cc_start: 0.2575 (OUTLIER) cc_final: 0.2242 (pt) REVERT: d 634 MET cc_start: 0.5994 (tmm) cc_final: 0.5485 (tpt) REVERT: e 256 TYR cc_start: 0.7450 (p90) cc_final: 0.7221 (p90) REVERT: f 14 PRO cc_start: 0.8278 (Cg_exo) cc_final: 0.8031 (Cg_endo) REVERT: g 57 MET cc_start: 0.7573 (tmm) cc_final: 0.7236 (ttp) REVERT: h 62 ARG cc_start: 0.1984 (mmm160) cc_final: 0.1650 (mmt180) REVERT: h 68 ASP cc_start: 0.8799 (m-30) cc_final: 0.8591 (t0) REVERT: h 130 MET cc_start: 0.7370 (ppp) cc_final: 0.7121 (ppp) REVERT: i 70 MET cc_start: 0.2616 (mmp) cc_final: 0.0752 (tpt) REVERT: i 95 MET cc_start: -0.3303 (ttm) cc_final: -0.5259 (ptt) REVERT: j 95 ARG cc_start: 0.1975 (ptt90) cc_final: 0.1706 (ptt180) REVERT: k 1 MET cc_start: 0.0333 (tpt) cc_final: -0.0713 (tpt) REVERT: k 2 ASN cc_start: 0.8090 (t0) cc_final: 0.7486 (p0) REVERT: l 453 MET cc_start: 0.4432 (ttp) cc_final: 0.3607 (ttt) REVERT: l 650 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8041 (p) REVERT: n 42 MET cc_start: -0.2388 (pmm) cc_final: -0.4407 (ptt) REVERT: p 9 GLU cc_start: 0.7283 (pp20) cc_final: 0.6537 (pm20) REVERT: v 90 MET cc_start: 0.0639 (tpt) cc_final: 0.0197 (tpt) outliers start: 156 outliers final: 96 residues processed: 766 average time/residue: 0.9714 time to fit residues: 1285.7492 Evaluate side-chains 701 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 599 time to evaluate : 9.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 350 HIS Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 1 residue 66 VAL Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 191 GLU Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 371 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain b residue 56 LYS Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 128 TYR Chi-restraints excluded: chain b residue 129 VAL Chi-restraints excluded: chain b residue 199 ASP Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain d residue 575 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 286 ILE Chi-restraints excluded: chain e residue 290 VAL Chi-restraints excluded: chain f residue 130 LEU Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 174 LEU Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain i residue 143 MET Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 104 LEU Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain l residue 650 VAL Chi-restraints excluded: chain p residue 43 PHE Chi-restraints excluded: chain x residue 101 THR Chi-restraints excluded: chain y residue 59 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 1068 optimal weight: 20.0000 chunk 728 optimal weight: 3.9990 chunk 18 optimal weight: 30.0000 chunk 955 optimal weight: 6.9990 chunk 529 optimal weight: 1.9990 chunk 1094 optimal weight: 9.9990 chunk 886 optimal weight: 30.0000 chunk 1 optimal weight: 8.9990 chunk 654 optimal weight: 4.9990 chunk 1151 optimal weight: 50.0000 chunk 323 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 416 HIS 7 230 ASN ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 HIS A 517 ASN A 906 HIS A1048 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 HIS ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 113 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN W 263 ASN ** W 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 66 GLN ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 84 GLN f 118 GLN ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 157 ASN ** i 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 116471 Z= 0.391 Angle : 0.600 11.553 159065 Z= 0.315 Chirality : 0.042 0.227 18052 Planarity : 0.004 0.080 18892 Dihedral : 17.156 177.606 18776 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.59 % Allowed : 11.07 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.50 (0.07), residues: 12842 helix: 1.30 (0.07), residues: 5942 sheet: -0.45 (0.13), residues: 1633 loop : -0.43 (0.09), residues: 5267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP l 632 HIS 0.011 0.001 HIS A 659 PHE 0.050 0.002 PHE 0 720 TYR 0.022 0.001 TYR A 465 ARG 0.014 0.000 ARG a 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 634 time to evaluate : 9.394 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 61 MET cc_start: 0.1855 (mmm) cc_final: 0.0575 (mtt) REVERT: 0 76 MET cc_start: 0.4829 (mmm) cc_final: 0.4580 (mmp) REVERT: 0 485 MET cc_start: -0.2605 (mtt) cc_final: -0.3014 (mtt) REVERT: 0 642 MET cc_start: 0.3317 (ttp) cc_final: 0.2811 (ppp) REVERT: 0 724 MET cc_start: -0.1539 (ptt) cc_final: -0.2007 (ptt) REVERT: 1 58 MET cc_start: -0.0491 (ttt) cc_final: -0.0976 (ttt) REVERT: 1 59 MET cc_start: 0.6566 (mmm) cc_final: 0.6290 (mmm) REVERT: 1 385 MET cc_start: 0.1966 (mtt) cc_final: 0.1085 (mmt) REVERT: 2 150 MET cc_start: -0.2944 (tpp) cc_final: -0.3354 (mmt) REVERT: 2 253 MET cc_start: -0.4735 (mmm) cc_final: -0.6200 (ptp) REVERT: 3 12 MET cc_start: 0.8544 (tmm) cc_final: 0.8268 (tmm) REVERT: 4 197 MET cc_start: 0.5543 (ptt) cc_final: 0.5249 (ptt) REVERT: 4 252 MET cc_start: -0.2490 (mmp) cc_final: -0.3736 (mmt) REVERT: 7 112 MET cc_start: -0.2310 (ttt) cc_final: -0.3485 (ppp) REVERT: 7 445 MET cc_start: 0.0691 (mmm) cc_final: -0.0226 (mpp) REVERT: 7 561 MET cc_start: -0.1275 (mtp) cc_final: -0.1968 (mmm) REVERT: A 22 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.9055 (m-10) REVERT: A 238 CYS cc_start: 0.8260 (t) cc_final: 0.7999 (t) REVERT: A 332 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6912 (mmmt) REVERT: A 368 LYS cc_start: 0.8507 (tttt) cc_final: 0.7728 (tttt) REVERT: A 780 VAL cc_start: 0.8507 (t) cc_final: 0.8280 (p) REVERT: A 1033 GLN cc_start: 0.7438 (tm-30) cc_final: 0.6876 (tm-30) REVERT: A 1112 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8098 (mttt) REVERT: A 1280 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6977 (tm-30) REVERT: A 1281 ARG cc_start: 0.7548 (ptt180) cc_final: 0.6847 (ptt180) REVERT: B 40 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: B 101 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7787 (ptt) REVERT: B 277 LYS cc_start: 0.7576 (pttm) cc_final: 0.7188 (ptpp) REVERT: B 282 ILE cc_start: 0.9203 (pt) cc_final: 0.8920 (mm) REVERT: B 328 GLU cc_start: 0.8121 (mp0) cc_final: 0.7731 (mp0) REVERT: B 378 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9394 (tt) REVERT: B 556 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8754 (p) REVERT: B 595 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.7467 (ttp80) REVERT: C 227 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8965 (p) REVERT: E 196 VAL cc_start: 0.9071 (OUTLIER) cc_final: 0.8867 (p) REVERT: G 106 MET cc_start: 0.8558 (ptm) cc_final: 0.8234 (ptm) REVERT: G 115 MET cc_start: 0.5827 (ptt) cc_final: 0.5619 (ppp) REVERT: H 137 GLN cc_start: 0.8029 (mm-40) cc_final: 0.7163 (pp30) REVERT: I 90 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: J 69 ARG cc_start: 0.5118 (ttp-170) cc_final: 0.4763 (mmm160) REVERT: K 84 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8368 (tttt) REVERT: M 104 MET cc_start: 0.8548 (pmm) cc_final: 0.8045 (tpp) REVERT: M 191 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: O 240 MET cc_start: 0.7212 (mtt) cc_final: 0.6626 (mmt) REVERT: Q 27 MET cc_start: 0.5022 (ppp) cc_final: 0.3197 (mmm) REVERT: W 111 ASP cc_start: 0.8159 (m-30) cc_final: 0.7654 (t0) REVERT: W 123 MET cc_start: 0.7105 (tmm) cc_final: 0.6594 (tmm) REVERT: X 262 MET cc_start: 0.8490 (ppp) cc_final: 0.7829 (ppp) REVERT: X 265 ASN cc_start: 0.8196 (m110) cc_final: 0.7910 (p0) REVERT: a 175 MET cc_start: 0.9116 (mmm) cc_final: 0.8831 (mmm) REVERT: a 281 ASP cc_start: 0.8791 (p0) cc_final: 0.8499 (m-30) REVERT: c 1 MET cc_start: 0.5228 (tpt) cc_final: 0.4290 (tmm) REVERT: c 23 MET cc_start: 0.7679 (mmt) cc_final: 0.7271 (mmt) REVERT: d 195 MET cc_start: 0.5606 (tmm) cc_final: 0.4909 (tpt) REVERT: d 207 MET cc_start: 0.8543 (mtt) cc_final: 0.8179 (mtt) REVERT: d 575 ILE cc_start: 0.2801 (OUTLIER) cc_final: 0.2447 (pt) REVERT: d 634 MET cc_start: 0.5886 (tmm) cc_final: 0.5617 (tpt) REVERT: e 256 TYR cc_start: 0.7570 (p90) cc_final: 0.7317 (p90) REVERT: f 14 PRO cc_start: 0.8345 (Cg_exo) cc_final: 0.8059 (Cg_endo) REVERT: h 68 ASP cc_start: 0.8835 (m-30) cc_final: 0.8591 (t0) REVERT: h 130 MET cc_start: 0.7368 (ppp) cc_final: 0.6823 (ppp) REVERT: i 70 MET cc_start: 0.2706 (mmp) cc_final: 0.0872 (tpt) REVERT: i 95 MET cc_start: -0.2634 (ttm) cc_final: -0.4801 (ptt) REVERT: k 1 MET cc_start: 0.0225 (tpt) cc_final: -0.0743 (tpt) REVERT: l 260 MET cc_start: -0.2643 (tpt) cc_final: -0.3392 (tpt) REVERT: l 453 MET cc_start: 0.4265 (ttp) cc_final: 0.3441 (ttt) REVERT: m 111 MET cc_start: -0.0457 (tmm) cc_final: -0.0793 (tmm) REVERT: n 42 MET cc_start: -0.2373 (pmm) cc_final: -0.4407 (ptt) REVERT: s 88 TYR cc_start: -0.1542 (OUTLIER) cc_final: -0.2014 (m-80) REVERT: v 90 MET cc_start: 0.0650 (tpt) cc_final: 0.0237 (tpt) outliers start: 187 outliers final: 115 residues processed: 774 average time/residue: 0.9750 time to fit residues: 1317.6978 Evaluate side-chains 728 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 601 time to evaluate : 9.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 350 HIS Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 7 residue 459 MET Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1225 PHE Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU 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 1072 MET Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain I residue 90 GLN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 191 GLU Chi-restraints excluded: chain M residue 210 MET Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 371 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain b residue 56 LYS Chi-restraints excluded: chain b residue 91 ASP Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 128 TYR Chi-restraints excluded: chain b residue 129 VAL Chi-restraints excluded: chain b residue 199 ASP Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain d residue 575 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 286 ILE Chi-restraints excluded: chain e residue 290 VAL Chi-restraints excluded: chain f residue 130 LEU Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 174 LEU Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain i residue 98 THR Chi-restraints excluded: chain i residue 143 MET Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain k residue 142 ASP Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain p residue 43 PHE Chi-restraints excluded: chain s residue 88 TYR Chi-restraints excluded: chain x residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 431 optimal weight: 10.0000 chunk 1155 optimal weight: 50.0000 chunk 253 optimal weight: 6.9990 chunk 753 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 chunk 1283 optimal weight: 50.0000 chunk 1065 optimal weight: 10.0000 chunk 594 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 424 optimal weight: 0.7980 chunk 674 optimal weight: 20.0000 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1178 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN L 66 GLN M 303 GLN Q 113 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN ** W 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 96 HIS ** k 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 116471 Z= 0.492 Angle : 0.641 14.467 159065 Z= 0.335 Chirality : 0.044 0.267 18052 Planarity : 0.004 0.096 18892 Dihedral : 17.165 177.030 18776 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.41 % Favored : 96.58 % Rotamer: Outliers : 1.55 % Allowed : 12.14 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.48 (0.08), residues: 12842 helix: 1.33 (0.07), residues: 5942 sheet: -0.53 (0.13), residues: 1667 loop : -0.49 (0.09), residues: 5233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP l 632 HIS 0.012 0.001 HIS A 659 PHE 0.040 0.002 PHE 0 720 TYR 0.033 0.001 TYR h 43 ARG 0.016 0.001 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 609 time to evaluate : 9.185 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 61 MET cc_start: 0.2132 (mmm) cc_final: 0.0713 (mtt) REVERT: 0 485 MET cc_start: -0.2340 (mtt) cc_final: -0.3057 (mtt) REVERT: 0 642 MET cc_start: 0.3548 (ttp) cc_final: 0.3144 (ppp) REVERT: 0 724 MET cc_start: -0.1361 (ptt) cc_final: -0.1609 (ptt) REVERT: 1 385 MET cc_start: 0.1994 (mtt) cc_final: 0.1107 (mmt) REVERT: 2 150 MET cc_start: -0.2947 (tpp) cc_final: -0.3266 (tpp) REVERT: 4 197 MET cc_start: 0.5409 (ptt) cc_final: 0.5049 (ptt) REVERT: 4 252 MET cc_start: -0.2031 (mmp) cc_final: -0.3245 (mmt) REVERT: 7 112 MET cc_start: -0.2087 (ttt) cc_final: -0.3603 (ppp) REVERT: 7 445 MET cc_start: 0.0798 (mmm) cc_final: -0.0147 (mpp) REVERT: 7 561 MET cc_start: -0.1167 (mtp) cc_final: -0.1882 (mmm) REVERT: A 22 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.9093 (m-10) REVERT: A 41 MET cc_start: 0.9266 (mmm) cc_final: 0.9029 (mmm) REVERT: A 238 CYS cc_start: 0.8296 (t) cc_final: 0.8005 (t) REVERT: A 257 ARG cc_start: 0.7769 (mmm160) cc_final: 0.7536 (mmm160) REVERT: A 332 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7211 (mmmt) REVERT: A 368 LYS cc_start: 0.8537 (tttt) cc_final: 0.7730 (tttt) REVERT: A 566 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9007 (mm) REVERT: A 780 VAL cc_start: 0.8522 (t) cc_final: 0.8304 (p) REVERT: A 1033 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7025 (tm-30) REVERT: A 1112 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8085 (tttt) REVERT: B 40 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: B 101 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7651 (ptt) REVERT: B 282 ILE cc_start: 0.9163 (pt) cc_final: 0.8894 (mm) REVERT: B 328 GLU cc_start: 0.8301 (mp0) cc_final: 0.7899 (mp0) REVERT: B 378 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9425 (tt) REVERT: B 595 ARG cc_start: 0.7802 (ptm-80) cc_final: 0.7503 (ttp80) REVERT: B 620 ARG cc_start: 0.8401 (mtp85) cc_final: 0.8084 (ttm-80) REVERT: C 227 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.9037 (p) REVERT: F 29 TYR cc_start: 0.5669 (m-80) cc_final: 0.5018 (m-80) REVERT: G 106 MET cc_start: 0.8615 (ptm) cc_final: 0.8302 (ptp) REVERT: G 115 MET cc_start: 0.5891 (ptt) cc_final: 0.5576 (ppp) REVERT: H 137 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7178 (pp30) REVERT: J 69 ARG cc_start: 0.5181 (ttp-170) cc_final: 0.4897 (mmm160) REVERT: K 84 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8442 (tttt) REVERT: M 141 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: O 240 MET cc_start: 0.7229 (mtt) cc_final: 0.6689 (mmt) REVERT: Q 27 MET cc_start: 0.5380 (ppp) cc_final: 0.3312 (mmm) REVERT: W 111 ASP cc_start: 0.8154 (m-30) cc_final: 0.7640 (t0) REVERT: X 262 MET cc_start: 0.8672 (ppp) cc_final: 0.8068 (ppp) REVERT: X 265 ASN cc_start: 0.8440 (m110) cc_final: 0.8040 (p0) REVERT: a 175 MET cc_start: 0.9125 (mmm) cc_final: 0.8830 (mmm) REVERT: a 281 ASP cc_start: 0.8806 (p0) cc_final: 0.8552 (m-30) REVERT: c 1 MET cc_start: 0.5441 (tpt) cc_final: 0.4370 (tmm) REVERT: c 23 MET cc_start: 0.7690 (mmt) cc_final: 0.7268 (mmt) REVERT: d 195 MET cc_start: 0.5864 (tmm) cc_final: 0.5058 (tpt) REVERT: d 575 ILE cc_start: 0.2980 (OUTLIER) cc_final: 0.2627 (pt) REVERT: f 14 PRO cc_start: 0.8449 (Cg_exo) cc_final: 0.8141 (Cg_endo) REVERT: h 68 ASP cc_start: 0.8836 (m-30) cc_final: 0.8597 (t0) REVERT: h 130 MET cc_start: 0.7359 (ppp) cc_final: 0.6832 (ppp) REVERT: i 70 MET cc_start: 0.2748 (mmp) cc_final: 0.0923 (tpt) REVERT: i 95 MET cc_start: -0.2652 (ttm) cc_final: -0.4839 (ptt) REVERT: k 1 MET cc_start: 0.0166 (tpt) cc_final: -0.0866 (tpt) REVERT: k 2 ASN cc_start: 0.8222 (t0) cc_final: 0.7537 (p0) REVERT: l 260 MET cc_start: -0.2256 (tpt) cc_final: -0.2717 (tpt) REVERT: l 453 MET cc_start: 0.4395 (ttp) cc_final: 0.3556 (ttt) REVERT: l 650 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.7906 (p) REVERT: m 111 MET cc_start: -0.0031 (tmm) cc_final: -0.0466 (tmm) REVERT: n 42 MET cc_start: -0.2922 (pmm) cc_final: -0.4776 (ptt) REVERT: v 90 MET cc_start: 0.0599 (tpt) cc_final: 0.0209 (tpt) outliers start: 182 outliers final: 135 residues processed: 745 average time/residue: 0.9749 time to fit residues: 1264.4008 Evaluate side-chains 715 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 570 time to evaluate : 9.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 350 HIS Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 3 residue 28 PHE Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1386 ARG Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU 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 1072 MET Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 127 GLU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 191 GLU Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 371 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain X residue 292 THR Chi-restraints excluded: chain b residue 91 ASP Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 128 TYR Chi-restraints excluded: chain b residue 129 VAL Chi-restraints excluded: chain b residue 199 ASP Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain d residue 575 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 259 VAL Chi-restraints excluded: chain e residue 286 ILE Chi-restraints excluded: chain e residue 290 VAL Chi-restraints excluded: chain f residue 130 LEU Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 174 LEU Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain i residue 98 THR Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain l residue 650 VAL Chi-restraints excluded: chain p residue 43 PHE Chi-restraints excluded: chain s residue 88 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 1237 optimal weight: 30.0000 chunk 144 optimal weight: 30.0000 chunk 731 optimal weight: 4.9990 chunk 937 optimal weight: 50.0000 chunk 726 optimal weight: 2.9990 chunk 1080 optimal weight: 6.9990 chunk 716 optimal weight: 0.8980 chunk 1279 optimal weight: 50.0000 chunk 800 optimal weight: 8.9990 chunk 779 optimal weight: 50.0000 chunk 590 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN 6 418 ASN ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 113 ASN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 ASN ** W 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 270 GLN ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 75 GLN ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 702 HIS ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 116471 Z= 0.317 Angle : 0.587 14.305 159065 Z= 0.306 Chirality : 0.042 0.348 18052 Planarity : 0.004 0.066 18892 Dihedral : 17.139 176.519 18776 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.09 % Favored : 96.90 % Rotamer: Outliers : 1.43 % Allowed : 13.21 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.59 (0.08), residues: 12842 helix: 1.42 (0.07), residues: 5944 sheet: -0.50 (0.13), residues: 1640 loop : -0.42 (0.09), residues: 5258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP l 632 HIS 0.017 0.001 HIS l 702 PHE 0.031 0.001 PHE 0 720 TYR 0.050 0.001 TYR h 43 ARG 0.007 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 612 time to evaluate : 9.282 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 61 MET cc_start: 0.2188 (mmm) cc_final: 0.0770 (mtt) REVERT: 0 485 MET cc_start: -0.2309 (mtt) cc_final: -0.2722 (mtt) REVERT: 0 642 MET cc_start: 0.3662 (ttp) cc_final: 0.3259 (ppp) REVERT: 1 385 MET cc_start: 0.1996 (mtt) cc_final: 0.1098 (mmt) REVERT: 2 150 MET cc_start: -0.2789 (tpp) cc_final: -0.3112 (mmt) REVERT: 3 12 MET cc_start: 0.8491 (tmm) cc_final: 0.7283 (tmm) REVERT: 4 197 MET cc_start: 0.5266 (ptt) cc_final: 0.4891 (ptt) REVERT: 4 252 MET cc_start: -0.1972 (mmp) cc_final: -0.3168 (mmt) REVERT: 7 112 MET cc_start: -0.2348 (ttt) cc_final: -0.3935 (ppp) REVERT: 7 445 MET cc_start: 0.0929 (mmm) cc_final: 0.0002 (mpp) REVERT: 7 561 MET cc_start: -0.1183 (mtp) cc_final: -0.1914 (mmm) REVERT: A 22 PHE cc_start: 0.9384 (OUTLIER) cc_final: 0.9030 (m-10) REVERT: A 238 CYS cc_start: 0.8229 (t) cc_final: 0.7970 (t) REVERT: A 332 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7014 (mmmt) REVERT: A 368 LYS cc_start: 0.8483 (tttt) cc_final: 0.7669 (tttt) REVERT: A 566 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8985 (mm) REVERT: A 658 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8180 (tp) REVERT: A 780 VAL cc_start: 0.8523 (t) cc_final: 0.8277 (p) REVERT: A 838 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: A 1033 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7014 (tm-30) REVERT: A 1112 LYS cc_start: 0.8361 (mmmt) cc_final: 0.8015 (tttt) REVERT: B 40 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: B 101 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7360 (ptt) REVERT: B 282 ILE cc_start: 0.9144 (pt) cc_final: 0.8894 (mm) REVERT: B 328 GLU cc_start: 0.8328 (mp0) cc_final: 0.8062 (mp0) REVERT: B 378 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9405 (tt) REVERT: B 595 ARG cc_start: 0.7683 (ptm-80) cc_final: 0.7351 (ttp80) REVERT: B 620 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8027 (ttm-80) REVERT: B 891 ASP cc_start: 0.7769 (p0) cc_final: 0.7516 (p0) REVERT: F 16 GLU cc_start: -0.1244 (OUTLIER) cc_final: -0.1692 (mm-30) REVERT: G 106 MET cc_start: 0.8680 (ptm) cc_final: 0.8361 (ptp) REVERT: G 115 MET cc_start: 0.5931 (ptt) cc_final: 0.5640 (ppp) REVERT: J 69 ARG cc_start: 0.5097 (ttp-170) cc_final: 0.4893 (mmm160) REVERT: K 20 LYS cc_start: 0.8098 (tppt) cc_final: 0.7895 (tppt) REVERT: K 84 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8396 (tttt) REVERT: M 104 MET cc_start: 0.8434 (pmm) cc_final: 0.7905 (tpp) REVERT: M 136 LEU cc_start: 0.9380 (mt) cc_final: 0.9144 (mt) REVERT: M 191 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: O 240 MET cc_start: 0.7152 (mtt) cc_final: 0.6687 (mmt) REVERT: Q 27 MET cc_start: 0.5377 (ppp) cc_final: 0.3264 (mmm) REVERT: Q 425 MET cc_start: 0.6866 (ppp) cc_final: 0.6046 (ppp) REVERT: W 111 ASP cc_start: 0.8106 (m-30) cc_final: 0.7595 (t0) REVERT: X 262 MET cc_start: 0.8656 (ppp) cc_final: 0.8045 (ppp) REVERT: X 265 ASN cc_start: 0.8445 (m110) cc_final: 0.8052 (p0) REVERT: a 101 MET cc_start: 0.7828 (mmm) cc_final: 0.7572 (mmm) REVERT: a 175 MET cc_start: 0.9145 (mmm) cc_final: 0.8880 (mmm) REVERT: a 281 ASP cc_start: 0.8832 (p0) cc_final: 0.8573 (m-30) REVERT: b 31 GLN cc_start: 0.9026 (pm20) cc_final: 0.8676 (pp30) REVERT: c 1 MET cc_start: 0.5261 (tpt) cc_final: 0.4284 (tmm) REVERT: c 23 MET cc_start: 0.7636 (mmt) cc_final: 0.7075 (mmt) REVERT: d 195 MET cc_start: 0.5746 (tmm) cc_final: 0.4986 (tpt) REVERT: d 207 MET cc_start: 0.8568 (mtt) cc_final: 0.8226 (mtt) REVERT: d 575 ILE cc_start: 0.3020 (OUTLIER) cc_final: 0.2729 (pt) REVERT: f 14 PRO cc_start: 0.8481 (Cg_exo) cc_final: 0.8176 (Cg_endo) REVERT: f 123 LYS cc_start: 0.8109 (tppp) cc_final: 0.7584 (pttm) REVERT: g 57 MET cc_start: 0.7550 (tmm) cc_final: 0.7321 (tpp) REVERT: h 68 ASP cc_start: 0.8894 (m-30) cc_final: 0.8650 (t0) REVERT: h 130 MET cc_start: 0.7324 (ppp) cc_final: 0.7088 (ppp) REVERT: i 70 MET cc_start: 0.2764 (mmp) cc_final: 0.0927 (tpt) REVERT: i 95 MET cc_start: -0.2689 (ttm) cc_final: -0.4855 (ptt) REVERT: k 1 MET cc_start: 0.0170 (tpt) cc_final: -0.0791 (tpt) REVERT: l 260 MET cc_start: -0.2115 (tpt) cc_final: -0.2506 (tpt) REVERT: l 453 MET cc_start: 0.4229 (ttp) cc_final: 0.3634 (ttt) REVERT: l 650 VAL cc_start: 0.8369 (OUTLIER) cc_final: 0.7896 (p) REVERT: m 111 MET cc_start: -0.0116 (tmm) cc_final: -0.0531 (tmm) REVERT: n 42 MET cc_start: -0.2753 (pmm) cc_final: -0.4577 (ptt) REVERT: v 90 MET cc_start: 0.1138 (tpt) cc_final: 0.0841 (tpt) outliers start: 168 outliers final: 120 residues processed: 737 average time/residue: 0.9716 time to fit residues: 1244.1837 Evaluate side-chains 719 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 587 time to evaluate : 9.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 350 HIS Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 3 residue 28 PHE Chi-restraints excluded: chain 6 residue 418 ASN Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain I residue 37 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 191 GLU Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain O residue 228 GLU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 371 ASP Chi-restraints excluded: chain R residue 83 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain b residue 91 ASP Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 128 TYR Chi-restraints excluded: chain b residue 129 VAL Chi-restraints excluded: chain b residue 199 ASP Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain d residue 575 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 259 VAL Chi-restraints excluded: chain e residue 286 ILE Chi-restraints excluded: chain f residue 130 LEU Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 174 LEU Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain i residue 98 THR Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain l residue 650 VAL Chi-restraints excluded: chain l residue 703 MET Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain p residue 43 PHE Chi-restraints excluded: chain s residue 88 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 791 optimal weight: 20.0000 chunk 510 optimal weight: 2.9990 chunk 763 optimal weight: 80.0000 chunk 385 optimal weight: 0.9990 chunk 251 optimal weight: 10.0000 chunk 247 optimal weight: 50.0000 chunk 813 optimal weight: 20.0000 chunk 871 optimal weight: 40.0000 chunk 632 optimal weight: 2.9990 chunk 119 optimal weight: 50.0000 chunk 1005 optimal weight: 40.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 23 ASN ** 0 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 8 HIS 6 212 ASN ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 660 ASN A 741 ASN A 906 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN K 92 ASN ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 GLN ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 104 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.149 116471 Z= 0.626 Angle : 0.704 12.125 159065 Z= 0.366 Chirality : 0.046 0.312 18052 Planarity : 0.005 0.135 18892 Dihedral : 17.197 176.324 18776 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.82 % Favored : 96.17 % Rotamer: Outliers : 1.71 % Allowed : 13.32 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.40 (0.08), residues: 12842 helix: 1.29 (0.07), residues: 5965 sheet: -0.62 (0.13), residues: 1660 loop : -0.55 (0.09), residues: 5217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP l 632 HIS 0.016 0.001 HIS A 659 PHE 0.036 0.002 PHE B 963 TYR 0.043 0.002 TYR h 43 ARG 0.013 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 597 time to evaluate : 9.240 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: 0 485 MET cc_start: -0.2530 (mtt) cc_final: -0.2919 (mtt) REVERT: 0 642 MET cc_start: 0.3916 (ttp) cc_final: 0.3477 (ppp) REVERT: 0 679 MET cc_start: 0.4948 (mpp) cc_final: 0.4397 (mmp) REVERT: 1 59 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5376 (mmt) REVERT: 1 385 MET cc_start: 0.1808 (mtt) cc_final: 0.0959 (mmt) REVERT: 2 150 MET cc_start: -0.2837 (tpp) cc_final: -0.3107 (mmt) REVERT: 2 373 MET cc_start: 0.3818 (pmm) cc_final: 0.3532 (pmm) REVERT: 3 12 MET cc_start: 0.8682 (tmm) cc_final: 0.8080 (tmm) REVERT: 4 197 MET cc_start: 0.5627 (ptt) cc_final: 0.5249 (ptt) REVERT: 4 252 MET cc_start: -0.1802 (mmp) cc_final: -0.3046 (mmt) REVERT: 5 13 ASP cc_start: 0.1537 (OUTLIER) cc_final: 0.1164 (p0) REVERT: 7 112 MET cc_start: -0.2375 (ttt) cc_final: -0.3071 (ptm) REVERT: 7 445 MET cc_start: 0.0722 (mmm) cc_final: -0.0508 (mpp) REVERT: 7 561 MET cc_start: -0.1025 (mtp) cc_final: -0.1524 (mmm) REVERT: A 22 PHE cc_start: 0.9378 (OUTLIER) cc_final: 0.9071 (m-10) REVERT: A 238 CYS cc_start: 0.8376 (t) cc_final: 0.8094 (t) REVERT: A 368 LYS cc_start: 0.8435 (tttt) cc_final: 0.7745 (tttt) REVERT: A 501 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 566 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8938 (mm) REVERT: A 780 VAL cc_start: 0.8526 (t) cc_final: 0.8311 (p) REVERT: A 838 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: A 1033 GLN cc_start: 0.7578 (tm-30) cc_final: 0.7069 (tm-30) REVERT: A 1112 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8010 (ttmt) REVERT: B 40 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: B 101 MET cc_start: 0.8574 (ptt) cc_final: 0.7881 (ptt) REVERT: B 115 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7959 (tp40) REVERT: B 282 ILE cc_start: 0.9172 (pt) cc_final: 0.8906 (mm) REVERT: B 328 GLU cc_start: 0.8330 (mp0) cc_final: 0.8031 (mp0) REVERT: B 378 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9441 (tt) REVERT: B 476 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6169 (mtp85) REVERT: B 595 ARG cc_start: 0.7804 (ptm-80) cc_final: 0.7511 (ttp80) REVERT: B 620 ARG cc_start: 0.8421 (mtp85) cc_final: 0.8097 (ttm-80) REVERT: F 29 TYR cc_start: 0.5543 (m-80) cc_final: 0.4743 (m-80) REVERT: F 63 GLN cc_start: 0.5753 (tp40) cc_final: 0.5108 (pt0) REVERT: G 1 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8292 (ppp) REVERT: I 60 GLN cc_start: 0.7056 (pm20) cc_final: 0.6845 (pp30) REVERT: J 34 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8516 (p) REVERT: J 69 ARG cc_start: 0.5138 (ttp-170) cc_final: 0.4904 (mmm160) REVERT: K 84 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8452 (tttt) REVERT: M 141 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: O 240 MET cc_start: 0.7211 (mtt) cc_final: 0.6719 (mmt) REVERT: Q 27 MET cc_start: 0.5326 (ppp) cc_final: 0.3134 (mmm) REVERT: W 123 MET cc_start: 0.7986 (tmm) cc_final: 0.7626 (tmm) REVERT: X 262 MET cc_start: 0.8766 (ppp) cc_final: 0.8358 (ppp) REVERT: a 101 MET cc_start: 0.7925 (mmm) cc_final: 0.7612 (mmm) REVERT: a 175 MET cc_start: 0.9172 (mmm) cc_final: 0.8900 (mmm) REVERT: b 31 GLN cc_start: 0.9048 (pm20) cc_final: 0.8714 (pp30) REVERT: c 1 MET cc_start: 0.5581 (tpt) cc_final: 0.4387 (tmm) REVERT: c 23 MET cc_start: 0.7773 (mmt) cc_final: 0.7302 (mmt) REVERT: d 195 MET cc_start: 0.5953 (tmm) cc_final: 0.5224 (tpt) REVERT: d 207 MET cc_start: 0.8655 (mtt) cc_final: 0.8304 (mtt) REVERT: d 575 ILE cc_start: 0.3118 (OUTLIER) cc_final: 0.2867 (pt) REVERT: d 634 MET cc_start: 0.6252 (tmm) cc_final: 0.5331 (tpt) REVERT: e 56 ASN cc_start: 0.7942 (m110) cc_final: 0.7594 (t0) REVERT: f 14 PRO cc_start: 0.8678 (Cg_exo) cc_final: 0.8389 (Cg_endo) REVERT: f 123 LYS cc_start: 0.8221 (tppp) cc_final: 0.7717 (pttm) REVERT: h 68 ASP cc_start: 0.8879 (m-30) cc_final: 0.8626 (t0) REVERT: h 130 MET cc_start: 0.7325 (ppp) cc_final: 0.6815 (ppp) REVERT: i 70 MET cc_start: 0.2594 (mmp) cc_final: 0.0790 (tpt) REVERT: i 95 MET cc_start: -0.2665 (ttm) cc_final: -0.4844 (ptt) REVERT: j 128 GLN cc_start: 0.9460 (pp30) cc_final: 0.9220 (pp30) REVERT: k 1 MET cc_start: 0.0221 (tpt) cc_final: -0.0680 (tpt) REVERT: l 260 MET cc_start: -0.1953 (tpt) cc_final: -0.2368 (tpt) REVERT: l 453 MET cc_start: 0.4147 (ttp) cc_final: 0.3551 (ttt) REVERT: m 111 MET cc_start: -0.0298 (tmm) cc_final: -0.0773 (tmm) REVERT: n 42 MET cc_start: -0.2792 (pmm) cc_final: -0.4595 (ptt) REVERT: t 104 GLN cc_start: -0.1603 (OUTLIER) cc_final: -0.2936 (mm-40) outliers start: 201 outliers final: 150 residues processed: 753 average time/residue: 0.9846 time to fit residues: 1290.1680 Evaluate side-chains 722 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 558 time to evaluate : 9.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 MET Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 350 HIS Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 2 residue 8 HIS Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 28 PHE Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 7 residue 415 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 905 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1003 LYS Chi-restraints excluded: chain A residue 1015 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 730 ARG Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain I residue 7 CYS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 191 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 371 ASP Chi-restraints excluded: chain R residue 83 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain b residue 91 ASP Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 128 TYR Chi-restraints excluded: chain b residue 129 VAL Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain d residue 575 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 225 LYS Chi-restraints excluded: chain e residue 259 VAL Chi-restraints excluded: chain e residue 286 ILE Chi-restraints excluded: chain e residue 290 VAL Chi-restraints excluded: chain f residue 130 LEU Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 174 LEU Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain i residue 98 THR Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain l residue 650 VAL Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain p residue 43 PHE Chi-restraints excluded: chain s residue 88 TYR Chi-restraints excluded: chain t residue 104 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 1163 optimal weight: 40.0000 chunk 1225 optimal weight: 10.0000 chunk 1117 optimal weight: 50.0000 chunk 1191 optimal weight: 9.9990 chunk 1224 optimal weight: 40.0000 chunk 717 optimal weight: 0.9980 chunk 519 optimal weight: 6.9990 chunk 935 optimal weight: 50.0000 chunk 365 optimal weight: 0.6980 chunk 1077 optimal weight: 8.9990 chunk 1127 optimal weight: 50.0000 overall best weight: 5.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 212 ASN ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN A 906 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 GLN ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 666 ASN ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 116471 Z= 0.472 Angle : 0.646 12.820 159065 Z= 0.336 Chirality : 0.044 0.256 18052 Planarity : 0.004 0.080 18892 Dihedral : 17.198 176.031 18776 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.56 % Allowed : 13.83 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.46 (0.08), residues: 12842 helix: 1.35 (0.07), residues: 5954 sheet: -0.62 (0.13), residues: 1647 loop : -0.51 (0.09), residues: 5241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP l 632 HIS 0.013 0.001 HIS 2 8 PHE 0.028 0.002 PHE K 71 TYR 0.035 0.001 TYR h 43 ARG 0.010 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 585 time to evaluate : 9.344 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: 0.0202 (mmt) cc_final: -0.1645 (mtt) REVERT: 0 485 MET cc_start: -0.2634 (mtt) cc_final: -0.3004 (mtt) REVERT: 0 642 MET cc_start: 0.3923 (ttp) cc_final: 0.3360 (ppp) REVERT: 0 679 MET cc_start: 0.4973 (mpp) cc_final: 0.4394 (mmp) REVERT: 0 724 MET cc_start: -0.1823 (ptt) cc_final: -0.2183 (ptp) REVERT: 1 385 MET cc_start: 0.1807 (mtt) cc_final: 0.0964 (mmt) REVERT: 2 150 MET cc_start: -0.3272 (tpp) cc_final: -0.3524 (mmt) REVERT: 2 253 MET cc_start: -0.4637 (mmm) cc_final: -0.4986 (mmp) REVERT: 3 12 MET cc_start: 0.8613 (tmm) cc_final: 0.8125 (tmm) REVERT: 4 197 MET cc_start: 0.5749 (ptt) cc_final: 0.5429 (ptt) REVERT: 4 252 MET cc_start: -0.2022 (mmp) cc_final: -0.3233 (mmt) REVERT: 5 13 ASP cc_start: 0.1576 (OUTLIER) cc_final: 0.1192 (p0) REVERT: 7 112 MET cc_start: -0.2404 (ttt) cc_final: -0.3112 (ptm) REVERT: 7 445 MET cc_start: 0.0622 (mmm) cc_final: -0.0435 (mpp) REVERT: 7 561 MET cc_start: -0.1116 (mtp) cc_final: -0.1632 (mmm) REVERT: 7 578 MET cc_start: 0.4674 (mmt) cc_final: 0.4201 (mpp) REVERT: A 22 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.9091 (m-10) REVERT: A 41 MET cc_start: 0.9166 (mmm) cc_final: 0.8609 (mmm) REVERT: A 238 CYS cc_start: 0.8298 (t) cc_final: 0.8040 (t) REVERT: A 368 LYS cc_start: 0.8443 (tttt) cc_final: 0.7732 (tttt) REVERT: A 501 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8178 (mp) REVERT: A 566 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8976 (mm) REVERT: A 780 VAL cc_start: 0.8537 (t) cc_final: 0.8328 (p) REVERT: A 838 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7124 (tm-30) REVERT: A 1033 GLN cc_start: 0.7578 (tm-30) cc_final: 0.7129 (tm-30) REVERT: A 1112 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8002 (ttmt) REVERT: A 1444 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7623 (mtp) REVERT: B 40 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: B 101 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7459 (ptt) REVERT: B 282 ILE cc_start: 0.9184 (pt) cc_final: 0.8923 (mm) REVERT: B 328 GLU cc_start: 0.8386 (mp0) cc_final: 0.8103 (mp0) REVERT: B 353 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8793 (mtmm) REVERT: B 378 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9420 (tt) REVERT: B 476 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6289 (mtp180) REVERT: B 595 ARG cc_start: 0.7762 (ptm-80) cc_final: 0.7459 (ttp80) REVERT: B 620 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8068 (ttm-80) REVERT: E 75 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8149 (ppp) REVERT: F 29 TYR cc_start: 0.5525 (m-80) cc_final: 0.4852 (m-80) REVERT: F 63 GLN cc_start: 0.5797 (tp40) cc_final: 0.5120 (pt0) REVERT: G 1 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8287 (ppp) REVERT: G 45 ILE cc_start: 0.9562 (OUTLIER) cc_final: 0.9339 (mp) REVERT: G 115 MET cc_start: 0.6119 (ptt) cc_final: 0.5856 (ppp) REVERT: I 60 GLN cc_start: 0.7261 (pm20) cc_final: 0.7029 (pp30) REVERT: J 34 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8511 (p) REVERT: J 69 ARG cc_start: 0.5136 (ttp-170) cc_final: 0.4911 (mmm160) REVERT: K 84 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8449 (tttt) REVERT: M 104 MET cc_start: 0.8464 (pmm) cc_final: 0.7865 (tpp) REVERT: M 116 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8460 (pttp) REVERT: M 136 LEU cc_start: 0.9367 (mt) cc_final: 0.9157 (mt) REVERT: M 141 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8030 (mt-10) REVERT: O 240 MET cc_start: 0.7158 (mtt) cc_final: 0.6724 (mmt) REVERT: Q 27 MET cc_start: 0.5531 (ppp) cc_final: 0.3110 (mmm) REVERT: W 123 MET cc_start: 0.7934 (tmm) cc_final: 0.7538 (tmm) REVERT: X 262 MET cc_start: 0.8818 (ppp) cc_final: 0.8224 (ppp) REVERT: X 265 ASN cc_start: 0.8667 (m-40) cc_final: 0.8007 (p0) REVERT: a 101 MET cc_start: 0.8068 (mmm) cc_final: 0.7710 (mmm) REVERT: a 175 MET cc_start: 0.9182 (mmm) cc_final: 0.8930 (mmm) REVERT: c 1 MET cc_start: 0.5480 (tpt) cc_final: 0.4353 (tmm) REVERT: c 23 MET cc_start: 0.7737 (mmt) cc_final: 0.7126 (mmt) REVERT: d 195 MET cc_start: 0.5925 (tmm) cc_final: 0.5302 (tpt) REVERT: d 207 MET cc_start: 0.8622 (mtt) cc_final: 0.8291 (mtt) REVERT: d 575 ILE cc_start: 0.3300 (OUTLIER) cc_final: 0.3018 (pt) REVERT: d 634 MET cc_start: 0.6230 (tmm) cc_final: 0.5573 (tpt) REVERT: e 215 TYR cc_start: 0.8084 (p90) cc_final: 0.7675 (p90) REVERT: f 14 PRO cc_start: 0.8739 (Cg_exo) cc_final: 0.8448 (Cg_endo) REVERT: f 123 LYS cc_start: 0.8166 (tppp) cc_final: 0.7644 (pttm) REVERT: g 57 MET cc_start: 0.7510 (ttp) cc_final: 0.7236 (tpp) REVERT: h 68 ASP cc_start: 0.8872 (m-30) cc_final: 0.8636 (t0) REVERT: h 130 MET cc_start: 0.7322 (ppp) cc_final: 0.7098 (ppp) REVERT: i 70 MET cc_start: 0.2587 (mmp) cc_final: 0.0768 (tpt) REVERT: i 95 MET cc_start: -0.2662 (ttm) cc_final: -0.4848 (ptt) REVERT: k 1 MET cc_start: 0.0331 (tpt) cc_final: -0.0623 (tpt) REVERT: l 260 MET cc_start: -0.1872 (tpt) cc_final: -0.2270 (tpt) REVERT: l 453 MET cc_start: 0.3875 (ttp) cc_final: 0.3289 (ttt) REVERT: m 111 MET cc_start: -0.0247 (tmm) cc_final: -0.0518 (tmm) REVERT: n 42 MET cc_start: -0.2790 (pmm) cc_final: -0.4611 (ptt) REVERT: v 90 MET cc_start: 0.2562 (tpt) cc_final: 0.1850 (tpt) outliers start: 184 outliers final: 146 residues processed: 726 average time/residue: 0.9976 time to fit residues: 1265.9421 Evaluate side-chains 727 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 564 time to evaluate : 9.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 MET Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 350 HIS Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 28 PHE Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 6 residue 169 MET Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 7 residue 415 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1390 ASN Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain A residue 1444 MET Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU 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 1072 MET Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 191 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 371 ASP Chi-restraints excluded: chain R residue 83 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain b residue 91 ASP Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 128 TYR Chi-restraints excluded: chain b residue 129 VAL Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain d residue 575 ILE Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 48 ASP Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 170 ASP Chi-restraints excluded: chain e residue 182 MET Chi-restraints excluded: chain e residue 259 VAL Chi-restraints excluded: chain e residue 286 ILE Chi-restraints excluded: chain e residue 290 VAL Chi-restraints excluded: chain f residue 130 LEU Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 174 LEU Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain i residue 98 THR Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain j residue 104 LEU Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain l residue 650 VAL Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain p residue 43 PHE Chi-restraints excluded: chain s residue 88 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 1187 optimal weight: 1.9990 chunk 782 optimal weight: 20.0000 chunk 1260 optimal weight: 10.0000 chunk 769 optimal weight: 220.0000 chunk 597 optimal weight: 4.9990 chunk 876 optimal weight: 50.0000 chunk 1322 optimal weight: 50.0000 chunk 1216 optimal weight: 7.9990 chunk 1052 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 813 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 8 HIS 6 212 ASN ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5565 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 116471 Z= 0.454 Angle : 0.650 14.021 159065 Z= 0.337 Chirality : 0.044 0.251 18052 Planarity : 0.004 0.086 18892 Dihedral : 17.199 175.536 18776 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.55 % Allowed : 14.04 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.48 (0.08), residues: 12842 helix: 1.37 (0.07), residues: 5946 sheet: -0.62 (0.13), residues: 1661 loop : -0.51 (0.09), residues: 5235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP l 632 HIS 0.011 0.001 HIS A 659 PHE 0.028 0.002 PHE A 219 TYR 0.035 0.001 TYR h 43 ARG 0.013 0.000 ARG j 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25684 Ramachandran restraints generated. 12842 Oldfield, 0 Emsley, 12842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 573 time to evaluate : 9.253 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: 0 485 MET cc_start: -0.2745 (mtt) cc_final: -0.3029 (mtt) REVERT: 0 642 MET cc_start: 0.3999 (ttp) cc_final: 0.3428 (ppp) REVERT: 0 679 MET cc_start: 0.4952 (mpp) cc_final: 0.4277 (mmp) REVERT: 0 724 MET cc_start: -0.1740 (ptt) cc_final: -0.1967 (ptp) REVERT: 1 58 MET cc_start: -0.1177 (OUTLIER) cc_final: -0.2250 (tmm) REVERT: 1 385 MET cc_start: 0.1836 (mtt) cc_final: 0.1001 (mmt) REVERT: 2 253 MET cc_start: -0.4583 (mmm) cc_final: -0.4907 (mmp) REVERT: 3 12 MET cc_start: 0.8628 (tmm) cc_final: 0.8207 (tmm) REVERT: 4 197 MET cc_start: 0.5728 (ptt) cc_final: 0.5441 (ptt) REVERT: 4 252 MET cc_start: -0.1948 (mmp) cc_final: -0.3191 (mmt) REVERT: 5 13 ASP cc_start: 0.1704 (OUTLIER) cc_final: 0.1301 (p0) REVERT: 6 322 MET cc_start: 0.2382 (tmm) cc_final: 0.2133 (tmm) REVERT: 7 112 MET cc_start: -0.2578 (ttt) cc_final: -0.3315 (ptm) REVERT: 7 445 MET cc_start: 0.0727 (mmm) cc_final: -0.0937 (mtm) REVERT: 7 561 MET cc_start: -0.1107 (mtp) cc_final: -0.1656 (mmm) REVERT: A 22 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.9083 (m-10) REVERT: A 238 CYS cc_start: 0.8251 (t) cc_final: 0.7992 (t) REVERT: A 368 LYS cc_start: 0.8440 (tttt) cc_final: 0.7733 (tttt) REVERT: A 501 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 566 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8962 (mm) REVERT: A 658 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 780 VAL cc_start: 0.8548 (t) cc_final: 0.8320 (p) REVERT: A 838 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: A 1033 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7175 (tm-30) REVERT: A 1112 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8007 (ttmt) REVERT: A 1281 ARG cc_start: 0.7583 (ptt180) cc_final: 0.7308 (ptt180) REVERT: B 40 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7791 (tt0) REVERT: B 282 ILE cc_start: 0.9138 (pt) cc_final: 0.8893 (mm) REVERT: B 304 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7389 (t70) REVERT: B 328 GLU cc_start: 0.8380 (mp0) cc_final: 0.8140 (mp0) REVERT: B 353 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8793 (mtmm) REVERT: B 476 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6307 (mtp180) REVERT: B 595 ARG cc_start: 0.7780 (ptm-80) cc_final: 0.7473 (ttp80) REVERT: B 620 ARG cc_start: 0.8374 (mtp85) cc_final: 0.8029 (ttm-80) REVERT: F 29 TYR cc_start: 0.5491 (m-80) cc_final: 0.4733 (m-80) REVERT: F 63 GLN cc_start: 0.5891 (tp40) cc_final: 0.5124 (pt0) REVERT: G 45 ILE cc_start: 0.9561 (OUTLIER) cc_final: 0.9347 (mp) REVERT: G 115 MET cc_start: 0.6112 (ptt) cc_final: 0.5762 (ppp) REVERT: I 60 GLN cc_start: 0.7383 (pm20) cc_final: 0.7046 (pp30) REVERT: J 34 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8586 (p) REVERT: K 84 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8445 (tttt) REVERT: M 104 MET cc_start: 0.8284 (pmm) cc_final: 0.8035 (tmm) REVERT: M 116 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8470 (pttp) REVERT: M 141 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: M 191 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: O 240 MET cc_start: 0.7112 (mtt) cc_final: 0.6721 (mmt) REVERT: Q 27 MET cc_start: 0.5608 (ppp) cc_final: 0.3116 (mmm) REVERT: Q 425 MET cc_start: 0.6943 (ptm) cc_final: 0.6694 (ptm) REVERT: V 111 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7178 (mt) REVERT: W 123 MET cc_start: 0.7892 (tmm) cc_final: 0.7491 (tmm) REVERT: X 262 MET cc_start: 0.8876 (ppp) cc_final: 0.8263 (ppp) REVERT: X 265 ASN cc_start: 0.8632 (m-40) cc_final: 0.7996 (p0) REVERT: a 101 MET cc_start: 0.8167 (mmm) cc_final: 0.7940 (mmm) REVERT: a 175 MET cc_start: 0.9175 (mmm) cc_final: 0.8911 (mmm) REVERT: b 31 GLN cc_start: 0.8921 (pm20) cc_final: 0.8604 (pp30) REVERT: c 1 MET cc_start: 0.5568 (tpt) cc_final: 0.4361 (tmm) REVERT: c 23 MET cc_start: 0.7633 (mmt) cc_final: 0.6965 (mmt) REVERT: d 195 MET cc_start: 0.5920 (tmm) cc_final: 0.5376 (tpt) REVERT: d 207 MET cc_start: 0.8655 (mtt) cc_final: 0.8338 (mtt) REVERT: d 411 MET cc_start: 0.1159 (tpt) cc_final: -0.0039 (mmt) REVERT: d 634 MET cc_start: 0.6364 (tmm) cc_final: 0.5683 (tpt) REVERT: e 56 ASN cc_start: 0.7880 (m110) cc_final: 0.7605 (t0) REVERT: e 215 TYR cc_start: 0.8106 (p90) cc_final: 0.7686 (p90) REVERT: f 123 LYS cc_start: 0.8145 (tppp) cc_final: 0.7610 (pttm) REVERT: g 57 MET cc_start: 0.7520 (ttp) cc_final: 0.7285 (tpp) REVERT: h 68 ASP cc_start: 0.8877 (m-30) cc_final: 0.8646 (t0) REVERT: h 130 MET cc_start: 0.7292 (ppp) cc_final: 0.7070 (ppp) REVERT: i 70 MET cc_start: 0.2561 (mmp) cc_final: 0.0834 (tpt) REVERT: i 95 MET cc_start: -0.2669 (ttm) cc_final: -0.4903 (ptt) REVERT: k 1 MET cc_start: 0.0263 (tpt) cc_final: -0.0620 (tpt) REVERT: l 260 MET cc_start: -0.1832 (tpt) cc_final: -0.2246 (tpt) REVERT: l 453 MET cc_start: 0.3915 (ttp) cc_final: 0.3397 (ttt) REVERT: m 111 MET cc_start: -0.0251 (tmm) cc_final: -0.0492 (tmm) REVERT: n 42 MET cc_start: -0.2957 (pmm) cc_final: -0.4742 (ptt) REVERT: v 90 MET cc_start: 0.2514 (tpt) cc_final: 0.1844 (tpt) outliers start: 182 outliers final: 153 residues processed: 712 average time/residue: 1.0041 time to fit residues: 1253.1571 Evaluate side-chains 736 residues out of total 11775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 567 time to evaluate : 9.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 MET Chi-restraints excluded: chain 0 residue 136 MET Chi-restraints excluded: chain 0 residue 350 HIS Chi-restraints excluded: chain 0 residue 367 THR Chi-restraints excluded: chain 0 residue 430 VAL Chi-restraints excluded: chain 0 residue 709 SER Chi-restraints excluded: chain 0 residue 711 ASP Chi-restraints excluded: chain 1 residue 58 MET Chi-restraints excluded: chain 1 residue 302 MET Chi-restraints excluded: chain 1 residue 477 MET Chi-restraints excluded: chain 2 residue 8 HIS Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 3 residue 28 PHE Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 6 residue 174 MET Chi-restraints excluded: chain 7 residue 415 VAL Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 618 GLU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 736 ASN Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1079 MET Chi-restraints excluded: chain A residue 1111 MET Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1295 THR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1359 ASP Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 468 GLU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 694 ASP Chi-restraints excluded: chain B residue 706 GLN Chi-restraints excluded: chain B residue 730 ARG Chi-restraints excluded: chain B residue 737 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 887 HIS Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 963 PHE Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1072 MET Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1124 ARG Chi-restraints excluded: chain B residue 1132 GLU Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 17 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 140 ASN Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 48 ARG Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 141 GLU Chi-restraints excluded: chain M residue 178 ILE Chi-restraints excluded: chain M residue 188 THR Chi-restraints excluded: chain M residue 191 GLU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 248 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain Q residue 119 LEU Chi-restraints excluded: chain Q residue 371 ASP Chi-restraints excluded: chain R residue 83 ASP Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 222 CYS Chi-restraints excluded: chain R residue 280 VAL Chi-restraints excluded: chain V residue 21 ASP Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 111 LEU Chi-restraints excluded: chain W residue 227 MET Chi-restraints excluded: chain b residue 91 ASP Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 128 TYR Chi-restraints excluded: chain b residue 129 VAL Chi-restraints excluded: chain d residue 238 MET Chi-restraints excluded: chain d residue 675 HIS Chi-restraints excluded: chain e residue 48 ASP Chi-restraints excluded: chain e residue 52 VAL Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 170 ASP Chi-restraints excluded: chain e residue 182 MET Chi-restraints excluded: chain e residue 259 VAL Chi-restraints excluded: chain e residue 286 ILE Chi-restraints excluded: chain e residue 290 VAL Chi-restraints excluded: chain f residue 130 LEU Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain f residue 144 SER Chi-restraints excluded: chain f residue 155 LEU Chi-restraints excluded: chain f residue 174 LEU Chi-restraints excluded: chain g residue 63 MET Chi-restraints excluded: chain h residue 59 SER Chi-restraints excluded: chain h residue 82 GLU Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain i residue 98 THR Chi-restraints excluded: chain j residue 15 LEU Chi-restraints excluded: chain j residue 87 LEU Chi-restraints excluded: chain k residue 53 LEU Chi-restraints excluded: chain l residue 650 VAL Chi-restraints excluded: chain m residue 18 ASP Chi-restraints excluded: chain p residue 43 PHE Chi-restraints excluded: chain s residue 88 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1327 random chunks: chunk 645 optimal weight: 3.9990 chunk 836 optimal weight: 6.9990 chunk 1121 optimal weight: 40.0000 chunk 322 optimal weight: 0.7980 chunk 970 optimal weight: 0.9990 chunk 155 optimal weight: 40.0000 chunk 292 optimal weight: 4.9990 chunk 1054 optimal weight: 10.0000 chunk 441 optimal weight: 6.9990 chunk 1082 optimal weight: 30.0000 chunk 133 optimal weight: 40.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 8 HIS 2 206 GLN 6 212 ASN ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1218 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 HIS ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 HIS ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 692 GLN ** m 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 57 ASN n 72 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.184381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.172601 restraints weight = 344972.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.170540 restraints weight = 452990.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.168883 restraints weight = 423882.061| |-----------------------------------------------------------------------------| r_work (final): 0.4582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5098 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 116471 Z= 0.333 Angle : 0.610 13.100 159065 Z= 0.316 Chirality : 0.042 0.207 18052 Planarity : 0.004 0.104 18892 Dihedral : 17.174 175.457 18776 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.18 % Favored : 96.81 % Rotamer: Outliers : 1.52 % Allowed : 14.18 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: 0.59 (0.08), residues: 12842 helix: 1.45 (0.07), residues: 5939 sheet: -0.58 (0.13), residues: 1639 loop : -0.43 (0.09), residues: 5264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP l 632 HIS 0.016 0.001 HIS 2 8 PHE 0.027 0.001 PHE j 70 TYR 0.035 0.001 TYR h 43 ARG 0.019 0.000 ARG k 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22437.19 seconds wall clock time: 397 minutes 26.79 seconds (23846.79 seconds total)