Starting phenix.real_space_refine on Thu Apr 11 04:05:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o75_12745/04_2024/7o75_12745_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o75_12745/04_2024/7o75_12745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o75_12745/04_2024/7o75_12745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o75_12745/04_2024/7o75_12745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o75_12745/04_2024/7o75_12745_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o75_12745/04_2024/7o75_12745_updated.pdb" } resolution = 3.2 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= 0.041 sd= 1.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 10 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 17 6.06 5 P 128 5.49 5 Mg 2 5.21 5 S 401 5.16 5 Be 1 3.05 5 C 46394 2.51 5 N 12762 2.21 5 O 14173 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 24": "OD1" <-> "OD2" Residue "7 PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 306": "OE1" <-> "OE2" Residue "O PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 73885 Number of models: 1 Model: "" Number of chains: 43 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4214 Classifications: {'peptide': 522} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 503} Chain breaks: 6 Chain: "2" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3597 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 4 Chain: "3" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2274 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 279} Chain breaks: 2 Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "6" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2946 Classifications: {'peptide': 374} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 352} Chain breaks: 2 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: 11254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1430, 11254 Classifications: {'peptide': 1430} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1363} Chain breaks: 3 Chain: "B" Number of atoms: 9404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9404 Classifications: {'peptide': 1180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1127} Chain breaks: 5 Chain: "C" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2092 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1343 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 697 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "G" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1120 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2360 Classifications: {'peptide': 308} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 295} Chain breaks: 2 Chain: "N" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1314 Inner-chain residues flagged as termini: ['pdbres=" DA N 57 "'] Classifications: {'DNA': 64} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 63} 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: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1849 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 208} 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: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1283 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain breaks: 1 Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 885 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 105} Chain breaks: 2 Chain: "V" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'TRANS': 103} Chain breaks: 1 Chain: "W" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2532 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 15, 'TRANS': 296} Chain breaks: 3 Chain: "X" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1661 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 938 SG CYS 0 115 75.833 89.986 186.436 1.00 53.96 S ATOM 1265 SG CYS 0 156 70.716 89.162 190.431 1.00 67.76 S ATOM 1080 SG CYS 0 133 72.749 95.152 188.538 1.00 60.17 S ATOM 1566 SG CYS 0 191 75.677 92.126 192.788 1.00 56.75 S ATOM 13941 SG CYS 3 13 61.015 121.027 141.508 1.00 93.97 S ATOM 13962 SG CYS 3 16 62.159 120.631 137.917 1.00 91.62 S ATOM 14157 SG CYS 3 39 63.525 123.504 140.005 1.00 90.08 S ATOM 14178 SG CYS 3 42 59.983 123.617 138.863 1.00 91.50 S ATOM 14110 SG CYS 3 34 54.055 126.162 150.899 1.00 86.05 S ATOM 14268 SG CYS 3 54 53.377 125.545 147.165 1.00 87.09 S ATOM 14306 SG CYS 3 59 50.671 124.745 149.733 1.00 90.13 S ATOM 16970 SG CYS 4 289 123.978 49.568 206.881 1.00 62.80 S ATOM 16989 SG CYS 4 292 127.523 50.066 208.150 1.00 60.03 S ATOM 17081 SG CYS 4 305 125.037 48.148 210.245 1.00 83.57 S ATOM 17099 SG CYS 4 308 124.595 51.899 209.815 1.00 76.57 S ATOM 19918 SG CYS 6 349 127.768 32.608 193.150 1.00 58.68 S ATOM 19939 SG CYS 6 352 125.828 30.305 190.768 1.00 72.94 S ATOM 20018 SG CYS 6 363 126.656 33.799 189.688 1.00 59.94 S ATOM 20037 SG CYS 6 366 124.139 33.300 192.482 1.00 67.35 S ATOM 20339 SG CYS 6 403 155.346 67.260 205.720 1.00 77.44 S ATOM 20362 SG CYS 6 406 157.364 66.255 202.600 1.00 63.72 S ATOM 20556 SG CYS 6 437 154.647 68.967 202.340 1.00 76.16 S ATOM 20577 SG CYS 6 440 153.765 65.428 202.753 1.00 66.98 S ATOM 20489 SG CYS 6 429 145.015 65.425 211.813 1.00 83.80 S ATOM 20512 SG CYS 6 432 148.187 64.013 213.453 1.00 81.37 S ATOM 20670 SG CYS 6 451 147.293 63.035 209.912 1.00 59.38 S ATOM 20687 SG CYS 6 454 145.222 61.745 212.811 1.00 66.62 S ATOM 19817 SG CYS 6 336 131.889 33.482 179.381 1.00 85.31 S ATOM 19829 SG CYS 6 338 130.480 36.266 181.618 1.00 75.83 S ATOM 19977 SG CYS 6 357 134.248 35.854 181.190 1.00 55.61 S ATOM 26499 SG CYS A 107 99.921 115.159 113.996 1.00 60.76 S ATOM 26523 SG CYS A 110 99.206 116.615 117.403 1.00 64.25 S ATOM 26828 SG CYS A 148 102.755 115.583 116.558 1.00 86.43 S ATOM 26966 SG CYS A 167 100.149 112.872 116.983 1.00 89.82 S ATOM 26194 SG CYS A 67 61.783 140.851 100.125 1.00 35.20 S ATOM 26216 SG CYS A 70 62.439 144.434 101.254 1.00 30.42 S ATOM 26269 SG CYS A 77 64.439 142.942 98.319 1.00 24.65 S ATOM 45843 SG CYS B1163 75.153 145.251 112.168 1.00 16.51 S ATOM 45861 SG CYS B1166 76.409 142.288 110.063 1.00 19.57 S ATOM 45986 SG CYS B1182 72.700 142.648 110.850 1.00 15.14 S ATOM 46005 SG CYS B1185 75.208 141.699 113.561 1.00 27.06 S ATOM 46990 SG CYS C 86 47.180 181.453 46.121 1.00 28.08 S ATOM 47007 SG CYS C 88 46.455 178.045 47.635 1.00 39.02 S ATOM 47040 SG CYS C 92 45.020 178.987 44.192 1.00 28.24 S ATOM 47063 SG CYS C 95 48.728 178.335 44.624 1.00 25.51 S ATOM 54733 SG CYS I 7 132.007 89.498 59.629 1.00 53.50 S ATOM 54758 SG CYS I 10 128.375 89.220 60.934 1.00 50.76 S ATOM 54924 SG CYS I 29 131.014 90.494 63.233 1.00 67.12 S ATOM 54948 SG CYS I 32 131.199 86.865 62.044 1.00 65.54 S ATOM 55275 SG CYS I 75 135.796 122.509 30.549 1.00 54.22 S ATOM 55297 SG CYS I 78 135.451 121.233 26.914 1.00 60.50 S ATOM 55513 SG CYS I 103 132.365 121.935 28.956 1.00 47.61 S ATOM 55533 SG CYS I 106 134.622 118.986 29.830 1.00 55.48 S ATOM 55678 SG CYS J 7 76.250 167.196 33.078 1.00 17.74 S ATOM 55701 SG CYS J 10 75.949 170.919 32.313 1.00 17.18 S ATOM 55981 SG CYS J 45 79.368 169.120 32.091 1.00 15.12 S ATOM 55987 SG CYS J 46 76.650 168.582 29.517 1.00 14.08 S ATOM 57167 SG CYS L 31 50.358 132.488 42.627 1.00 51.39 S ATOM 57187 SG CYS L 34 48.336 132.107 39.442 1.00 52.94 S ATOM 57291 SG CYS L 48 46.833 130.969 42.698 1.00 55.72 S ATOM 57314 SG CYS L 51 49.771 129.030 41.249 1.00 57.86 S ATOM 57558 SG CYS M 24 48.968 161.468 89.326 1.00 64.75 S ATOM 57580 SG CYS M 27 46.317 163.251 87.294 1.00 69.54 S ATOM 57724 SG CYS M 45 48.531 160.703 85.559 1.00 52.19 S ATOM 57743 SG CYS M 48 50.071 163.970 86.861 1.00 50.21 S ATOM 70644 SG CYS W 124 48.044 138.280 108.998 1.00 90.46 S ATOM 70665 SG CYS W 127 51.461 137.497 107.673 1.00 90.54 S ATOM 70850 SG CYS W 149 50.437 141.126 108.434 1.00 72.48 S ATOM 70870 SG CYS W 152 48.911 139.270 105.437 1.00 77.86 S Time building chain proxies: 27.67, per 1000 atoms: 0.37 Number of scatterers: 73885 At special positions: 0 Unit cell: (213.15, 229.95, 241.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 10 Type Number sf(0) Zn 17 29.99 Fe 4 26.01 S 401 16.00 P 128 15.00 Mg 2 11.99 F 3 9.00 O 14173 8.00 N 12762 7.00 C 46394 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.55 Conformation dependent library (CDL) restraints added in 10.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE2 SF4 0 801 " - pdb=" SG CYS 0 156 " pdb="FE1 SF4 0 801 " - pdb=" SG CYS 0 115 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 3 401 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 39 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 42 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 401 " - pdb=" SG CYS 3 13 " pdb=" ZN 3 402 " pdb="ZN ZN 3 402 " - pdb=" ND1 HIS 3 36 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 54 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 34 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb=" ZN 6 504 " pdb="ZN ZN 6 504 " - pdb=" ND1 HIS 6 339 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 357 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 6 504 " - pdb=" SG CYS 6 336 " pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " Number of angles added : 93 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 348 helices and 72 sheets defined 39.9% alpha, 12.7% beta 59 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 23.99 Creating SS restraints... Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 49 through 62 Processing helix chain '0' and resid 76 through 97 Processing helix chain '0' and resid 126 through 137 Processing helix chain '0' and resid 140 through 147 Processing helix chain '0' and resid 157 through 164 removed outlier: 3.685A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN 0 164 " --> pdb=" O GLU 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 167 through 169 No H-bonds generated for 'chain '0' and resid 167 through 169' Processing helix chain '0' and resid 178 through 188 Processing helix chain '0' and resid 192 through 202 removed outlier: 5.328A pdb=" N SER 0 201 " --> pdb=" O ARG 0 197 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU 0 202 " --> pdb=" O ARG 0 198 " (cutoff:3.500A) Processing helix chain '0' and resid 211 through 214 No H-bonds generated for 'chain '0' and resid 211 through 214' Processing helix chain '0' and resid 216 through 225 removed outlier: 3.762A pdb=" N GLU 0 220 " --> pdb=" O PRO 0 216 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG 0 221 " --> pdb=" O LYS 0 217 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL 0 222 " --> pdb=" O ILE 0 218 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU 0 225 " --> pdb=" O ARG 0 221 " (cutoff:3.500A) Processing helix chain '0' and resid 240 through 248 removed outlier: 4.083A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 removed outlier: 3.508A pdb=" N VAL 0 277 " --> pdb=" O GLU 0 273 " (cutoff:3.500A) Processing helix chain '0' and resid 280 through 291 Processing helix chain '0' and resid 295 through 298 No H-bonds generated for 'chain '0' and resid 295 through 298' Processing helix chain '0' and resid 313 through 315 No H-bonds generated for 'chain '0' and resid 313 through 315' Processing helix chain '0' and resid 328 through 346 Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 375 Processing helix chain '0' and resid 377 through 388 Processing helix chain '0' and resid 395 through 411 removed outlier: 4.030A pdb=" N ALA 0 398 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE 0 409 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER 0 410 " --> pdb=" O THR 0 407 " (cutoff:3.500A) Processing helix chain '0' and resid 443 through 452 Proline residue: 0 448 - end of helix Processing helix chain '0' and resid 466 through 472 Proline residue: 0 470 - end of helix No H-bonds generated for 'chain '0' and resid 466 through 472' Processing helix chain '0' and resid 510 through 512 No H-bonds generated for 'chain '0' and resid 510 through 512' Processing helix chain '0' and resid 516 through 532 removed outlier: 3.707A pdb=" N ILE 0 532 " --> pdb=" O GLU 0 528 " (cutoff:3.500A) Processing helix chain '0' and resid 544 through 557 Processing helix chain '0' and resid 559 through 566 removed outlier: 3.634A pdb=" N LYS 0 565 " --> pdb=" O ASP 0 561 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS 0 566 " --> pdb=" O GLU 0 562 " (cutoff:3.500A) Processing helix chain '0' and resid 576 through 592 Processing helix chain '0' and resid 614 through 616 No H-bonds generated for 'chain '0' and resid 614 through 616' Processing helix chain '0' and resid 633 through 645 Processing helix chain '0' and resid 650 through 668 removed outlier: 3.682A pdb=" N HIS 0 661 " --> pdb=" O ASP 0 657 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) Processing helix chain '0' and resid 684 through 692 removed outlier: 3.575A pdb=" N SER 0 687 " --> pdb=" O ARG 0 684 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG 0 688 " --> pdb=" O ARG 0 685 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 695 through 700 removed outlier: 3.905A pdb=" N GLY 0 700 " --> pdb=" O TRP 0 696 " (cutoff:3.500A) Processing helix chain '0' and resid 703 through 705 No H-bonds generated for 'chain '0' and resid 703 through 705' Processing helix chain '0' and resid 710 through 725 Processing helix chain '0' and resid 730 through 733 Processing helix chain '0' and resid 741 through 751 Processing helix chain '1' and resid 42 through 44 No H-bonds generated for 'chain '1' and resid 42 through 44' Processing helix chain '1' and resid 94 through 120 Processing helix chain '1' and resid 171 through 176 Processing helix chain '1' and resid 178 through 187 removed outlier: 3.513A pdb=" N GLY 1 187 " --> pdb=" O SER 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 189 through 199 Processing helix chain '1' and resid 206 through 211 Processing helix chain '1' and resid 214 through 224 removed outlier: 3.709A pdb=" N THR 1 224 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 253 through 262 Processing helix chain '1' and resid 264 through 271 Processing helix chain '1' and resid 280 through 289 Processing helix chain '1' and resid 291 through 297 Processing helix chain '1' and resid 309 through 329 removed outlier: 3.658A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR 1 314 " --> pdb=" O ILE 1 310 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU 1 315 " --> pdb=" O ILE 1 311 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR 1 316 " --> pdb=" O ASP 1 312 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU 1 317 " --> pdb=" O ARG 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 335 through 337 No H-bonds generated for 'chain '1' and resid 335 through 337' Processing helix chain '1' and resid 339 through 343 removed outlier: 3.563A pdb=" N ILE 1 343 " --> pdb=" O LEU 1 339 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 339 through 343' Processing helix chain '1' and resid 356 through 358 No H-bonds generated for 'chain '1' and resid 356 through 358' Processing helix chain '1' and resid 371 through 389 removed outlier: 3.543A pdb=" N LEU 1 375 " --> pdb=" O THR 1 371 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 419 Processing helix chain '1' and resid 466 through 482 Processing helix chain '1' and resid 487 through 489 No H-bonds generated for 'chain '1' and resid 487 through 489' Processing helix chain '1' and resid 495 through 516 removed outlier: 3.505A pdb=" N ALA 1 506 " --> pdb=" O ARG 1 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N HIS 1 516 " --> pdb=" O LYS 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 544 through 568 removed outlier: 3.529A pdb=" N HIS 1 563 " --> pdb=" O GLU 1 559 " (cutoff:3.500A) Processing helix chain '1' and resid 573 through 604 removed outlier: 4.701A pdb=" N SER 1 577 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS 1 585 " --> pdb=" O LEU 1 582 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASN 1 602 " --> pdb=" O ASP 1 599 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP 1 604 " --> pdb=" O LEU 1 601 " (cutoff:3.500A) Processing helix chain '1' and resid 609 through 638 Proline residue: 1 618 - end of helix removed outlier: 3.730A pdb=" N GLU 1 636 " --> pdb=" O GLU 1 632 " (cutoff:3.500A) Processing helix chain '2' and resid 6 through 16 Processing helix chain '2' and resid 19 through 27 removed outlier: 3.887A pdb=" N ARG 2 24 " --> pdb=" O GLN 2 20 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR 2 27 " --> pdb=" O ASN 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 38 removed outlier: 3.695A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 51 Processing helix chain '2' and resid 59 through 65 removed outlier: 3.604A pdb=" N ASP 2 63 " --> pdb=" O LEU 2 59 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP 2 65 " --> pdb=" O ASP 2 61 " (cutoff:3.500A) Processing helix chain '2' and resid 69 through 83 removed outlier: 4.501A pdb=" N LEU 2 72 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE 2 78 " --> pdb=" O GLN 2 75 " (cutoff:3.500A) Processing helix chain '2' and resid 102 through 113 Processing helix chain '2' and resid 135 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 193 Processing helix chain '2' and resid 196 through 210 removed outlier: 3.723A pdb=" N LEU 2 203 " --> pdb=" O GLN 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 230 removed outlier: 3.639A pdb=" N GLY 2 229 " --> pdb=" O ILE 2 225 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA 2 230 " --> pdb=" O PHE 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 244 through 256 removed outlier: 3.898A pdb=" N ILE 2 248 " --> pdb=" O GLU 2 244 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG 2 254 " --> pdb=" O LEU 2 250 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP 2 255 " --> pdb=" O GLN 2 251 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR 2 256 " --> pdb=" O ASP 2 252 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 278 Processing helix chain '2' and resid 354 through 362 removed outlier: 3.609A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 389 Processing helix chain '2' and resid 393 through 402 Processing helix chain '2' and resid 406 through 422 Processing helix chain '2' and resid 435 through 448 Processing helix chain '2' and resid 465 through 477 Processing helix chain '2' and resid 498 through 506 Processing helix chain '3' and resid 40 through 47 Processing helix chain '3' and resid 65 through 67 No H-bonds generated for 'chain '3' and resid 65 through 67' Processing helix chain '3' and resid 76 through 91 removed outlier: 3.799A pdb=" N VAL 3 91 " --> pdb=" O ARG 3 87 " (cutoff:3.500A) Processing helix chain '3' and resid 96 through 99 Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 126 through 138 removed outlier: 3.595A pdb=" N GLU 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU 3 138 " --> pdb=" O ARG 3 134 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 43 removed outlier: 3.577A pdb=" N PHE 4 40 " --> pdb=" O LEU 4 36 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 67 Processing helix chain '4' and resid 116 through 138 removed outlier: 4.150A pdb=" N THR 4 124 " --> pdb=" O ASN 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 166 Processing helix chain '4' and resid 191 through 206 Proline residue: 4 195 - end of helix Processing helix chain '4' and resid 224 through 231 Processing helix chain '4' and resid 244 through 250 Processing helix chain '4' and resid 256 through 258 No H-bonds generated for 'chain '4' and resid 256 through 258' Processing helix chain '4' and resid 301 through 303 No H-bonds generated for 'chain '4' and resid 301 through 303' Processing helix chain '4' and resid 314 through 321 removed outlier: 3.654A pdb=" N LEU 4 320 " --> pdb=" O VAL 4 316 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 26 removed outlier: 3.585A pdb=" N LEU 5 19 " --> pdb=" O SER 5 15 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS 5 26 " --> pdb=" O GLN 5 22 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 61 removed outlier: 4.506A pdb=" N GLU 5 48 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN 5 61 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) Processing helix chain '6' and resid 75 through 78 No H-bonds generated for 'chain '6' and resid 75 through 78' Processing helix chain '6' and resid 83 through 86 No H-bonds generated for 'chain '6' and resid 83 through 86' Processing helix chain '6' and resid 97 through 113 removed outlier: 3.568A pdb=" N ILE 6 102 " --> pdb=" O LEU 6 98 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA 6 105 " --> pdb=" O SER 6 101 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 199 Processing helix chain '6' and resid 210 through 220 Processing helix chain '6' and resid 247 through 257 Processing helix chain '6' and resid 271 through 281 Processing helix chain '6' and resid 294 through 305 removed outlier: 3.653A pdb=" N ALA 6 304 " --> pdb=" O LEU 6 300 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL 6 305 " --> pdb=" O PHE 6 301 " (cutoff:3.500A) Processing helix chain '6' and resid 373 through 383 removed outlier: 4.216A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU 6 383 " --> pdb=" O SER 6 379 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 446 Processing helix chain '6' and resid 452 through 456 Processing helix chain '7' and resid 110 through 112 No H-bonds generated for 'chain '7' and resid 110 through 112' Processing helix chain '7' and resid 125 through 128 removed outlier: 4.379A pdb=" N ALA 7 128 " --> pdb=" O PRO 7 125 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 125 through 128' Processing helix chain '7' and resid 150 through 160 removed outlier: 4.261A pdb=" N ASP 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL 7 158 " --> pdb=" O GLN 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 177 through 185 Processing helix chain '7' and resid 190 through 200 Processing helix chain '7' and resid 207 through 217 removed outlier: 3.547A pdb=" N ALA 7 216 " --> pdb=" O PHE 7 212 " (cutoff:3.500A) Processing helix chain '7' and resid 239 through 245 removed outlier: 3.524A pdb=" N LEU 7 245 " --> pdb=" O LEU 7 242 " (cutoff:3.500A) Processing helix chain '7' and resid 321 through 332 removed outlier: 3.786A pdb=" N GLU 7 324 " --> pdb=" O GLU 7 321 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS 7 327 " --> pdb=" O GLU 7 324 " (cutoff:3.500A) Processing helix chain '7' and resid 343 through 345 No H-bonds generated for 'chain '7' and resid 343 through 345' Processing helix chain '7' and resid 364 through 373 Processing helix chain '7' and resid 392 through 403 Processing helix chain '7' and resid 415 through 427 Processing helix chain '7' and resid 432 through 434 No H-bonds generated for 'chain '7' and resid 432 through 434' Processing helix chain '7' and resid 457 through 461 Processing helix chain '7' and resid 468 through 479 removed outlier: 3.912A pdb=" N VAL 7 473 " --> pdb=" O ASP 7 469 " (cutoff:3.500A) Processing helix chain '7' and resid 490 through 492 No H-bonds generated for 'chain '7' and resid 490 through 492' Processing helix chain '7' and resid 498 through 504 Processing helix chain '7' and resid 524 through 530 removed outlier: 3.527A pdb=" N LEU 7 530 " --> pdb=" O LEU 7 527 " (cutoff:3.500A) Processing helix chain '7' and resid 540 through 545 Processing helix chain '7' and resid 563 through 571 removed outlier: 3.838A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 582 removed outlier: 4.631A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 601 Processing helix chain '7' and resid 612 through 622 Processing helix chain '7' and resid 633 through 645 Processing helix chain '7' and resid 656 through 658 No H-bonds generated for 'chain '7' and resid 656 through 658' Processing helix chain '7' and resid 681 through 692 removed outlier: 3.671A pdb=" N ARG 7 689 " --> pdb=" O GLN 7 685 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE 7 690 " --> pdb=" O ARG 7 686 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG 7 692 " --> pdb=" O GLY 7 688 " (cutoff:3.500A) Processing helix chain '7' and resid 714 through 729 removed outlier: 4.105A pdb=" N ALA 7 724 " --> pdb=" O THR 7 720 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N PHE 7 725 " --> pdb=" O LYS 7 721 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU 7 726 " --> pdb=" O ARG 7 722 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL 7 727 " --> pdb=" O GLN 7 723 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP 7 728 " --> pdb=" O ALA 7 724 " (cutoff:3.500A) Processing helix chain '7' and resid 753 through 766 Processing helix chain '7' and resid 831 through 835 removed outlier: 3.995A pdb=" N LYS 7 835 " --> pdb=" O PRO 7 831 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 831 through 835' Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 93 through 105 removed outlier: 3.779A pdb=" N ILE A 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.218A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.669A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.648A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 660 removed outlier: 3.508A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 699 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 810 through 844 Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 916 through 919 No H-bonds generated for 'chain 'A' and resid 916 through 919' Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.588A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 removed outlier: 3.835A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 3.529A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1078 Proline residue: A1075 - end of helix removed outlier: 3.690A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1105 Processing helix chain 'A' and resid 1122 through 1124 No H-bonds generated for 'chain 'A' and resid 1122 through 1124' Processing helix chain 'A' and resid 1129 through 1138 Processing helix chain 'A' and resid 1143 through 1146 Processing helix chain 'A' and resid 1165 through 1176 removed outlier: 3.839A pdb=" N GLU A1168 " --> pdb=" O GLU A1165 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A1169 " --> pdb=" O ASP A1166 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE A1170 " --> pdb=" O GLU A1167 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A1173 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE A1174 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1256 through 1269 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.815A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1341 through 1358 Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1389 through 1391 No H-bonds generated for 'chain 'A' and resid 1389 through 1391' Processing helix chain 'A' and resid 1396 through 1401 Processing helix chain 'A' and resid 1405 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.642A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.658A pdb=" N GLU B 40 " --> pdb=" O PHE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 114 through 120 removed outlier: 3.565A pdb=" N LEU B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.588A 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 371 through 389 Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 438 Processing helix chain 'B' and resid 444 through 447 No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 667 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 695 through 700 removed outlier: 3.730A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 700' Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 776 removed outlier: 3.995A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 810 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1014 through 1020 Proline residue: B1018 - end of helix Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.618A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 267 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 157 through 170 removed outlier: 5.231A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N THR D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'E' and resid 3 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'E' and resid 118 through 122 Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 33 Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'H' and resid 89 through 92 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 39 Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.610A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 Processing helix chain 'K' and resid 6 through 9 Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.882A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 removed outlier: 3.511A pdb=" N LEU K 111 " --> pdb=" O THR K 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 115 removed outlier: 3.559A pdb=" N GLU M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 118 through 140 removed outlier: 4.028A pdb=" N LYS M 122 " --> pdb=" O VAL M 118 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL M 126 " --> pdb=" O LYS M 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 168 through 182 Processing helix chain 'M' and resid 189 through 195 removed outlier: 4.089A pdb=" N LEU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 220 removed outlier: 3.624A pdb=" N GLU M 219 " --> pdb=" O ARG M 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 230 No H-bonds generated for 'chain 'M' and resid 228 through 230' Processing helix chain 'M' and resid 235 through 246 removed outlier: 3.673A pdb=" N ILE M 239 " --> pdb=" O ASN M 235 " (cutoff:3.500A) Proline residue: M 240 - end of helix Processing helix chain 'M' and resid 250 through 265 removed outlier: 3.806A pdb=" N LYS M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 270 No H-bonds generated for 'chain 'M' and resid 267 through 270' Processing helix chain 'M' and resid 274 through 289 Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 306 through 319 removed outlier: 3.761A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU M 318 " --> pdb=" O LYS M 314 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS M 319 " --> pdb=" O ILE M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 323 No H-bonds generated for 'chain 'M' and resid 321 through 323' Processing helix chain 'M' and resid 326 through 331 Processing helix chain 'M' and resid 336 through 338 No H-bonds generated for 'chain 'M' and resid 336 through 338' Processing helix chain 'O' and resid 82 through 88 Processing helix chain 'O' and resid 129 through 146 Processing helix chain 'O' and resid 172 through 178 Processing helix chain 'O' and resid 220 through 237 removed outlier: 3.520A pdb=" N PHE O 227 " --> pdb=" O ILE O 223 " (cutoff:3.500A) Proline residue: O 232 - end of helix removed outlier: 4.209A pdb=" N PHE O 237 " --> pdb=" O VAL O 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 34 Processing helix chain 'Q' and resid 153 through 167 removed outlier: 3.594A pdb=" N SER Q 164 " --> pdb=" O GLN Q 160 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU Q 165 " --> pdb=" O LYS Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 337 through 347 Processing helix chain 'Q' and resid 406 through 413 Processing helix chain 'Q' and resid 424 through 431 removed outlier: 3.523A pdb=" N ILE Q 431 " --> pdb=" O HIS Q 427 " (cutoff:3.500A) Processing helix chain 'Q' and resid 437 through 447 removed outlier: 3.573A pdb=" N ARG Q 443 " --> pdb=" O ASP Q 439 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS Q 444 " --> pdb=" O ARG Q 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 52 No H-bonds generated for 'chain 'R' and resid 49 through 52' Processing helix chain 'R' and resid 75 through 81 removed outlier: 3.974A pdb=" N LYS R 80 " --> pdb=" O PHE R 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing helix chain 'R' and resid 235 through 244 removed outlier: 3.949A pdb=" N VAL R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 265 removed outlier: 4.668A pdb=" N HIS R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 286 removed outlier: 3.559A pdb=" N LYS R 286 " --> pdb=" O ARG R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 309 removed outlier: 4.450A pdb=" N ASP R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE R 304 " --> pdb=" O LEU R 300 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS R 305 " --> pdb=" O ASP R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 315 through 322 Processing helix chain 'R' and resid 326 through 336 removed outlier: 3.671A pdb=" N GLU R 331 " --> pdb=" O ALA R 327 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS R 332 " --> pdb=" O HIS R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 353 through 356 No H-bonds generated for 'chain 'R' and resid 353 through 356' Processing helix chain 'U' and resid 4 through 20 Processing helix chain 'U' and resid 22 through 28 Processing helix chain 'U' and resid 32 through 49 removed outlier: 3.734A pdb=" N ILE U 41 " --> pdb=" O LEU U 38 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP U 42 " --> pdb=" O LYS U 39 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR U 47 " --> pdb=" O LYS U 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 12 Processing helix chain 'V' and resid 14 through 29 Processing helix chain 'V' and resid 34 through 54 removed outlier: 3.530A pdb=" N ASP V 45 " --> pdb=" O LEU V 41 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS V 46 " --> pdb=" O GLU V 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 20 Processing helix chain 'W' and resid 23 through 34 Processing helix chain 'W' and resid 40 through 47 Processing helix chain 'W' and resid 51 through 63 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 91 through 117 Processing helix chain 'W' and resid 133 through 139 removed outlier: 3.923A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 165 through 178 removed outlier: 3.896A pdb=" N GLN W 169 " --> pdb=" O ASN W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 191 Processing helix chain 'W' and resid 199 through 205 removed outlier: 3.846A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG W 205 " --> pdb=" O ILE W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 288 removed outlier: 3.872A pdb=" N LYS W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN W 287 " --> pdb=" O GLU W 283 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN W 288 " --> pdb=" O LYS W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 292 through 295 No H-bonds generated for 'chain 'W' and resid 292 through 295' Processing helix chain 'W' and resid 350 through 368 Processing helix chain 'X' and resid 107 through 115 Processing helix chain 'X' and resid 124 through 136 removed outlier: 3.516A pdb=" N LEU X 128 " --> pdb=" O ASP X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 150 Processing helix chain 'X' and resid 158 through 165 removed outlier: 3.504A pdb=" N LYS X 164 " --> pdb=" O ILE X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 189 through 198 Processing helix chain 'X' and resid 207 through 211 Processing helix chain 'X' and resid 218 through 227 Processing helix chain 'X' and resid 257 through 265 removed outlier: 3.639A pdb=" N MET X 262 " --> pdb=" O GLU X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 271 through 281 Proline residue: X 275 - end of helix Processing helix chain 'X' and resid 290 through 292 No H-bonds generated for 'chain 'X' and resid 290 through 292' Processing sheet with id= A, first strand: chain '0' and resid 2 through 4 Processing sheet with id= B, first strand: chain '0' and resid 479 through 482 removed outlier: 3.990A pdb=" N LEU 0 479 " --> pdb=" O ASN 0 37 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL 0 456 " --> pdb=" O SER 0 38 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU 0 40 " --> pdb=" O VAL 0 456 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE 0 458 " --> pdb=" O LEU 0 40 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL 0 232 " --> pdb=" O ILE 0 457 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR 0 459 " --> pdb=" O VAL 0 232 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N PHE 0 234 " --> pdb=" O THR 0 459 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 0 106 " --> pdb=" O ILE 0 205 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY 0 174 " --> pdb=" O GLY 0 105 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N GLY 0 107 " --> pdb=" O GLY 0 174 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N PHE 0 176 " --> pdb=" O GLY 0 107 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 250 through 253 Processing sheet with id= D, first strand: chain '0' and resid 492 through 497 removed outlier: 7.247A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N MET 0 495 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE 0 497 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU 0 681 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR 0 619 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA 0 596 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL 0 539 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 4 through 9 Processing sheet with id= F, first strand: chain '1' and resid 86 through 90 Processing sheet with id= G, first strand: chain '2' and resid 87 through 92 Processing sheet with id= H, first strand: chain '2' and resid 339 through 341 removed outlier: 6.179A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '2' and resid 456 through 459 removed outlier: 3.639A pdb=" N PHE 2 491 " --> pdb=" O TYR 2 459 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 28 through 30 Processing sheet with id= K, first strand: chain '4' and resid 82 through 87 removed outlier: 6.404A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ALA 4 74 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '5' and resid 8 through 11 removed outlier: 3.535A pdb=" N VAL 5 42 " --> pdb=" O ALA 5 8 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '6' and resid 178 through 183 removed outlier: 6.325A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG 6 260 " --> pdb=" O VAL 6 232 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE 6 234 " --> pdb=" O ARG 6 260 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS 6 262 " --> pdb=" O ILE 6 234 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE 6 236 " --> pdb=" O LYS 6 262 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU 6 264 " --> pdb=" O PHE 6 236 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '6' and resid 427 through 429 removed outlier: 3.779A pdb=" N GLN 6 434 " --> pdb=" O CYS 6 429 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '7' and resid 132 through 134 removed outlier: 3.541A pdb=" N SER 7 165 " --> pdb=" O GLU 7 172 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '7' and resid 224 through 228 removed outlier: 4.404A pdb=" N TYR 7 232 " --> pdb=" O ILE 7 318 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE 7 316 " --> pdb=" O VAL 7 234 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '7' and resid 484 through 488 removed outlier: 6.781A pdb=" N ALA 7 509 " --> pdb=" O ILE 7 485 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU 7 487 " --> pdb=" O ALA 7 509 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU 7 511 " --> pdb=" O LEU 7 487 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL 7 385 " --> pdb=" O PRO 7 533 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N LEU 7 535 " --> pdb=" O VAL 7 385 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '7' and resid 407 through 411 removed outlier: 3.644A pdb=" N PHE 7 438 " --> pdb=" O VAL 7 454 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR 7 456 " --> pdb=" O PHE 7 438 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '7' and resid 734 through 736 removed outlier: 7.123A pdb=" N ALA 7 703 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA 7 555 " --> pdb=" O ALA 7 703 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE 7 705 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL 7 557 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N SER 7 707 " --> pdb=" O VAL 7 557 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N CYS 7 559 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL 7 709 " --> pdb=" O CYS 7 559 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS 7 604 " --> pdb=" O THR 7 668 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU 7 670 " --> pdb=" O LYS 7 604 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE 7 606 " --> pdb=" O LEU 7 670 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN 7 672 " --> pdb=" O ILE 7 606 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE 7 608 " --> pdb=" O GLN 7 672 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= U, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= V, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.502A pdb=" N ARG A 200 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.598A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.439A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'A' and resid 375 through 379 removed outlier: 6.218A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 588 through 590 removed outlier: 3.777A pdb=" N PHE A 614 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= AB, first strand: chain 'A' and resid 1115 through 1119 removed outlier: 3.690A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.108A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 69 through 73 removed outlier: 4.178A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 132 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS B 164 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LYS B 134 " --> pdb=" O GLU B 157 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLU B 157 " --> pdb=" O LYS B 134 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR B 136 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B 155 " --> pdb=" O THR B 136 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= AF, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= AG, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= AH, first strand: chain 'B' and resid 498 through 500 removed outlier: 6.477A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 224 through 227 removed outlier: 7.014A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= AK, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.322A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.559A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 4.327A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B1088 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET B 839 " --> pdb=" O LYS B 987 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR B 989 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N MET B 841 " --> pdb=" O THR B 989 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLY B 991 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 872 through 874 Processing sheet with id= AO, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= AP, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= AQ, first strand: chain 'C' and resid 176 through 179 removed outlier: 6.787A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 97 through 104 removed outlier: 6.058A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AT, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AU, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.635A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.556A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AX, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.190A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'G' and resid 142 through 146 removed outlier: 7.327A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ILE G 157 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N PHE G 109 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA G 159 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR G 111 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY G 161 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= BA, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.507A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'I' and resid 15 through 19 Processing sheet with id= BC, first strand: chain 'I' and resid 69 through 71 removed outlier: 3.522A pdb=" N PHE I 85 " --> pdb=" O PRO I 69 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= BE, first strand: chain 'L' and resid 37 through 40 Processing sheet with id= BF, first strand: chain 'M' and resid 34 through 37 Processing sheet with id= BG, first strand: chain 'O' and resid 155 through 157 removed outlier: 3.554A pdb=" N LYS O 156 " --> pdb=" O THR O 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 192 through 197 removed outlier: 3.634A pdb=" N ILE O 202 " --> pdb=" O MET O 197 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS O 211 " --> pdb=" O PHE O 207 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY O 216 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE O 160 " --> pdb=" O GLY O 216 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER O 163 " --> pdb=" O LEU O 67 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU O 67 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Q' and resid 103 through 105 removed outlier: 6.444A pdb=" N PHE Q 384 " --> pdb=" O ARG Q 104 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'Q' and resid 117 through 121 removed outlier: 6.615A pdb=" N LYS Q 391 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LYS Q 120 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR Q 393 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL Q 392 " --> pdb=" O GLU Q 366 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'R' and resid 94 through 97 removed outlier: 4.450A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU R 70 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU R 221 " --> pdb=" O LEU R 70 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG R 72 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN R 223 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'R' and resid 337 through 340 removed outlier: 3.630A pdb=" N VAL R 340 " --> pdb=" O LYS R 348 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS R 348 " --> pdb=" O VAL R 340 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'R' and resid 133 through 135 removed outlier: 3.743A pdb=" N GLY R 216 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'U' and resid 243 through 245 Processing sheet with id= BO, first strand: chain 'U' and resid 278 through 284 removed outlier: 3.753A pdb=" N LYS U 250 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS U 263 " --> pdb=" O TYR U 248 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR U 248 " --> pdb=" O LYS U 263 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'V' and resid 60 through 63 removed outlier: 3.649A pdb=" N CYS V 83 " --> pdb=" O VAL V 108 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'V' and resid 110 through 116 removed outlier: 6.210A pdb=" N LYS V 81 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU V 66 " --> pdb=" O LYS V 81 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'W' and resid 68 through 74 Processing sheet with id= BS, first strand: chain 'X' and resid 169 through 172 Processing sheet with id= BT, first strand: chain 'X' and resid 230 through 234 removed outlier: 4.366A pdb=" N TYR X 243 " --> pdb=" O LEU X 233 " (cutoff:3.500A) 2642 hydrogen bonds defined for protein. 7386 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 136 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 59 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 35.13 Time building geometry restraints manager: 24.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 30986 1.43 - 1.64: 43833 1.64 - 1.85: 628 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 75459 Sorted by residual: bond pdb=" C4 ADP 7 903 " pdb=" C5 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" BE BEF 7 901 " pdb=" F2 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C5 ADP 7 903 " pdb=" C6 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" BE BEF 7 901 " pdb=" F3 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.547 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" BE BEF 7 901 " pdb=" F1 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.532 -0.056 2.00e-02 2.50e+03 7.85e+00 ... (remaining 75454 not shown) Histogram of bond angle deviations from ideal: 73.69 - 85.88: 12 85.88 - 98.07: 0 98.07 - 110.26: 16296 110.26 - 122.45: 75956 122.45 - 134.64: 10125 Bond angle restraints: 102389 Sorted by residual: angle pdb=" N HIS 7 676 " pdb=" CA HIS 7 676 " pdb=" C HIS 7 676 " ideal model delta sigma weight residual 109.39 119.95 -10.56 1.59e+00 3.96e-01 4.41e+01 angle pdb=" C1' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C3' ADP 7 903 " ideal model delta sigma weight residual 111.00 98.42 12.58 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N TRP B 466 " pdb=" CA TRP B 466 " pdb=" C TRP B 466 " ideal model delta sigma weight residual 108.52 101.78 6.74 1.63e+00 3.76e-01 1.71e+01 angle pdb=" C PRO R 295 " pdb=" N LYS R 296 " pdb=" CA LYS R 296 " ideal model delta sigma weight residual 120.44 125.54 -5.10 1.30e+00 5.92e-01 1.54e+01 angle pdb=" N GLN A 525 " pdb=" CA GLN A 525 " pdb=" CB GLN A 525 " ideal model delta sigma weight residual 110.49 104.23 6.26 1.69e+00 3.50e-01 1.37e+01 ... (remaining 102384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 44819 34.56 - 69.11: 1108 69.11 - 103.67: 115 103.67 - 138.23: 2 138.23 - 172.79: 1 Dihedral angle restraints: 46045 sinusoidal: 20001 harmonic: 26044 Sorted by residual: dihedral pdb=" O1B ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PB ADP 7 903 " pdb=" PA ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 112.78 -172.79 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 70.06 -130.06 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" C5' ADP 7 903 " pdb=" O5' ADP 7 903 " pdb=" PA ADP 7 903 " pdb=" O2A ADP 7 903 " ideal model delta sinusoidal sigma weight residual -60.00 -166.41 106.41 1 2.00e+01 2.50e-03 3.08e+01 ... (remaining 46042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 10433 0.066 - 0.131: 1117 0.131 - 0.197: 15 0.197 - 0.263: 3 0.263 - 0.328: 2 Chirality restraints: 11570 Sorted by residual: chirality pdb=" CA GLN 0 615 " pdb=" N GLN 0 615 " pdb=" C GLN 0 615 " pdb=" CB GLN 0 615 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA HIS 0 614 " pdb=" N HIS 0 614 " pdb=" C HIS 0 614 " pdb=" CB HIS 0 614 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA HIS 7 676 " pdb=" N HIS 7 676 " pdb=" C HIS 7 676 " pdb=" CB HIS 7 676 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 11567 not shown) Planarity restraints: 12699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP W 293 " 0.036 2.00e-02 2.50e+03 4.61e-02 5.32e+01 pdb=" CG TRP W 293 " -0.110 2.00e-02 2.50e+03 pdb=" CD1 TRP W 293 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP W 293 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP W 293 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 TRP W 293 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP W 293 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 293 " 0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 293 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP W 293 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS 7 676 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.74e+01 pdb=" C HIS 7 676 " 0.072 2.00e-02 2.50e+03 pdb=" O HIS 7 676 " -0.027 2.00e-02 2.50e+03 pdb=" N TYR 7 677 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA N 25 " -0.028 2.00e-02 2.50e+03 1.34e-02 4.97e+00 pdb=" N9 DA N 25 " 0.033 2.00e-02 2.50e+03 pdb=" C8 DA N 25 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA N 25 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA N 25 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA N 25 " 0.000 2.00e-02 2.50e+03 pdb=" N6 DA N 25 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA N 25 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA N 25 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA N 25 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA N 25 " 0.000 2.00e-02 2.50e+03 ... (remaining 12696 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 320 2.52 - 3.11: 55404 3.11 - 3.71: 111800 3.71 - 4.30: 161888 4.30 - 4.90: 267889 Nonbonded interactions: 597301 Sorted by model distance: nonbonded pdb=" OD1 ASP B 326 " pdb=" OG1 THR B 329 " model vdw 1.921 2.440 nonbonded pdb="MG MG 7 902 " pdb=" O3B ADP 7 903 " model vdw 2.000 2.170 nonbonded pdb=" F1 BEF 7 901 " pdb="MG MG 7 902 " model vdw 2.000 2.120 nonbonded pdb=" OD2 ASP A 483 " pdb="MG MG A1803 " model vdw 2.035 2.170 nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 2.035 2.170 ... (remaining 597296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.070 Extract box with map and model: 13.560 Check model and map are aligned: 0.820 Set scattering table: 0.500 Process input model: 186.910 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 208.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.109 75459 Z= 0.144 Angle : 0.452 12.583 102389 Z= 0.259 Chirality : 0.039 0.328 11570 Planarity : 0.002 0.053 12699 Dihedral : 14.818 172.787 29129 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.36 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.09), residues: 8769 helix: 2.33 (0.09), residues: 3488 sheet: 0.52 (0.15), residues: 1284 loop : 0.14 (0.10), residues: 3997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.001 TRP W 293 HIS 0.006 0.000 HIS 0 614 PHE 0.019 0.001 PHE M 189 TYR 0.015 0.001 TYR 7 677 ARG 0.005 0.000 ARG R 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1733 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1733 time to evaluate : 6.028 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: 0 199 MET cc_start: 0.7630 (ttt) cc_final: 0.7363 (ttm) REVERT: 0 214 LEU cc_start: 0.9138 (mm) cc_final: 0.8899 (mt) REVERT: 0 309 THR cc_start: 0.8369 (t) cc_final: 0.7944 (p) REVERT: 0 378 SER cc_start: 0.8461 (p) cc_final: 0.8247 (m) REVERT: 0 468 MET cc_start: 0.7419 (tpp) cc_final: 0.6840 (tpp) REVERT: 1 57 LYS cc_start: 0.7215 (mtmm) cc_final: 0.6827 (mtmm) REVERT: 1 112 LYS cc_start: 0.8583 (mttt) cc_final: 0.8375 (tppp) REVERT: 1 177 ASN cc_start: 0.6881 (t0) cc_final: 0.6609 (t0) REVERT: 1 189 LYS cc_start: 0.8194 (tptp) cc_final: 0.7669 (tptp) REVERT: 1 359 GLN cc_start: 0.7178 (mt0) cc_final: 0.6827 (tt0) REVERT: 1 420 LYS cc_start: 0.7703 (mmtm) cc_final: 0.7487 (mmtt) REVERT: 1 568 PHE cc_start: 0.8820 (t80) cc_final: 0.8460 (t80) REVERT: 1 583 TYR cc_start: 0.7725 (t80) cc_final: 0.7459 (t80) REVERT: 1 636 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7810 (tm-30) REVERT: 2 17 ILE cc_start: 0.9014 (mm) cc_final: 0.8735 (mm) REVERT: 2 59 LEU cc_start: 0.8779 (tp) cc_final: 0.8568 (tp) REVERT: 2 72 LEU cc_start: 0.7721 (tp) cc_final: 0.7415 (tt) REVERT: 2 409 ARG cc_start: 0.7842 (ttm110) cc_final: 0.7527 (mtt90) REVERT: 2 418 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8198 (mmpt) REVERT: 3 17 LYS cc_start: 0.7522 (mttp) cc_final: 0.7123 (mttp) REVERT: 3 112 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7283 (mt-10) REVERT: 3 116 ILE cc_start: 0.8083 (mt) cc_final: 0.7759 (mt) REVERT: 6 131 ASP cc_start: 0.8133 (t0) cc_final: 0.7844 (t0) REVERT: 6 164 ASN cc_start: 0.8141 (m-40) cc_final: 0.7821 (m-40) REVERT: 6 298 LYS cc_start: 0.7648 (tttt) cc_final: 0.7413 (ttpp) REVERT: 6 351 ASN cc_start: 0.7945 (t0) cc_final: 0.7474 (t0) REVERT: 6 373 SER cc_start: 0.7750 (t) cc_final: 0.7323 (p) REVERT: 6 410 PHE cc_start: 0.6762 (m-10) cc_final: 0.6012 (m-80) REVERT: 7 613 TYR cc_start: 0.7918 (t80) cc_final: 0.7538 (t80) REVERT: 7 640 LEU cc_start: 0.6617 (tt) cc_final: 0.6352 (tt) REVERT: 7 715 GLU cc_start: 0.7142 (tt0) cc_final: 0.6441 (tt0) REVERT: A 414 ASP cc_start: 0.7684 (t0) cc_final: 0.7478 (t0) REVERT: A 509 LEU cc_start: 0.9256 (mt) cc_final: 0.9046 (mt) REVERT: A 624 SER cc_start: 0.8229 (p) cc_final: 0.7974 (p) REVERT: A 676 MET cc_start: 0.6532 (mmm) cc_final: 0.6095 (mmm) REVERT: A 939 ASP cc_start: 0.7509 (m-30) cc_final: 0.7161 (m-30) REVERT: A 941 LYS cc_start: 0.7724 (tttp) cc_final: 0.7488 (tttp) REVERT: A 1194 ARG cc_start: 0.7073 (ttt-90) cc_final: 0.6840 (ttm-80) REVERT: A 1373 ASP cc_start: 0.7381 (m-30) cc_final: 0.6824 (m-30) REVERT: A 1386 ARG cc_start: 0.8030 (ptt-90) cc_final: 0.7709 (ptp-170) REVERT: B 65 GLU cc_start: 0.7212 (mm-30) cc_final: 0.7008 (mm-30) REVERT: B 69 LEU cc_start: 0.8123 (mt) cc_final: 0.7886 (mm) REVERT: B 323 VAL cc_start: 0.9274 (m) cc_final: 0.8964 (p) REVERT: B 353 LYS cc_start: 0.7581 (ttmm) cc_final: 0.7123 (mttt) REVERT: B 358 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7360 (ptpt) REVERT: B 367 LEU cc_start: 0.8740 (mp) cc_final: 0.8505 (mt) REVERT: B 426 LYS cc_start: 0.8376 (tttp) cc_final: 0.8114 (ttmt) REVERT: B 433 GLN cc_start: 0.7256 (tt0) cc_final: 0.6901 (tt0) REVERT: B 567 GLU cc_start: 0.8086 (mp0) cc_final: 0.7857 (mp0) REVERT: B 599 THR cc_start: 0.8138 (m) cc_final: 0.7708 (p) REVERT: B 623 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7644 (mt-10) REVERT: B 665 GLU cc_start: 0.6803 (tt0) cc_final: 0.6419 (tp30) REVERT: B 697 GLU cc_start: 0.7727 (tt0) cc_final: 0.7353 (tt0) REVERT: B 698 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7969 (mm-30) REVERT: B 906 SER cc_start: 0.8760 (p) cc_final: 0.8254 (m) REVERT: B 1072 MET cc_start: 0.8799 (mtp) cc_final: 0.8567 (mtm) REVERT: C 260 LEU cc_start: 0.8700 (tt) cc_final: 0.8419 (tp) REVERT: D 60 LYS cc_start: 0.7827 (tttt) cc_final: 0.7475 (ttmt) REVERT: D 61 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6845 (mt-10) REVERT: D 185 CYS cc_start: 0.7556 (m) cc_final: 0.7316 (m) REVERT: E 29 PHE cc_start: 0.8373 (t80) cc_final: 0.8138 (t80) REVERT: E 61 GLN cc_start: 0.7883 (tt0) cc_final: 0.7576 (tt0) REVERT: E 83 CYS cc_start: 0.6083 (t) cc_final: 0.5878 (t) REVERT: F 137 TYR cc_start: 0.8953 (m-80) cc_final: 0.8276 (m-80) REVERT: G 140 LYS cc_start: 0.8057 (tppt) cc_final: 0.7834 (mmtm) REVERT: H 37 LYS cc_start: 0.8610 (pttt) cc_final: 0.8177 (pttm) REVERT: I 98 VAL cc_start: 0.8521 (p) cc_final: 0.8150 (t) REVERT: I 109 ILE cc_start: 0.8786 (mp) cc_final: 0.8584 (mt) REVERT: K 89 ASN cc_start: 0.8071 (m110) cc_final: 0.7858 (m110) REVERT: L 36 SER cc_start: 0.8141 (t) cc_final: 0.7687 (m) REVERT: L 37 LYS cc_start: 0.8264 (tttt) cc_final: 0.8001 (tttt) REVERT: L 47 ARG cc_start: 0.8219 (ptm-80) cc_final: 0.7885 (ptm160) REVERT: M 134 THR cc_start: 0.7288 (m) cc_final: 0.6916 (p) REVERT: M 138 ASP cc_start: 0.6193 (m-30) cc_final: 0.5920 (m-30) REVERT: M 208 ASN cc_start: 0.7995 (t0) cc_final: 0.7766 (t0) REVERT: M 261 LYS cc_start: 0.7657 (tttt) cc_final: 0.6921 (ttpp) REVERT: O 67 LEU cc_start: 0.8558 (mt) cc_final: 0.8128 (pt) REVERT: O 121 MET cc_start: 0.5112 (ttt) cc_final: 0.4838 (ptm) REVERT: Q 356 ASP cc_start: 0.6177 (m-30) cc_final: 0.5841 (t0) REVERT: R 253 THR cc_start: 0.7966 (m) cc_final: 0.7756 (p) REVERT: R 303 LEU cc_start: 0.6701 (mp) cc_final: 0.6432 (pp) REVERT: X 197 ARG cc_start: 0.7300 (mtt180) cc_final: 0.6975 (ttm170) REVERT: X 214 TRP cc_start: 0.8011 (t60) cc_final: 0.7579 (t60) REVERT: X 292 THR cc_start: 0.7577 (m) cc_final: 0.7275 (p) outliers start: 0 outliers final: 0 residues processed: 1733 average time/residue: 0.7053 time to fit residues: 2071.5506 Evaluate side-chains 1339 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1339 time to evaluate : 6.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 751 optimal weight: 50.0000 chunk 674 optimal weight: 3.9990 chunk 374 optimal weight: 0.0670 chunk 230 optimal weight: 0.0770 chunk 455 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 697 optimal weight: 5.9990 chunk 269 optimal weight: 50.0000 chunk 424 optimal weight: 4.9990 chunk 519 optimal weight: 2.9990 chunk 808 optimal weight: 30.0000 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 66 HIS ** 0 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 719 GLN 1 93 ASN 1 500 ASN 2 19 GLN 2 148 HIS 2 261 GLN ** 2 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 246 GLN 6 281 ASN ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 169 HIS ** 7 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 491 HIS 7 551 ASN A 109 HIS ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A1270 ASN B 309 GLN B 357 GLN B 776 GLN B1013 ASN B1104 HIS B1195 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN D 31 GLN D 165 GLN G 131 GLN H 139 ASN ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN W 180 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 75459 Z= 0.287 Angle : 0.566 11.696 102389 Z= 0.297 Chirality : 0.043 0.200 11570 Planarity : 0.004 0.078 12699 Dihedral : 11.720 150.798 11078 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.46 % Allowed : 7.44 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.92 (0.09), residues: 8769 helix: 1.56 (0.09), residues: 3552 sheet: 0.29 (0.14), residues: 1337 loop : -0.07 (0.10), residues: 3880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP W 293 HIS 0.016 0.001 HIS W 261 PHE 0.029 0.002 PHE A 219 TYR 0.027 0.002 TYR 4 79 ARG 0.014 0.001 ARG 7 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1503 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1387 time to evaluate : 6.414 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: 0 132 LYS cc_start: 0.7552 (mttt) cc_final: 0.7100 (mmmt) REVERT: 0 199 MET cc_start: 0.7872 (ttt) cc_final: 0.7575 (ttm) REVERT: 0 214 LEU cc_start: 0.9266 (mm) cc_final: 0.8957 (mt) REVERT: 0 270 ARG cc_start: 0.7600 (tpt170) cc_final: 0.7371 (tpt170) REVERT: 0 347 LYS cc_start: 0.8329 (mmtt) cc_final: 0.8090 (mttt) REVERT: 0 468 MET cc_start: 0.7847 (tpp) cc_final: 0.7287 (tpp) REVERT: 1 57 LYS cc_start: 0.7044 (mtmm) cc_final: 0.6807 (mtmm) REVERT: 1 177 ASN cc_start: 0.6804 (t0) cc_final: 0.6535 (t0) REVERT: 1 286 ARG cc_start: 0.7181 (mmt90) cc_final: 0.6426 (mmt90) REVERT: 1 359 GLN cc_start: 0.7272 (mt0) cc_final: 0.6991 (tt0) REVERT: 1 636 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8006 (tm-30) REVERT: 2 17 ILE cc_start: 0.9133 (mm) cc_final: 0.8751 (mt) REVERT: 2 22 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7702 (mm-40) REVERT: 2 72 LEU cc_start: 0.7739 (tp) cc_final: 0.7479 (tt) REVERT: 2 183 LYS cc_start: 0.7436 (mmtt) cc_final: 0.7107 (mmmt) REVERT: 2 277 MET cc_start: 0.7478 (ttm) cc_final: 0.7122 (tpp) REVERT: 2 373 MET cc_start: 0.5948 (ppp) cc_final: 0.5436 (ppp) REVERT: 2 409 ARG cc_start: 0.7928 (ttm110) cc_final: 0.7348 (mtm-85) REVERT: 2 418 LYS cc_start: 0.8412 (mtpp) cc_final: 0.8202 (mmpt) REVERT: 3 17 LYS cc_start: 0.7578 (mttp) cc_final: 0.7084 (mttp) REVERT: 3 112 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7392 (mt-10) REVERT: 3 114 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7587 (tm-30) REVERT: 3 116 ILE cc_start: 0.8105 (mt) cc_final: 0.7804 (mt) REVERT: 4 71 ASN cc_start: 0.7796 (m110) cc_final: 0.7559 (m-40) REVERT: 4 323 LYS cc_start: 0.8793 (mtpt) cc_final: 0.8500 (mtmm) REVERT: 6 131 ASP cc_start: 0.8079 (t0) cc_final: 0.7841 (t0) REVERT: 6 298 LYS cc_start: 0.7824 (tttt) cc_final: 0.7474 (ttpp) REVERT: 7 493 VAL cc_start: 0.7768 (p) cc_final: 0.7562 (t) REVERT: 7 613 TYR cc_start: 0.7843 (t80) cc_final: 0.7282 (t80) REVERT: 7 637 MET cc_start: 0.8252 (tpp) cc_final: 0.7873 (mmm) REVERT: 7 677 TYR cc_start: 0.6779 (m-80) cc_final: 0.6475 (m-80) REVERT: 7 738 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.7111 (p-80) REVERT: A 141 LEU cc_start: 0.8585 (mp) cc_final: 0.8363 (mm) REVERT: A 186 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7722 (mmmt) REVERT: A 414 ASP cc_start: 0.7884 (t0) cc_final: 0.7599 (t0) REVERT: A 509 LEU cc_start: 0.9259 (mt) cc_final: 0.9046 (mt) REVERT: A 555 ASP cc_start: 0.7292 (p0) cc_final: 0.7082 (p0) REVERT: A 609 ASP cc_start: 0.7791 (t70) cc_final: 0.7421 (t70) REVERT: A 676 MET cc_start: 0.6848 (mmm) cc_final: 0.6345 (mmm) REVERT: A 1139 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7488 (tm-30) REVERT: A 1141 THR cc_start: 0.8893 (t) cc_final: 0.8677 (p) REVERT: A 1194 ARG cc_start: 0.7211 (ttt-90) cc_final: 0.6989 (ttm-80) REVERT: A 1267 MET cc_start: 0.7394 (ttm) cc_final: 0.7005 (ttm) REVERT: A 1290 LYS cc_start: 0.7953 (mttt) cc_final: 0.7655 (mtpp) REVERT: A 1373 ASP cc_start: 0.7493 (m-30) cc_final: 0.6920 (m-30) REVERT: B 103 ASN cc_start: 0.8410 (p0) cc_final: 0.8199 (p0) REVERT: B 353 LYS cc_start: 0.7460 (ttmm) cc_final: 0.6939 (mtpp) REVERT: B 433 GLN cc_start: 0.7420 (tt0) cc_final: 0.7105 (tt0) REVERT: B 449 ASN cc_start: 0.7617 (p0) cc_final: 0.7391 (p0) REVERT: B 906 SER cc_start: 0.8819 (p) cc_final: 0.8318 (m) REVERT: B 1072 MET cc_start: 0.8839 (mtp) cc_final: 0.8627 (mtm) REVERT: B 1104 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8222 (p90) REVERT: C 179 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: C 260 LEU cc_start: 0.8783 (tt) cc_final: 0.8490 (tp) REVERT: D 60 LYS cc_start: 0.7841 (tttt) cc_final: 0.7460 (ttmt) REVERT: E 20 LYS cc_start: 0.8438 (mmtp) cc_final: 0.8195 (mttt) REVERT: E 61 GLN cc_start: 0.7931 (tt0) cc_final: 0.7558 (tt0) REVERT: E 171 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7548 (mttt) REVERT: F 137 TYR cc_start: 0.8973 (m-80) cc_final: 0.8265 (m-80) REVERT: I 98 VAL cc_start: 0.8536 (p) cc_final: 0.8190 (t) REVERT: L 36 SER cc_start: 0.8212 (t) cc_final: 0.7821 (m) REVERT: L 47 ARG cc_start: 0.8352 (ptm-80) cc_final: 0.8021 (ptm160) REVERT: M 108 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7335 (mtpt) REVERT: M 159 ASP cc_start: 0.6708 (m-30) cc_final: 0.6289 (p0) REVERT: M 181 ARG cc_start: 0.7338 (mtt-85) cc_final: 0.7079 (mtt-85) REVERT: M 208 ASN cc_start: 0.7950 (t0) cc_final: 0.7703 (t0) REVERT: M 261 LYS cc_start: 0.7712 (tttt) cc_final: 0.6979 (ttpp) REVERT: O 67 LEU cc_start: 0.8699 (mt) cc_final: 0.8477 (tt) REVERT: O 106 ILE cc_start: 0.8039 (pt) cc_final: 0.7727 (mp) REVERT: Q 352 MET cc_start: 0.7628 (ttt) cc_final: 0.7307 (ttt) REVERT: Q 387 ILE cc_start: 0.7671 (mt) cc_final: 0.7270 (pt) REVERT: Q 394 LYS cc_start: 0.7421 (mtmt) cc_final: 0.7137 (mtmt) REVERT: R 116 ILE cc_start: 0.8185 (mp) cc_final: 0.7863 (tt) REVERT: R 210 LYS cc_start: 0.8232 (mmmm) cc_final: 0.7748 (mmmt) REVERT: V 20 VAL cc_start: 0.8129 (m) cc_final: 0.7838 (p) REVERT: W 5 ILE cc_start: 0.8892 (tp) cc_final: 0.8686 (mt) REVERT: W 74 GLU cc_start: 0.6740 (tt0) cc_final: 0.6525 (mt-10) REVERT: W 96 ASP cc_start: 0.7326 (t0) cc_final: 0.7035 (t0) REVERT: W 179 ILE cc_start: 0.8165 (tt) cc_final: 0.7887 (tt) REVERT: W 195 GLU cc_start: 0.6825 (tp30) cc_final: 0.6495 (tm-30) REVERT: W 218 THR cc_start: 0.8658 (p) cc_final: 0.8446 (t) REVERT: X 153 MET cc_start: 0.1133 (ppp) cc_final: -0.0213 (ppp) REVERT: X 214 TRP cc_start: 0.7977 (t60) cc_final: 0.7438 (t60) REVERT: X 292 THR cc_start: 0.7586 (m) cc_final: 0.7272 (p) outliers start: 116 outliers final: 73 residues processed: 1436 average time/residue: 0.6833 time to fit residues: 1671.4041 Evaluate side-chains 1338 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1262 time to evaluate : 6.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 61 MET Chi-restraints excluded: chain 0 residue 75 THR Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 395 ASP Chi-restraints excluded: chain 0 residue 455 SER Chi-restraints excluded: chain 0 residue 580 SER Chi-restraints excluded: chain 0 residue 630 THR Chi-restraints excluded: chain 0 residue 634 ILE Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 0 residue 701 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 289 SER Chi-restraints excluded: chain 1 residue 306 ARG Chi-restraints excluded: chain 2 residue 38 ILE Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 190 GLN Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 278 LEU Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 301 PHE Chi-restraints excluded: chain 6 residue 439 ASP Chi-restraints excluded: chain 7 residue 586 THR Chi-restraints excluded: chain 7 residue 588 PHE Chi-restraints excluded: chain 7 residue 646 ASN Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1270 ASN Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 510 LYS Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 281 SER Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain X residue 210 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 449 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 672 optimal weight: 1.9990 chunk 550 optimal weight: 0.9990 chunk 222 optimal weight: 20.0000 chunk 809 optimal weight: 6.9990 chunk 874 optimal weight: 20.0000 chunk 721 optimal weight: 5.9990 chunk 802 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 649 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 66 HIS ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 427 ASN 0 664 GLN ** 0 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 199 GLN 2 344 ASN 4 71 ASN 6 164 ASN 6 281 ASN 7 366 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN B1104 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 252 GLN G 131 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 220 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 75459 Z= 0.296 Angle : 0.541 11.693 102389 Z= 0.282 Chirality : 0.043 0.190 11570 Planarity : 0.004 0.051 12699 Dihedral : 11.802 122.483 11078 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.20 % Allowed : 9.77 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8769 helix: 1.30 (0.09), residues: 3553 sheet: 0.21 (0.14), residues: 1357 loop : -0.21 (0.10), residues: 3859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 7 133 HIS 0.022 0.001 HIS B1104 PHE 0.031 0.002 PHE A 219 TYR 0.025 0.001 TYR 4 115 ARG 0.018 0.000 ARG 7 757 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1490 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1315 time to evaluate : 6.221 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: 0 132 LYS cc_start: 0.7519 (mttt) cc_final: 0.7140 (mmmt) REVERT: 0 199 MET cc_start: 0.7937 (ttt) cc_final: 0.7641 (ttm) REVERT: 0 270 ARG cc_start: 0.7603 (tpt170) cc_final: 0.7393 (tpt170) REVERT: 0 347 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8145 (mttt) REVERT: 0 468 MET cc_start: 0.7897 (tpp) cc_final: 0.7291 (tpp) REVERT: 0 557 MET cc_start: 0.7695 (mtp) cc_final: 0.7335 (ptp) REVERT: 1 11 LYS cc_start: 0.8603 (mttm) cc_final: 0.8274 (ptpp) REVERT: 1 48 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6202 (pp) REVERT: 1 57 LYS cc_start: 0.7120 (mtmm) cc_final: 0.6886 (mtmm) REVERT: 1 177 ASN cc_start: 0.6782 (t0) cc_final: 0.6467 (t0) REVERT: 1 180 LEU cc_start: 0.8035 (tp) cc_final: 0.7727 (tp) REVERT: 1 184 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7600 (pt) REVERT: 1 249 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7696 (p) REVERT: 1 359 GLN cc_start: 0.7306 (mt0) cc_final: 0.7027 (tt0) REVERT: 2 17 ILE cc_start: 0.9101 (mm) cc_final: 0.8767 (mm) REVERT: 2 22 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7757 (mm-40) REVERT: 2 183 LYS cc_start: 0.7281 (mmtt) cc_final: 0.6934 (mmmt) REVERT: 2 373 MET cc_start: 0.5849 (ppp) cc_final: 0.5493 (ppp) REVERT: 2 409 ARG cc_start: 0.7866 (ttm110) cc_final: 0.7280 (mtm-85) REVERT: 2 418 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8211 (mmpt) REVERT: 3 11 ASP cc_start: 0.8064 (t0) cc_final: 0.7573 (t0) REVERT: 3 17 LYS cc_start: 0.7741 (mttp) cc_final: 0.7476 (mmtp) REVERT: 3 112 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7417 (mt-10) REVERT: 3 114 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: 3 115 ASP cc_start: 0.7160 (t0) cc_final: 0.6787 (t0) REVERT: 3 116 ILE cc_start: 0.8099 (mt) cc_final: 0.7783 (mt) REVERT: 4 210 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6223 (mt) REVERT: 4 323 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8546 (mtmm) REVERT: 6 180 GLN cc_start: 0.7504 (tp40) cc_final: 0.7288 (mm-40) REVERT: 6 298 LYS cc_start: 0.7753 (tttt) cc_final: 0.7445 (ttpp) REVERT: 6 341 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7594 (ttmm) REVERT: 6 441 ASP cc_start: 0.7901 (t0) cc_final: 0.7593 (t0) REVERT: 7 199 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7029 (tpm170) REVERT: 7 392 LYS cc_start: 0.7043 (pttt) cc_final: 0.6633 (pttt) REVERT: 7 613 TYR cc_start: 0.7741 (t80) cc_final: 0.7283 (t80) REVERT: 7 637 MET cc_start: 0.8242 (tpp) cc_final: 0.7899 (mmm) REVERT: 7 677 TYR cc_start: 0.6761 (m-80) cc_final: 0.6520 (m-10) REVERT: 7 711 LYS cc_start: 0.7757 (ttmt) cc_final: 0.7540 (ttmt) REVERT: 7 738 HIS cc_start: 0.7445 (OUTLIER) cc_final: 0.7156 (p-80) REVERT: A 389 THR cc_start: 0.8709 (m) cc_final: 0.8385 (m) REVERT: A 414 ASP cc_start: 0.7867 (t0) cc_final: 0.7577 (t0) REVERT: A 544 ASP cc_start: 0.8151 (p0) cc_final: 0.7863 (p0) REVERT: A 545 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7514 (tt0) REVERT: A 609 ASP cc_start: 0.7921 (t70) cc_final: 0.7554 (t70) REVERT: A 676 MET cc_start: 0.6951 (mmm) cc_final: 0.6531 (mmm) REVERT: A 906 HIS cc_start: 0.7733 (m-70) cc_final: 0.7315 (m-70) REVERT: A 985 ASP cc_start: 0.7184 (t0) cc_final: 0.6875 (t70) REVERT: A 1074 GLU cc_start: 0.7811 (tt0) cc_final: 0.7598 (tt0) REVERT: A 1194 ARG cc_start: 0.7207 (ttt-90) cc_final: 0.6936 (ttm-80) REVERT: A 1290 LYS cc_start: 0.8083 (mttt) cc_final: 0.7795 (mtpp) REVERT: A 1373 ASP cc_start: 0.7492 (m-30) cc_final: 0.6920 (m-30) REVERT: A 1454 MET cc_start: 0.6865 (tpp) cc_final: 0.6661 (ttt) REVERT: B 103 ASN cc_start: 0.8484 (p0) cc_final: 0.7647 (p0) REVERT: B 136 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7987 (t) REVERT: B 358 LYS cc_start: 0.7649 (ptpt) cc_final: 0.7325 (ttpt) REVERT: B 433 GLN cc_start: 0.7399 (tt0) cc_final: 0.7049 (tt0) REVERT: B 434 ARG cc_start: 0.7033 (ttt90) cc_final: 0.6790 (tpp80) REVERT: B 906 SER cc_start: 0.8785 (p) cc_final: 0.8429 (m) REVERT: B 1053 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6954 (mm-30) REVERT: B 1072 MET cc_start: 0.8856 (mtp) cc_final: 0.8633 (mtm) REVERT: C 260 LEU cc_start: 0.8759 (tt) cc_final: 0.8420 (tp) REVERT: D 60 LYS cc_start: 0.7839 (tttt) cc_final: 0.7463 (ttmt) REVERT: E 20 LYS cc_start: 0.8436 (mmtp) cc_final: 0.8196 (mttt) REVERT: E 171 LYS cc_start: 0.8052 (mtmt) cc_final: 0.7680 (mttt) REVERT: F 127 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6612 (mt-10) REVERT: F 137 TYR cc_start: 0.8983 (m-80) cc_final: 0.8237 (m-80) REVERT: I 30 ARG cc_start: 0.8412 (mtp180) cc_final: 0.7995 (mtm180) REVERT: I 48 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8667 (mm) REVERT: I 98 VAL cc_start: 0.8523 (p) cc_final: 0.8187 (t) REVERT: L 36 SER cc_start: 0.8308 (t) cc_final: 0.7941 (m) REVERT: L 47 ARG cc_start: 0.8374 (ptm-80) cc_final: 0.8017 (ptm160) REVERT: M 22 LEU cc_start: 0.8022 (pt) cc_final: 0.7797 (mp) REVERT: M 119 MET cc_start: 0.4190 (ppp) cc_final: 0.3190 (ptm) REVERT: M 141 GLU cc_start: 0.7109 (tp30) cc_final: 0.6440 (tm-30) REVERT: M 157 CYS cc_start: 0.7321 (m) cc_final: 0.6870 (m) REVERT: M 181 ARG cc_start: 0.7454 (mtt-85) cc_final: 0.7185 (mtt-85) REVERT: M 208 ASN cc_start: 0.7937 (t0) cc_final: 0.7687 (t0) REVERT: M 261 LYS cc_start: 0.7895 (tttt) cc_final: 0.7185 (ttpp) REVERT: O 67 LEU cc_start: 0.8702 (mt) cc_final: 0.8441 (tt) REVERT: Q 394 LYS cc_start: 0.7406 (mtmt) cc_final: 0.7204 (mtmt) REVERT: R 210 LYS cc_start: 0.8236 (mmmm) cc_final: 0.7754 (mmmm) REVERT: U 267 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8374 (p) REVERT: W 5 ILE cc_start: 0.8913 (tp) cc_final: 0.8709 (mt) REVERT: W 74 GLU cc_start: 0.6731 (tt0) cc_final: 0.6517 (mt-10) REVERT: W 96 ASP cc_start: 0.7400 (t0) cc_final: 0.6988 (t0) REVERT: W 179 ILE cc_start: 0.8041 (tt) cc_final: 0.7799 (tt) REVERT: W 195 GLU cc_start: 0.6823 (tp30) cc_final: 0.6500 (tm-30) REVERT: W 218 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8476 (t) REVERT: X 153 MET cc_start: 0.1361 (ppp) cc_final: -0.0001 (ppp) REVERT: X 214 TRP cc_start: 0.7973 (t60) cc_final: 0.7325 (t60) REVERT: X 292 THR cc_start: 0.7664 (m) cc_final: 0.7410 (p) outliers start: 175 outliers final: 108 residues processed: 1408 average time/residue: 0.6964 time to fit residues: 1663.4129 Evaluate side-chains 1367 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1247 time to evaluate : 6.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 61 MET Chi-restraints excluded: chain 0 residue 75 THR Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 395 ASP Chi-restraints excluded: chain 0 residue 455 SER Chi-restraints excluded: chain 0 residue 580 SER Chi-restraints excluded: chain 0 residue 630 THR Chi-restraints excluded: chain 0 residue 701 LEU Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 1 residue 48 LEU Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 289 SER Chi-restraints excluded: chain 1 residue 306 ARG Chi-restraints excluded: chain 1 residue 367 ASN Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 190 GLN Chi-restraints excluded: chain 2 residue 341 VAL Chi-restraints excluded: chain 3 residue 114 GLU Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 66 MET Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 231 GLU Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 301 PHE Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 439 ASP Chi-restraints excluded: chain 6 residue 456 SER Chi-restraints excluded: chain 7 residue 199 ARG Chi-restraints excluded: chain 7 residue 244 MET Chi-restraints excluded: chain 7 residue 366 GLN Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 586 THR Chi-restraints excluded: chain 7 residue 588 PHE Chi-restraints excluded: chain 7 residue 646 ASN Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 545 GLN Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 281 SER Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain M residue 321 ASP Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain U residue 251 VAL Chi-restraints excluded: chain U residue 267 VAL Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 218 THR Chi-restraints excluded: chain W residue 225 SER Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 254 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 799 optimal weight: 9.9990 chunk 608 optimal weight: 2.9990 chunk 420 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 386 optimal weight: 6.9990 chunk 543 optimal weight: 2.9990 chunk 812 optimal weight: 0.8980 chunk 860 optimal weight: 5.9990 chunk 424 optimal weight: 3.9990 chunk 770 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 0 66 HIS ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 664 GLN ** 0 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 554 HIS 2 199 GLN 2 344 ASN 7 366 GLN A 517 ASN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 165 GLN E 101 GLN G 131 GLN I 114 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 220 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 75459 Z= 0.368 Angle : 0.571 11.815 102389 Z= 0.296 Chirality : 0.044 0.246 11570 Planarity : 0.004 0.056 12699 Dihedral : 11.901 119.771 11078 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.75 % Allowed : 11.43 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.42 (0.09), residues: 8769 helix: 1.13 (0.09), residues: 3532 sheet: 0.07 (0.14), residues: 1344 loop : -0.35 (0.10), residues: 3893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 1 284 HIS 0.008 0.001 HIS W 261 PHE 0.035 0.002 PHE A 219 TYR 0.018 0.002 TYR G 51 ARG 0.007 0.000 ARG A 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1517 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1298 time to evaluate : 7.208 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: 0 80 GLU cc_start: 0.7549 (tp30) cc_final: 0.7255 (mm-30) REVERT: 0 132 LYS cc_start: 0.7577 (mttt) cc_final: 0.7172 (mmmt) REVERT: 0 199 MET cc_start: 0.7903 (ttt) cc_final: 0.7633 (ttm) REVERT: 0 270 ARG cc_start: 0.7671 (tpt170) cc_final: 0.7392 (tpt170) REVERT: 0 468 MET cc_start: 0.7972 (tpp) cc_final: 0.7298 (tpp) REVERT: 1 11 LYS cc_start: 0.8591 (mttm) cc_final: 0.8293 (ptpp) REVERT: 1 87 HIS cc_start: 0.7764 (m-70) cc_final: 0.7335 (m-70) REVERT: 1 177 ASN cc_start: 0.6835 (t0) cc_final: 0.6519 (t0) REVERT: 1 180 LEU cc_start: 0.8156 (tp) cc_final: 0.7913 (tp) REVERT: 1 184 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7776 (pt) REVERT: 1 249 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7778 (p) REVERT: 1 439 ARG cc_start: 0.6471 (mtt-85) cc_final: 0.6151 (ttm110) REVERT: 2 17 ILE cc_start: 0.9131 (mm) cc_final: 0.8813 (mm) REVERT: 2 183 LYS cc_start: 0.7280 (mmtt) cc_final: 0.7027 (ptmt) REVERT: 2 277 MET cc_start: 0.7437 (ttm) cc_final: 0.6938 (tpp) REVERT: 2 373 MET cc_start: 0.5739 (ppp) cc_final: 0.5392 (ppp) REVERT: 2 409 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7309 (mtm-85) REVERT: 2 418 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8169 (mmpt) REVERT: 2 446 LEU cc_start: 0.7983 (mm) cc_final: 0.7781 (tp) REVERT: 3 17 LYS cc_start: 0.7757 (mttp) cc_final: 0.7371 (mmtt) REVERT: 3 112 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7402 (mt-10) REVERT: 3 114 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: 3 115 ASP cc_start: 0.7182 (t0) cc_final: 0.6694 (t0) REVERT: 3 116 ILE cc_start: 0.8112 (mt) cc_final: 0.7778 (mt) REVERT: 4 210 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6485 (mt) REVERT: 4 323 LYS cc_start: 0.8797 (mtpt) cc_final: 0.8552 (mtmm) REVERT: 6 180 GLN cc_start: 0.7454 (tp40) cc_final: 0.7173 (mm-40) REVERT: 6 298 LYS cc_start: 0.7731 (tttt) cc_final: 0.7430 (ttpp) REVERT: 6 341 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7679 (ttmm) REVERT: 6 441 ASP cc_start: 0.7981 (t0) cc_final: 0.7702 (t0) REVERT: 7 121 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7925 (pp) REVERT: 7 199 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7168 (tpm170) REVERT: 7 367 GLU cc_start: 0.7823 (tt0) cc_final: 0.7242 (tp30) REVERT: 7 392 LYS cc_start: 0.7074 (pttt) cc_final: 0.6654 (pttt) REVERT: 7 613 TYR cc_start: 0.7755 (t80) cc_final: 0.7330 (t80) REVERT: 7 637 MET cc_start: 0.8252 (tpp) cc_final: 0.7916 (mmm) REVERT: 7 677 TYR cc_start: 0.6802 (m-80) cc_final: 0.6519 (m-10) REVERT: 7 711 LYS cc_start: 0.7740 (ttmt) cc_final: 0.7508 (ttmt) REVERT: 7 738 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.7088 (p-80) REVERT: A 133 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7913 (mttp) REVERT: A 389 THR cc_start: 0.8807 (m) cc_final: 0.8554 (m) REVERT: A 545 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: A 609 ASP cc_start: 0.7957 (t70) cc_final: 0.7624 (t70) REVERT: A 676 MET cc_start: 0.7081 (mmm) cc_final: 0.6845 (mmm) REVERT: A 702 LEU cc_start: 0.8436 (tp) cc_final: 0.8212 (tp) REVERT: A 906 HIS cc_start: 0.7894 (m-70) cc_final: 0.7678 (m-70) REVERT: A 985 ASP cc_start: 0.7084 (t0) cc_final: 0.6776 (t70) REVERT: A 1157 ASP cc_start: 0.7474 (p0) cc_final: 0.7221 (m-30) REVERT: A 1194 ARG cc_start: 0.7251 (ttt-90) cc_final: 0.6863 (ttm-80) REVERT: A 1373 ASP cc_start: 0.7486 (m-30) cc_final: 0.6910 (m-30) REVERT: A 1453 TYR cc_start: 0.7978 (m-10) cc_final: 0.7657 (m-10) REVERT: A 1454 MET cc_start: 0.6936 (tpp) cc_final: 0.6597 (ttt) REVERT: B 136 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7952 (t) REVERT: B 227 LYS cc_start: 0.8174 (mtmt) cc_final: 0.7907 (ttmt) REVERT: B 312 GLU cc_start: 0.7595 (tp30) cc_final: 0.7308 (tp30) REVERT: B 353 LYS cc_start: 0.7538 (ttmm) cc_final: 0.6985 (mttt) REVERT: B 358 LYS cc_start: 0.7757 (ptpt) cc_final: 0.7342 (pttt) REVERT: B 433 GLN cc_start: 0.7414 (tt0) cc_final: 0.7198 (tt0) REVERT: B 434 ARG cc_start: 0.6963 (ttt90) cc_final: 0.6739 (tpp80) REVERT: B 662 MET cc_start: 0.8138 (mtp) cc_final: 0.7625 (mmm) REVERT: B 824 ILE cc_start: 0.8726 (mm) cc_final: 0.8496 (mm) REVERT: B 906 SER cc_start: 0.8793 (p) cc_final: 0.8380 (t) REVERT: B 1072 MET cc_start: 0.8869 (mtp) cc_final: 0.8611 (mtm) REVERT: C 12 GLU cc_start: 0.6966 (tt0) cc_final: 0.6646 (mt-10) REVERT: C 252 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: C 260 LEU cc_start: 0.8749 (tt) cc_final: 0.8422 (tp) REVERT: F 104 ASN cc_start: 0.8413 (t0) cc_final: 0.8077 (t0) REVERT: F 127 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6742 (mt-10) REVERT: F 137 TYR cc_start: 0.9005 (m-80) cc_final: 0.8225 (m-80) REVERT: G 115 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7839 (mtt) REVERT: I 17 ARG cc_start: 0.7485 (tpp80) cc_final: 0.7095 (tpp80) REVERT: I 48 LEU cc_start: 0.8958 (mm) cc_final: 0.8708 (mm) REVERT: I 98 VAL cc_start: 0.8519 (p) cc_final: 0.8184 (t) REVERT: L 36 SER cc_start: 0.8378 (t) cc_final: 0.8022 (m) REVERT: L 37 LYS cc_start: 0.8396 (tttt) cc_final: 0.8102 (tttt) REVERT: M 22 LEU cc_start: 0.8207 (pt) cc_final: 0.7872 (mp) REVERT: M 101 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7424 (p) REVERT: M 108 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7538 (mmtt) REVERT: M 119 MET cc_start: 0.4321 (ppp) cc_final: 0.3426 (ptm) REVERT: M 157 CYS cc_start: 0.7388 (m) cc_final: 0.7017 (m) REVERT: M 208 ASN cc_start: 0.7945 (t0) cc_final: 0.7683 (t0) REVERT: M 261 LYS cc_start: 0.7889 (tttt) cc_final: 0.7158 (ttpp) REVERT: M 315 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7465 (mp) REVERT: O 67 LEU cc_start: 0.8665 (mt) cc_final: 0.8452 (tt) REVERT: Q 34 MET cc_start: 0.1073 (ppp) cc_final: 0.0709 (ppp) REVERT: R 266 THR cc_start: 0.9028 (m) cc_final: 0.8744 (p) REVERT: W 74 GLU cc_start: 0.6777 (tt0) cc_final: 0.6537 (mt-10) REVERT: W 96 ASP cc_start: 0.7524 (t0) cc_final: 0.7077 (t0) REVERT: W 179 ILE cc_start: 0.7993 (tt) cc_final: 0.7761 (tt) REVERT: W 195 GLU cc_start: 0.6796 (tp30) cc_final: 0.6501 (tm-30) REVERT: W 218 THR cc_start: 0.8735 (OUTLIER) cc_final: 0.8484 (t) REVERT: X 214 TRP cc_start: 0.8000 (t60) cc_final: 0.7367 (t60) outliers start: 219 outliers final: 142 residues processed: 1424 average time/residue: 0.6998 time to fit residues: 1691.7859 Evaluate side-chains 1395 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1239 time to evaluate : 6.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 61 MET Chi-restraints excluded: chain 0 residue 75 THR Chi-restraints excluded: chain 0 residue 171 LEU Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 395 ASP Chi-restraints excluded: chain 0 residue 409 ILE Chi-restraints excluded: chain 0 residue 455 SER Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 580 SER Chi-restraints excluded: chain 0 residue 630 THR Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 0 residue 701 LEU Chi-restraints excluded: chain 0 residue 745 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 248 ASN Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 286 ARG Chi-restraints excluded: chain 1 residue 289 SER Chi-restraints excluded: chain 1 residue 306 ARG Chi-restraints excluded: chain 1 residue 349 VAL Chi-restraints excluded: chain 1 residue 367 ASN Chi-restraints excluded: chain 1 residue 470 LEU Chi-restraints excluded: chain 1 residue 504 ILE Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 341 VAL Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 114 GLU Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 231 GLU Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 301 PHE Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 439 ASP Chi-restraints excluded: chain 6 residue 456 SER Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 199 ARG Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 586 THR Chi-restraints excluded: chain 7 residue 588 PHE Chi-restraints excluded: chain 7 residue 646 ASN Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 545 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1224 LEU Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 152 GLU Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 281 SER Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain M residue 315 ILE Chi-restraints excluded: chain M residue 321 ASP Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 118 GLU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 143 ASP Chi-restraints excluded: chain W residue 218 THR Chi-restraints excluded: chain W residue 225 SER Chi-restraints excluded: chain X residue 210 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 716 optimal weight: 7.9990 chunk 488 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 640 optimal weight: 3.9990 chunk 354 optimal weight: 0.1980 chunk 734 optimal weight: 5.9990 chunk 594 optimal weight: 0.0670 chunk 1 optimal weight: 0.6980 chunk 439 optimal weight: 20.0000 chunk 772 optimal weight: 4.9990 chunk 217 optimal weight: 30.0000 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 0 66 HIS ** 0 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 664 GLN 1 331 HIS 1 442 HIS 1 516 HIS 2 169 HIS 2 344 ASN ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN 7 366 GLN A 171 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A1270 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN ** W 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 220 ASN W 294 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 75459 Z= 0.242 Angle : 0.519 11.873 102389 Z= 0.269 Chirality : 0.041 0.204 11570 Planarity : 0.004 0.051 12699 Dihedral : 11.867 115.524 11078 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.31 % Allowed : 13.18 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.53 (0.09), residues: 8769 helix: 1.26 (0.09), residues: 3530 sheet: 0.12 (0.14), residues: 1329 loop : -0.32 (0.10), residues: 3910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 7 133 HIS 0.007 0.001 HIS W 261 PHE 0.030 0.001 PHE 2 269 TYR 0.035 0.001 TYR 4 79 ARG 0.008 0.000 ARG 7 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1301 time to evaluate : 6.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 132 LYS cc_start: 0.7545 (mttt) cc_final: 0.7165 (mmmt) REVERT: 0 270 ARG cc_start: 0.7621 (tpt170) cc_final: 0.7343 (tpt170) REVERT: 0 468 MET cc_start: 0.7892 (tpp) cc_final: 0.7223 (tpp) REVERT: 0 557 MET cc_start: 0.7659 (mtp) cc_final: 0.7433 (ptp) REVERT: 1 11 LYS cc_start: 0.8582 (mttm) cc_final: 0.8261 (ptpp) REVERT: 1 87 HIS cc_start: 0.7784 (m-70) cc_final: 0.7337 (m-70) REVERT: 1 177 ASN cc_start: 0.6781 (t0) cc_final: 0.6468 (t0) REVERT: 1 180 LEU cc_start: 0.8144 (tp) cc_final: 0.7889 (tp) REVERT: 1 184 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7744 (pt) REVERT: 1 249 VAL cc_start: 0.7982 (OUTLIER) cc_final: 0.7762 (p) REVERT: 1 566 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7925 (mt) REVERT: 2 17 ILE cc_start: 0.9053 (mm) cc_final: 0.8530 (mm) REVERT: 2 183 LYS cc_start: 0.7249 (mmtt) cc_final: 0.7046 (ptmt) REVERT: 2 205 LEU cc_start: 0.8473 (tp) cc_final: 0.8214 (mm) REVERT: 2 249 MET cc_start: 0.8042 (tpt) cc_final: 0.7767 (tpt) REVERT: 2 373 MET cc_start: 0.5710 (ppp) cc_final: 0.5426 (ppp) REVERT: 2 409 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7279 (mtm-85) REVERT: 2 418 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8183 (mmpt) REVERT: 2 446 LEU cc_start: 0.7987 (mm) cc_final: 0.7765 (tp) REVERT: 3 112 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7342 (mt-10) REVERT: 3 114 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: 3 115 ASP cc_start: 0.7174 (t0) cc_final: 0.6767 (t0) REVERT: 3 116 ILE cc_start: 0.8065 (mt) cc_final: 0.7732 (mt) REVERT: 4 190 ILE cc_start: 0.7989 (mm) cc_final: 0.7660 (mt) REVERT: 4 210 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6282 (mt) REVERT: 4 323 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8529 (mtmm) REVERT: 6 180 GLN cc_start: 0.7412 (tp40) cc_final: 0.7143 (mm-40) REVERT: 6 298 LYS cc_start: 0.7727 (tttt) cc_final: 0.7427 (ttpp) REVERT: 6 341 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7828 (ttmm) REVERT: 6 441 ASP cc_start: 0.7927 (t0) cc_final: 0.7631 (t0) REVERT: 6 447 ILE cc_start: 0.7935 (mm) cc_final: 0.7721 (mm) REVERT: 7 121 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7912 (pp) REVERT: 7 190 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7992 (m) REVERT: 7 231 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7086 (ptt-90) REVERT: 7 392 LYS cc_start: 0.7091 (pttt) cc_final: 0.6642 (pttt) REVERT: 7 613 TYR cc_start: 0.7735 (t80) cc_final: 0.7350 (t80) REVERT: 7 637 MET cc_start: 0.8250 (tpp) cc_final: 0.7918 (mmm) REVERT: 7 675 SER cc_start: 0.7931 (p) cc_final: 0.7608 (p) REVERT: 7 677 TYR cc_start: 0.6696 (m-80) cc_final: 0.6448 (m-10) REVERT: 7 738 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6999 (p-80) REVERT: A 133 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7934 (mttp) REVERT: A 186 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7858 (mmmt) REVERT: A 545 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: A 609 ASP cc_start: 0.7866 (t70) cc_final: 0.7519 (t70) REVERT: A 676 MET cc_start: 0.7039 (mmm) cc_final: 0.6596 (mmm) REVERT: A 702 LEU cc_start: 0.8385 (tp) cc_final: 0.8161 (tp) REVERT: A 985 ASP cc_start: 0.6952 (t0) cc_final: 0.6604 (t70) REVERT: A 1040 GLN cc_start: 0.7431 (tt0) cc_final: 0.7146 (pt0) REVERT: A 1373 ASP cc_start: 0.7494 (m-30) cc_final: 0.6921 (m-30) REVERT: A 1453 TYR cc_start: 0.8060 (m-10) cc_final: 0.7576 (m-10) REVERT: A 1454 MET cc_start: 0.7045 (tpp) cc_final: 0.6652 (ttt) REVERT: B 65 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7025 (mm-30) REVERT: B 227 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7921 (ttmt) REVERT: B 312 GLU cc_start: 0.7576 (tp30) cc_final: 0.7239 (tp30) REVERT: B 353 LYS cc_start: 0.7505 (ttmm) cc_final: 0.6859 (mttt) REVERT: B 358 LYS cc_start: 0.7806 (ptpt) cc_final: 0.7386 (pttt) REVERT: B 433 GLN cc_start: 0.7387 (tt0) cc_final: 0.7162 (tt0) REVERT: B 434 ARG cc_start: 0.6946 (ttt90) cc_final: 0.6726 (tpp80) REVERT: B 662 MET cc_start: 0.8116 (mtp) cc_final: 0.7595 (mmm) REVERT: B 824 ILE cc_start: 0.8692 (mm) cc_final: 0.8451 (mm) REVERT: B 906 SER cc_start: 0.8786 (p) cc_final: 0.8369 (t) REVERT: B 1072 MET cc_start: 0.8855 (mtp) cc_final: 0.8588 (mtm) REVERT: C 12 GLU cc_start: 0.6971 (tt0) cc_final: 0.6621 (mt-10) REVERT: C 260 LEU cc_start: 0.8751 (tt) cc_final: 0.8430 (tp) REVERT: E 20 LYS cc_start: 0.8564 (mmtm) cc_final: 0.7964 (mttt) REVERT: E 171 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7742 (mttt) REVERT: F 104 ASN cc_start: 0.8358 (t0) cc_final: 0.7968 (t0) REVERT: F 127 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6631 (mt-10) REVERT: F 137 TYR cc_start: 0.8982 (m-80) cc_final: 0.8203 (m-80) REVERT: G 41 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7884 (mtpp) REVERT: I 17 ARG cc_start: 0.7567 (tpp80) cc_final: 0.7197 (tpp80) REVERT: I 25 LEU cc_start: 0.8403 (tp) cc_final: 0.8193 (tp) REVERT: I 48 LEU cc_start: 0.8911 (mm) cc_final: 0.8684 (mm) REVERT: I 80 SER cc_start: 0.7408 (m) cc_final: 0.7012 (m) REVERT: I 98 VAL cc_start: 0.8511 (p) cc_final: 0.8176 (t) REVERT: L 36 SER cc_start: 0.8393 (t) cc_final: 0.8036 (m) REVERT: M 22 LEU cc_start: 0.8239 (pt) cc_final: 0.7931 (mp) REVERT: M 101 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7362 (p) REVERT: M 119 MET cc_start: 0.4417 (ppp) cc_final: 0.3417 (ptm) REVERT: M 157 CYS cc_start: 0.7314 (m) cc_final: 0.6951 (m) REVERT: M 208 ASN cc_start: 0.7920 (t0) cc_final: 0.7663 (t0) REVERT: M 261 LYS cc_start: 0.7847 (tttt) cc_final: 0.7127 (ttpp) REVERT: M 315 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7444 (mp) REVERT: O 67 LEU cc_start: 0.8652 (mt) cc_final: 0.8360 (tt) REVERT: Q 34 MET cc_start: 0.1338 (ppp) cc_final: 0.1027 (ppp) REVERT: R 266 THR cc_start: 0.9036 (m) cc_final: 0.8740 (p) REVERT: R 284 LYS cc_start: 0.6548 (mtpt) cc_final: 0.6314 (mtpt) REVERT: W 74 GLU cc_start: 0.6794 (tt0) cc_final: 0.6501 (mt-10) REVERT: W 96 ASP cc_start: 0.7532 (t0) cc_final: 0.7058 (t0) REVERT: W 179 ILE cc_start: 0.7952 (tt) cc_final: 0.7729 (tt) REVERT: W 201 ILE cc_start: 0.8575 (mm) cc_final: 0.8349 (mm) REVERT: X 214 TRP cc_start: 0.7921 (t60) cc_final: 0.7236 (t60) outliers start: 184 outliers final: 127 residues processed: 1404 average time/residue: 0.6869 time to fit residues: 1641.4583 Evaluate side-chains 1391 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1252 time to evaluate : 6.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 61 MET Chi-restraints excluded: chain 0 residue 75 THR Chi-restraints excluded: chain 0 residue 171 LEU Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 395 ASP Chi-restraints excluded: chain 0 residue 409 ILE Chi-restraints excluded: chain 0 residue 478 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 580 SER Chi-restraints excluded: chain 0 residue 630 THR Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 0 residue 701 LEU Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 248 ASN Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 286 ARG Chi-restraints excluded: chain 1 residue 306 ARG Chi-restraints excluded: chain 1 residue 367 ASN Chi-restraints excluded: chain 1 residue 504 ILE Chi-restraints excluded: chain 1 residue 566 ILE Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 341 VAL Chi-restraints excluded: chain 3 residue 114 GLU Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 231 GLU Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 410 PHE Chi-restraints excluded: chain 6 residue 439 ASP Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 190 THR Chi-restraints excluded: chain 7 residue 231 ARG Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 586 THR Chi-restraints excluded: chain 7 residue 588 PHE Chi-restraints excluded: chain 7 residue 646 ASN Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 545 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 281 SER Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain M residue 315 ILE Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 118 GLU Chi-restraints excluded: chain W residue 218 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 254 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 289 optimal weight: 6.9990 chunk 774 optimal weight: 6.9990 chunk 170 optimal weight: 0.3980 chunk 505 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 861 optimal weight: 5.9990 chunk 714 optimal weight: 2.9990 chunk 398 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 284 optimal weight: 40.0000 chunk 452 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 0 66 HIS ** 0 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 471 GLN 1 516 HIS ** 2 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 395 GLN ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN 7 366 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A1270 ASN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN G 131 GLN K 89 ASN L 53 HIS ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 75459 Z= 0.299 Angle : 0.542 11.385 102389 Z= 0.279 Chirality : 0.042 0.227 11570 Planarity : 0.004 0.053 12699 Dihedral : 11.891 111.589 11078 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.79 % Allowed : 13.58 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.09), residues: 8769 helix: 1.22 (0.09), residues: 3529 sheet: 0.08 (0.14), residues: 1335 loop : -0.35 (0.10), residues: 3905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 7 133 HIS 0.006 0.001 HIS A 451 PHE 0.033 0.002 PHE 2 269 TYR 0.026 0.001 TYR G 51 ARG 0.007 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1490 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1268 time to evaluate : 6.206 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: 0 132 LYS cc_start: 0.7468 (mttt) cc_final: 0.7093 (mmmt) REVERT: 0 270 ARG cc_start: 0.7633 (tpt170) cc_final: 0.7357 (tpt170) REVERT: 0 468 MET cc_start: 0.7907 (tpp) cc_final: 0.7231 (tpp) REVERT: 1 11 LYS cc_start: 0.8604 (mttm) cc_final: 0.8288 (ptpp) REVERT: 1 177 ASN cc_start: 0.6832 (t0) cc_final: 0.6512 (t0) REVERT: 1 180 LEU cc_start: 0.8221 (tp) cc_final: 0.7992 (tp) REVERT: 1 184 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7770 (pt) REVERT: 1 197 GLU cc_start: 0.7010 (tp30) cc_final: 0.6780 (tp30) REVERT: 1 249 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7694 (p) REVERT: 1 291 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8406 (mtmt) REVERT: 1 566 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7943 (mt) REVERT: 2 17 ILE cc_start: 0.9116 (mm) cc_final: 0.8830 (mt) REVERT: 2 22 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7715 (mm-40) REVERT: 2 205 LEU cc_start: 0.8543 (tp) cc_final: 0.8282 (mm) REVERT: 2 249 MET cc_start: 0.8068 (tpt) cc_final: 0.7795 (tpt) REVERT: 2 270 TYR cc_start: 0.7326 (m-80) cc_final: 0.6938 (m-80) REVERT: 2 277 MET cc_start: 0.7146 (tpp) cc_final: 0.6782 (tpp) REVERT: 2 409 ARG cc_start: 0.7881 (ttm110) cc_final: 0.7277 (mtm-85) REVERT: 2 418 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8213 (mmpt) REVERT: 2 446 LEU cc_start: 0.8025 (mm) cc_final: 0.7803 (tp) REVERT: 3 11 ASP cc_start: 0.8149 (t0) cc_final: 0.7783 (t0) REVERT: 3 112 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7331 (mt-10) REVERT: 3 114 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7542 (tm-30) REVERT: 3 115 ASP cc_start: 0.7180 (t0) cc_final: 0.6774 (t0) REVERT: 3 116 ILE cc_start: 0.8081 (mt) cc_final: 0.7745 (mt) REVERT: 4 190 ILE cc_start: 0.8035 (mm) cc_final: 0.7671 (mt) REVERT: 4 210 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6378 (mt) REVERT: 4 323 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8529 (mtmm) REVERT: 6 180 GLN cc_start: 0.7438 (tp40) cc_final: 0.7151 (mm-40) REVERT: 6 298 LYS cc_start: 0.7703 (tttt) cc_final: 0.7399 (ttpp) REVERT: 6 341 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7893 (ttmm) REVERT: 6 351 ASN cc_start: 0.8266 (t0) cc_final: 0.7722 (t0) REVERT: 6 441 ASP cc_start: 0.7924 (t0) cc_final: 0.7639 (t0) REVERT: 6 447 ILE cc_start: 0.8056 (mm) cc_final: 0.7809 (mm) REVERT: 7 121 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7951 (pp) REVERT: 7 190 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.8120 (m) REVERT: 7 231 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.7070 (ptt-90) REVERT: 7 367 GLU cc_start: 0.7927 (tt0) cc_final: 0.7310 (tp30) REVERT: 7 392 LYS cc_start: 0.7006 (pttt) cc_final: 0.6582 (pttt) REVERT: 7 613 TYR cc_start: 0.7750 (t80) cc_final: 0.7350 (t80) REVERT: 7 637 MET cc_start: 0.8255 (tpp) cc_final: 0.7924 (mmm) REVERT: 7 677 TYR cc_start: 0.6732 (m-80) cc_final: 0.6508 (m-10) REVERT: 7 738 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.7012 (p-80) REVERT: A 133 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7907 (mttp) REVERT: A 186 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7917 (mmmt) REVERT: A 545 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: A 609 ASP cc_start: 0.7950 (t70) cc_final: 0.7619 (t70) REVERT: A 676 MET cc_start: 0.7086 (mmm) cc_final: 0.6731 (mmm) REVERT: A 702 LEU cc_start: 0.8463 (tp) cc_final: 0.8249 (tp) REVERT: A 838 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8119 (tp-100) REVERT: A 898 ARG cc_start: 0.7948 (tpt170) cc_final: 0.7711 (tpt90) REVERT: A 985 ASP cc_start: 0.6950 (t0) cc_final: 0.6595 (t70) REVERT: A 1040 GLN cc_start: 0.7364 (tt0) cc_final: 0.6938 (pt0) REVERT: A 1373 ASP cc_start: 0.7499 (m-30) cc_final: 0.6925 (m-30) REVERT: A 1442 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: A 1454 MET cc_start: 0.7088 (tpp) cc_final: 0.6672 (ttt) REVERT: B 22 SER cc_start: 0.8179 (p) cc_final: 0.7934 (t) REVERT: B 65 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7051 (mm-30) REVERT: B 227 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7917 (ttmt) REVERT: B 312 GLU cc_start: 0.7643 (tp30) cc_final: 0.7304 (tp30) REVERT: B 358 LYS cc_start: 0.7874 (ptpt) cc_final: 0.7418 (pttt) REVERT: B 433 GLN cc_start: 0.7418 (tt0) cc_final: 0.7192 (tt0) REVERT: B 434 ARG cc_start: 0.6937 (ttt90) cc_final: 0.6726 (tpp80) REVERT: B 592 ASN cc_start: 0.8449 (t0) cc_final: 0.8207 (t0) REVERT: B 662 MET cc_start: 0.8169 (mtp) cc_final: 0.7588 (mmm) REVERT: B 665 GLU cc_start: 0.6952 (tt0) cc_final: 0.6693 (tp30) REVERT: B 824 ILE cc_start: 0.8715 (mm) cc_final: 0.8466 (mm) REVERT: B 906 SER cc_start: 0.8786 (p) cc_final: 0.8384 (t) REVERT: B 1072 MET cc_start: 0.8876 (mtp) cc_final: 0.8607 (mtm) REVERT: B 1104 HIS cc_start: 0.8665 (OUTLIER) cc_final: 0.8215 (p90) REVERT: C 12 GLU cc_start: 0.6942 (tt0) cc_final: 0.6618 (mt-10) REVERT: C 252 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: C 260 LEU cc_start: 0.8738 (tt) cc_final: 0.8414 (tp) REVERT: E 20 LYS cc_start: 0.8543 (mmtm) cc_final: 0.7957 (mttt) REVERT: E 171 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7738 (mttt) REVERT: F 104 ASN cc_start: 0.8374 (t0) cc_final: 0.7941 (t0) REVERT: F 127 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6667 (mt-10) REVERT: F 137 TYR cc_start: 0.9001 (m-80) cc_final: 0.8207 (m-80) REVERT: G 41 LYS cc_start: 0.8141 (mtpp) cc_final: 0.7826 (mtpp) REVERT: G 115 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7848 (mtt) REVERT: I 17 ARG cc_start: 0.7558 (tpp80) cc_final: 0.7166 (tpp80) REVERT: I 25 LEU cc_start: 0.8439 (tp) cc_final: 0.8214 (tp) REVERT: I 48 LEU cc_start: 0.8919 (mm) cc_final: 0.8694 (mm) REVERT: I 80 SER cc_start: 0.7373 (m) cc_final: 0.6974 (m) REVERT: I 98 VAL cc_start: 0.8527 (p) cc_final: 0.8213 (t) REVERT: L 36 SER cc_start: 0.8445 (t) cc_final: 0.8063 (m) REVERT: M 22 LEU cc_start: 0.8312 (pt) cc_final: 0.7967 (mp) REVERT: M 101 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7357 (p) REVERT: M 108 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7469 (mtpt) REVERT: M 119 MET cc_start: 0.4441 (ppp) cc_final: 0.3511 (ptm) REVERT: M 152 GLU cc_start: 0.7261 (tt0) cc_final: 0.7049 (pt0) REVERT: M 157 CYS cc_start: 0.7336 (m) cc_final: 0.6958 (m) REVERT: M 202 GLU cc_start: 0.7709 (pm20) cc_final: 0.7508 (pm20) REVERT: M 208 ASN cc_start: 0.7928 (t0) cc_final: 0.7656 (t0) REVERT: M 261 LYS cc_start: 0.7830 (tttt) cc_final: 0.7095 (ttpp) REVERT: M 315 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7415 (mp) REVERT: O 67 LEU cc_start: 0.8657 (mt) cc_final: 0.8453 (tt) REVERT: O 121 MET cc_start: 0.4920 (ppp) cc_final: 0.3941 (ttp) REVERT: Q 34 MET cc_start: 0.1382 (ppp) cc_final: 0.1162 (ppp) REVERT: R 266 THR cc_start: 0.9082 (m) cc_final: 0.8790 (p) REVERT: R 284 LYS cc_start: 0.6588 (mtpt) cc_final: 0.6342 (mtpt) REVERT: W 96 ASP cc_start: 0.7608 (t0) cc_final: 0.7124 (t0) REVERT: W 179 ILE cc_start: 0.7863 (tt) cc_final: 0.7657 (tt) REVERT: X 214 TRP cc_start: 0.7916 (t60) cc_final: 0.7214 (t60) outliers start: 222 outliers final: 168 residues processed: 1396 average time/residue: 0.6980 time to fit residues: 1662.1778 Evaluate side-chains 1421 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1235 time to evaluate : 6.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 60 GLN Chi-restraints excluded: chain 0 residue 75 THR Chi-restraints excluded: chain 0 residue 171 LEU Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 385 VAL Chi-restraints excluded: chain 0 residue 395 ASP Chi-restraints excluded: chain 0 residue 409 ILE Chi-restraints excluded: chain 0 residue 455 SER Chi-restraints excluded: chain 0 residue 478 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 580 SER Chi-restraints excluded: chain 0 residue 630 THR Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 0 residue 701 LEU Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 248 ASN Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 286 ARG Chi-restraints excluded: chain 1 residue 291 LYS Chi-restraints excluded: chain 1 residue 306 ARG Chi-restraints excluded: chain 1 residue 367 ASN Chi-restraints excluded: chain 1 residue 504 ILE Chi-restraints excluded: chain 1 residue 566 ILE Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 341 VAL Chi-restraints excluded: chain 3 residue 114 GLU Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 231 GLU Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 410 PHE Chi-restraints excluded: chain 6 residue 439 ASP Chi-restraints excluded: chain 6 residue 456 SER Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 190 THR Chi-restraints excluded: chain 7 residue 231 ARG Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 455 SER Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 586 THR Chi-restraints excluded: chain 7 residue 588 PHE Chi-restraints excluded: chain 7 residue 646 ASN Chi-restraints excluded: chain 7 residue 647 ASP Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 545 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 619 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 281 SER Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain M residue 315 ILE Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 36 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 118 GLU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 140 LEU Chi-restraints excluded: chain W residue 225 SER Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 254 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 830 optimal weight: 50.0000 chunk 97 optimal weight: 5.9990 chunk 490 optimal weight: 3.9990 chunk 628 optimal weight: 0.4980 chunk 487 optimal weight: 0.9990 chunk 724 optimal weight: 7.9990 chunk 480 optimal weight: 0.6980 chunk 857 optimal weight: 0.9990 chunk 536 optimal weight: 3.9990 chunk 522 optimal weight: 4.9990 chunk 396 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 0 66 HIS 0 521 ASN 1 493 ASN 1 516 HIS ** 2 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN 7 366 GLN A 75 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A 994 GLN A1270 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN G 131 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 220 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 75459 Z= 0.222 Angle : 0.512 11.377 102389 Z= 0.265 Chirality : 0.041 0.203 11570 Planarity : 0.004 0.051 12699 Dihedral : 11.857 107.864 11078 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.60 % Allowed : 14.09 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.09), residues: 8769 helix: 1.33 (0.09), residues: 3526 sheet: 0.07 (0.14), residues: 1355 loop : -0.32 (0.10), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 7 133 HIS 0.007 0.001 HIS A 451 PHE 0.033 0.001 PHE 2 269 TYR 0.024 0.001 TYR 4 79 ARG 0.009 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1264 time to evaluate : 6.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 132 LYS cc_start: 0.7451 (mttt) cc_final: 0.7106 (mmmt) REVERT: 0 225 GLU cc_start: 0.6440 (mm-30) cc_final: 0.5747 (mm-30) REVERT: 0 270 ARG cc_start: 0.7612 (tpt170) cc_final: 0.7340 (tpt170) REVERT: 0 468 MET cc_start: 0.7890 (tpp) cc_final: 0.7218 (tpp) REVERT: 0 712 MET cc_start: 0.7008 (mtm) cc_final: 0.6749 (mtm) REVERT: 1 11 LYS cc_start: 0.8556 (mttm) cc_final: 0.8246 (ptpp) REVERT: 1 177 ASN cc_start: 0.6795 (t0) cc_final: 0.6489 (t0) REVERT: 1 180 LEU cc_start: 0.8227 (tp) cc_final: 0.8021 (tp) REVERT: 1 184 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7744 (pt) REVERT: 1 197 GLU cc_start: 0.7043 (tp30) cc_final: 0.6578 (tp30) REVERT: 1 199 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6647 (p) REVERT: 1 249 VAL cc_start: 0.7914 (OUTLIER) cc_final: 0.7680 (p) REVERT: 1 291 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8252 (mtmt) REVERT: 1 566 ILE cc_start: 0.8162 (mm) cc_final: 0.7950 (mt) REVERT: 2 17 ILE cc_start: 0.9121 (mm) cc_final: 0.8810 (mt) REVERT: 2 22 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7700 (mm-40) REVERT: 2 183 LYS cc_start: 0.7016 (ptmt) cc_final: 0.6717 (ptmt) REVERT: 2 184 ILE cc_start: 0.8484 (mp) cc_final: 0.8279 (mt) REVERT: 2 205 LEU cc_start: 0.8539 (tp) cc_final: 0.8299 (mm) REVERT: 2 249 MET cc_start: 0.8058 (tpt) cc_final: 0.7784 (tpt) REVERT: 2 270 TYR cc_start: 0.7354 (m-80) cc_final: 0.6965 (m-80) REVERT: 2 277 MET cc_start: 0.6999 (tpp) cc_final: 0.6684 (tpp) REVERT: 2 409 ARG cc_start: 0.7813 (ttm110) cc_final: 0.7234 (mtm-85) REVERT: 2 446 LEU cc_start: 0.8027 (mm) cc_final: 0.7815 (tp) REVERT: 3 112 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7239 (mt-10) REVERT: 3 114 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: 3 115 ASP cc_start: 0.7157 (t0) cc_final: 0.6786 (t0) REVERT: 3 116 ILE cc_start: 0.8116 (mt) cc_final: 0.7780 (mt) REVERT: 4 190 ILE cc_start: 0.7985 (mm) cc_final: 0.7605 (mt) REVERT: 4 210 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6198 (mt) REVERT: 4 323 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8516 (mtmm) REVERT: 6 180 GLN cc_start: 0.7416 (tp40) cc_final: 0.7140 (mm-40) REVERT: 6 296 HIS cc_start: 0.7378 (t-90) cc_final: 0.7104 (t-170) REVERT: 6 298 LYS cc_start: 0.7683 (tttt) cc_final: 0.7393 (ttpp) REVERT: 6 341 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7726 (tttm) REVERT: 6 351 ASN cc_start: 0.8265 (t0) cc_final: 0.7715 (t0) REVERT: 6 441 ASP cc_start: 0.7911 (t0) cc_final: 0.7666 (t0) REVERT: 6 447 ILE cc_start: 0.8043 (mm) cc_final: 0.7779 (mm) REVERT: 7 121 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7977 (pp) REVERT: 7 190 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8161 (m) REVERT: 7 231 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.7052 (ptt-90) REVERT: 7 392 LYS cc_start: 0.7024 (pttt) cc_final: 0.6608 (pttt) REVERT: 7 613 TYR cc_start: 0.7719 (t80) cc_final: 0.7378 (t80) REVERT: 7 637 MET cc_start: 0.8257 (tpp) cc_final: 0.7930 (mmm) REVERT: 7 677 TYR cc_start: 0.6694 (m-80) cc_final: 0.6491 (m-10) REVERT: 7 738 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6897 (p-80) REVERT: A 133 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7885 (mttp) REVERT: A 186 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7984 (mmmt) REVERT: A 609 ASP cc_start: 0.7850 (t70) cc_final: 0.7514 (t70) REVERT: A 676 MET cc_start: 0.7007 (mmm) cc_final: 0.6474 (mmm) REVERT: A 702 LEU cc_start: 0.8449 (tp) cc_final: 0.8239 (tp) REVERT: A 898 ARG cc_start: 0.7939 (tpt170) cc_final: 0.7713 (tpt90) REVERT: A 985 ASP cc_start: 0.6911 (t0) cc_final: 0.6545 (t70) REVERT: A 1040 GLN cc_start: 0.7305 (tt0) cc_final: 0.6919 (pt0) REVERT: A 1240 CYS cc_start: 0.7283 (m) cc_final: 0.7017 (t) REVERT: A 1373 ASP cc_start: 0.7514 (m-30) cc_final: 0.6909 (m-30) REVERT: A 1442 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: A 1454 MET cc_start: 0.7073 (tpp) cc_final: 0.6681 (ttt) REVERT: B 22 SER cc_start: 0.8194 (p) cc_final: 0.7933 (t) REVERT: B 65 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7027 (mm-30) REVERT: B 227 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7919 (ttmt) REVERT: B 257 LYS cc_start: 0.8276 (mtmt) cc_final: 0.8042 (mtpt) REVERT: B 312 GLU cc_start: 0.7619 (tp30) cc_final: 0.7291 (tp30) REVERT: B 353 LYS cc_start: 0.7447 (ttmm) cc_final: 0.7082 (mttm) REVERT: B 358 LYS cc_start: 0.7846 (ptpt) cc_final: 0.7413 (pttt) REVERT: B 433 GLN cc_start: 0.7413 (tt0) cc_final: 0.7191 (tt0) REVERT: B 434 ARG cc_start: 0.6931 (ttt90) cc_final: 0.6722 (tpp80) REVERT: B 662 MET cc_start: 0.8137 (mtp) cc_final: 0.7599 (mmm) REVERT: B 665 GLU cc_start: 0.6946 (tt0) cc_final: 0.6695 (tp30) REVERT: B 906 SER cc_start: 0.8785 (p) cc_final: 0.8381 (t) REVERT: B 1072 MET cc_start: 0.8865 (mtp) cc_final: 0.8593 (mtm) REVERT: B 1104 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.8190 (p90) REVERT: C 260 LEU cc_start: 0.8747 (tt) cc_final: 0.8430 (tp) REVERT: E 20 LYS cc_start: 0.8549 (mmtm) cc_final: 0.7956 (mttt) REVERT: E 171 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7754 (mttt) REVERT: F 104 ASN cc_start: 0.8295 (t0) cc_final: 0.7829 (t0) REVERT: F 127 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6652 (mt-10) REVERT: F 137 TYR cc_start: 0.8985 (m-80) cc_final: 0.8198 (m-80) REVERT: G 41 LYS cc_start: 0.8148 (mtpp) cc_final: 0.7821 (mtpp) REVERT: G 115 MET cc_start: 0.8159 (mtm) cc_final: 0.7819 (mtt) REVERT: I 17 ARG cc_start: 0.7510 (tpp80) cc_final: 0.7123 (tpp80) REVERT: I 25 LEU cc_start: 0.8380 (tp) cc_final: 0.8176 (tp) REVERT: I 48 LEU cc_start: 0.8902 (mm) cc_final: 0.8674 (mm) REVERT: I 80 SER cc_start: 0.7386 (m) cc_final: 0.6987 (m) REVERT: I 98 VAL cc_start: 0.8525 (p) cc_final: 0.8214 (t) REVERT: L 36 SER cc_start: 0.8453 (t) cc_final: 0.8134 (m) REVERT: L 47 ARG cc_start: 0.8349 (ptm-80) cc_final: 0.8114 (ptm160) REVERT: M 22 LEU cc_start: 0.8366 (pt) cc_final: 0.8005 (mp) REVERT: M 101 THR cc_start: 0.7794 (OUTLIER) cc_final: 0.7324 (p) REVERT: M 108 LYS cc_start: 0.7756 (mmtt) cc_final: 0.7516 (mmtt) REVERT: M 119 MET cc_start: 0.4463 (ppp) cc_final: 0.3515 (ptm) REVERT: M 208 ASN cc_start: 0.7922 (t0) cc_final: 0.7632 (t0) REVERT: M 261 LYS cc_start: 0.7823 (tttt) cc_final: 0.7104 (ttpp) REVERT: O 67 LEU cc_start: 0.8631 (mt) cc_final: 0.8428 (tt) REVERT: O 121 MET cc_start: 0.4939 (ppp) cc_final: 0.4029 (ttp) REVERT: Q 34 MET cc_start: 0.1339 (ppp) cc_final: 0.1136 (ppp) REVERT: R 266 THR cc_start: 0.9105 (m) cc_final: 0.8824 (p) REVERT: W 96 ASP cc_start: 0.7616 (t0) cc_final: 0.7132 (t0) REVERT: W 179 ILE cc_start: 0.7805 (tt) cc_final: 0.7587 (tt) REVERT: X 210 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8210 (mp) REVERT: X 214 TRP cc_start: 0.7827 (t60) cc_final: 0.7083 (t60) outliers start: 207 outliers final: 162 residues processed: 1382 average time/residue: 0.6958 time to fit residues: 1640.8195 Evaluate side-chains 1416 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1240 time to evaluate : 6.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 75 THR Chi-restraints excluded: chain 0 residue 171 LEU Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 366 LEU Chi-restraints excluded: chain 0 residue 385 VAL Chi-restraints excluded: chain 0 residue 395 ASP Chi-restraints excluded: chain 0 residue 409 ILE Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 580 SER Chi-restraints excluded: chain 0 residue 630 THR Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 0 residue 701 LEU Chi-restraints excluded: chain 1 residue 48 LEU Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 1 residue 248 ASN Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 286 ARG Chi-restraints excluded: chain 1 residue 289 SER Chi-restraints excluded: chain 1 residue 291 LYS Chi-restraints excluded: chain 1 residue 306 ARG Chi-restraints excluded: chain 1 residue 367 ASN Chi-restraints excluded: chain 1 residue 493 ASN Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 2 residue 341 VAL Chi-restraints excluded: chain 3 residue 114 GLU Chi-restraints excluded: chain 4 residue 32 ILE Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 231 GLU Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 410 PHE Chi-restraints excluded: chain 6 residue 438 VAL Chi-restraints excluded: chain 6 residue 439 ASP Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 190 THR Chi-restraints excluded: chain 7 residue 231 ARG Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 539 ASN Chi-restraints excluded: chain 7 residue 586 THR Chi-restraints excluded: chain 7 residue 588 PHE Chi-restraints excluded: chain 7 residue 646 ASN Chi-restraints excluded: chain 7 residue 647 ASP Chi-restraints excluded: chain 7 residue 675 SER Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 916 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 281 SER Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 36 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 118 GLU Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 140 LEU Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 254 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 530 optimal weight: 2.9990 chunk 342 optimal weight: 0.9980 chunk 512 optimal weight: 0.9980 chunk 258 optimal weight: 30.0000 chunk 168 optimal weight: 10.0000 chunk 166 optimal weight: 40.0000 chunk 545 optimal weight: 1.9990 chunk 584 optimal weight: 0.6980 chunk 424 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 674 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 66 HIS 1 516 HIS ** 2 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN 7 366 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A1270 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN G 131 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 120 ASN W 165 ASN ** W 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 220 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 75459 Z= 0.211 Angle : 0.511 13.739 102389 Z= 0.263 Chirality : 0.041 0.252 11570 Planarity : 0.004 0.051 12699 Dihedral : 11.840 104.613 11078 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.77 % Allowed : 14.33 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.59 (0.09), residues: 8769 helix: 1.36 (0.09), residues: 3545 sheet: 0.10 (0.14), residues: 1350 loop : -0.32 (0.10), residues: 3874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 0 696 HIS 0.006 0.001 HIS A 451 PHE 0.035 0.001 PHE 2 269 TYR 0.024 0.001 TYR B 88 ARG 0.008 0.000 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1256 time to evaluate : 6.228 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: 0 132 LYS cc_start: 0.7463 (mttt) cc_final: 0.7144 (mmmt) REVERT: 0 225 GLU cc_start: 0.6444 (mm-30) cc_final: 0.5755 (mm-30) REVERT: 0 270 ARG cc_start: 0.7611 (tpt170) cc_final: 0.7339 (tpt170) REVERT: 0 468 MET cc_start: 0.7887 (tpp) cc_final: 0.7212 (tpp) REVERT: 1 11 LYS cc_start: 0.8587 (mttm) cc_final: 0.8336 (ptpp) REVERT: 1 177 ASN cc_start: 0.6799 (t0) cc_final: 0.6492 (t0) REVERT: 1 184 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7730 (pt) REVERT: 1 197 GLU cc_start: 0.7066 (tp30) cc_final: 0.6602 (tp30) REVERT: 1 249 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7636 (p) REVERT: 1 291 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8251 (mtmt) REVERT: 1 566 ILE cc_start: 0.8184 (mm) cc_final: 0.7973 (mt) REVERT: 2 17 ILE cc_start: 0.9125 (mm) cc_final: 0.8766 (mm) REVERT: 2 22 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7700 (mm-40) REVERT: 2 183 LYS cc_start: 0.7001 (ptmt) cc_final: 0.6711 (ptmt) REVERT: 2 205 LEU cc_start: 0.8508 (tp) cc_final: 0.8287 (mm) REVERT: 2 249 MET cc_start: 0.8072 (tpt) cc_final: 0.7805 (tpt) REVERT: 2 270 TYR cc_start: 0.7376 (m-80) cc_final: 0.7012 (m-80) REVERT: 2 277 MET cc_start: 0.6952 (tpp) cc_final: 0.6645 (tpp) REVERT: 2 397 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8598 (tt) REVERT: 2 409 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7218 (mtm-85) REVERT: 2 446 LEU cc_start: 0.8016 (mm) cc_final: 0.7799 (tp) REVERT: 3 31 ASN cc_start: 0.8644 (t0) cc_final: 0.8212 (t0) REVERT: 3 112 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7223 (mt-10) REVERT: 3 115 ASP cc_start: 0.7150 (t0) cc_final: 0.6821 (t0) REVERT: 3 116 ILE cc_start: 0.8093 (mt) cc_final: 0.7745 (mt) REVERT: 4 190 ILE cc_start: 0.8010 (mm) cc_final: 0.7633 (mt) REVERT: 4 210 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6195 (mt) REVERT: 4 323 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8516 (mtmm) REVERT: 6 180 GLN cc_start: 0.7432 (tp40) cc_final: 0.7219 (mm-40) REVERT: 6 296 HIS cc_start: 0.7352 (t-90) cc_final: 0.7065 (t-170) REVERT: 6 298 LYS cc_start: 0.7669 (tttt) cc_final: 0.7386 (ttpp) REVERT: 6 341 LYS cc_start: 0.8134 (ttpt) cc_final: 0.7750 (tttm) REVERT: 6 351 ASN cc_start: 0.8263 (t0) cc_final: 0.7713 (t0) REVERT: 6 441 ASP cc_start: 0.7924 (t0) cc_final: 0.7679 (t0) REVERT: 6 447 ILE cc_start: 0.8037 (mm) cc_final: 0.7772 (mm) REVERT: 7 121 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7949 (pp) REVERT: 7 190 THR cc_start: 0.8324 (OUTLIER) cc_final: 0.8120 (m) REVERT: 7 231 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.7075 (ptt-90) REVERT: 7 392 LYS cc_start: 0.7029 (pttt) cc_final: 0.6626 (pttt) REVERT: 7 613 TYR cc_start: 0.7685 (t80) cc_final: 0.7331 (t80) REVERT: 7 637 MET cc_start: 0.8272 (tpp) cc_final: 0.7950 (mmm) REVERT: 7 738 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6895 (p-80) REVERT: A 133 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7869 (mttp) REVERT: A 186 LYS cc_start: 0.8219 (mmmt) cc_final: 0.8014 (mmmt) REVERT: A 501 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8419 (mt) REVERT: A 545 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: A 609 ASP cc_start: 0.7926 (t70) cc_final: 0.7589 (t70) REVERT: A 676 MET cc_start: 0.6983 (mmm) cc_final: 0.6398 (mmm) REVERT: A 702 LEU cc_start: 0.8449 (tp) cc_final: 0.8234 (tp) REVERT: A 740 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8717 (pp) REVERT: A 838 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8109 (tp-100) REVERT: A 898 ARG cc_start: 0.7870 (tpt170) cc_final: 0.7660 (tpt90) REVERT: A 985 ASP cc_start: 0.6926 (t0) cc_final: 0.6556 (t70) REVERT: A 1036 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7689 (mtp85) REVERT: A 1040 GLN cc_start: 0.7267 (tt0) cc_final: 0.6875 (pt0) REVERT: A 1240 CYS cc_start: 0.7269 (m) cc_final: 0.7009 (t) REVERT: A 1373 ASP cc_start: 0.7532 (m-30) cc_final: 0.6921 (m-30) REVERT: A 1454 MET cc_start: 0.6872 (tpp) cc_final: 0.6550 (ttt) REVERT: B 22 SER cc_start: 0.8209 (p) cc_final: 0.7942 (t) REVERT: B 65 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7026 (mm-30) REVERT: B 227 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7950 (ttmt) REVERT: B 257 LYS cc_start: 0.8273 (mtmt) cc_final: 0.8039 (mtpt) REVERT: B 312 GLU cc_start: 0.7644 (tp30) cc_final: 0.7292 (tp30) REVERT: B 353 LYS cc_start: 0.7492 (ttmm) cc_final: 0.7067 (mttm) REVERT: B 358 LYS cc_start: 0.7827 (ptpt) cc_final: 0.7383 (pttt) REVERT: B 433 GLN cc_start: 0.7409 (tt0) cc_final: 0.7190 (tt0) REVERT: B 434 ARG cc_start: 0.6929 (ttt90) cc_final: 0.6728 (tpp80) REVERT: B 592 ASN cc_start: 0.8489 (t0) cc_final: 0.8268 (t0) REVERT: B 662 MET cc_start: 0.8137 (mtp) cc_final: 0.7609 (mmm) REVERT: B 665 GLU cc_start: 0.6944 (tt0) cc_final: 0.6698 (tp30) REVERT: B 824 ILE cc_start: 0.8679 (mm) cc_final: 0.8458 (mm) REVERT: B 906 SER cc_start: 0.8821 (p) cc_final: 0.8394 (t) REVERT: B 1072 MET cc_start: 0.8866 (mtp) cc_final: 0.8593 (mtm) REVERT: B 1104 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.8180 (p90) REVERT: B 1129 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7971 (ttt-90) REVERT: C 252 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: C 260 LEU cc_start: 0.8704 (tt) cc_final: 0.8385 (tp) REVERT: E 171 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7758 (mttt) REVERT: F 127 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6666 (mt-10) REVERT: F 128 LYS cc_start: 0.7708 (mtpt) cc_final: 0.7328 (mmmm) REVERT: F 137 TYR cc_start: 0.8979 (m-80) cc_final: 0.8195 (m-80) REVERT: G 41 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7735 (mtpp) REVERT: G 115 MET cc_start: 0.8188 (mtm) cc_final: 0.7846 (mtt) REVERT: I 17 ARG cc_start: 0.7477 (tpp80) cc_final: 0.7076 (tpp80) REVERT: I 25 LEU cc_start: 0.8383 (tp) cc_final: 0.8173 (tp) REVERT: I 48 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8671 (mm) REVERT: I 80 SER cc_start: 0.7370 (m) cc_final: 0.6983 (m) REVERT: I 98 VAL cc_start: 0.8524 (p) cc_final: 0.8221 (t) REVERT: L 36 SER cc_start: 0.8461 (t) cc_final: 0.8150 (m) REVERT: L 47 ARG cc_start: 0.8429 (ptm-80) cc_final: 0.8168 (ptm160) REVERT: M 101 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7305 (p) REVERT: M 108 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7523 (mmtt) REVERT: M 119 MET cc_start: 0.4543 (ppp) cc_final: 0.3819 (ptm) REVERT: M 152 GLU cc_start: 0.7269 (tt0) cc_final: 0.6733 (pp20) REVERT: M 208 ASN cc_start: 0.7921 (t0) cc_final: 0.7640 (t0) REVERT: M 261 LYS cc_start: 0.7824 (tttt) cc_final: 0.7138 (ttpp) REVERT: O 67 LEU cc_start: 0.8603 (mt) cc_final: 0.8398 (tt) REVERT: O 121 MET cc_start: 0.4966 (ppp) cc_final: 0.4170 (ttp) REVERT: Q 333 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8161 (mmmm) REVERT: R 266 THR cc_start: 0.9067 (m) cc_final: 0.8778 (p) REVERT: R 348 LYS cc_start: 0.3829 (tttt) cc_final: 0.3291 (mmtp) REVERT: W 96 ASP cc_start: 0.7542 (t0) cc_final: 0.7081 (t0) REVERT: W 179 ILE cc_start: 0.7799 (tt) cc_final: 0.7584 (tt) REVERT: X 210 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8207 (mp) REVERT: X 214 TRP cc_start: 0.7800 (t60) cc_final: 0.7048 (t60) outliers start: 220 outliers final: 171 residues processed: 1380 average time/residue: 0.7013 time to fit residues: 1653.7207 Evaluate side-chains 1426 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1236 time to evaluate : 6.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 171 LEU Chi-restraints excluded: chain 0 residue 195 ILE Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 366 LEU Chi-restraints excluded: chain 0 residue 385 VAL Chi-restraints excluded: chain 0 residue 395 ASP Chi-restraints excluded: chain 0 residue 409 ILE Chi-restraints excluded: chain 0 residue 476 LYS Chi-restraints excluded: chain 0 residue 478 VAL Chi-restraints excluded: chain 0 residue 539 VAL Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 580 SER Chi-restraints excluded: chain 0 residue 630 THR Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 0 residue 701 LEU Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 248 ASN Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 286 ARG Chi-restraints excluded: chain 1 residue 289 SER Chi-restraints excluded: chain 1 residue 291 LYS Chi-restraints excluded: chain 1 residue 306 ARG Chi-restraints excluded: chain 1 residue 367 ASN Chi-restraints excluded: chain 1 residue 504 ILE Chi-restraints excluded: chain 1 residue 507 ILE Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 2 residue 397 ILE Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 231 GLU Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 410 PHE Chi-restraints excluded: chain 6 residue 439 ASP Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 190 THR Chi-restraints excluded: chain 7 residue 231 ARG Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 455 SER Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 539 ASN Chi-restraints excluded: chain 7 residue 586 THR Chi-restraints excluded: chain 7 residue 588 PHE Chi-restraints excluded: chain 7 residue 646 ASN Chi-restraints excluded: chain 7 residue 647 ASP Chi-restraints excluded: chain 7 residue 675 SER Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 545 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 861 ASP Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 281 SER Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 36 SER Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 118 GLU Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 139 LEU Chi-restraints excluded: chain W residue 140 LEU Chi-restraints excluded: chain W residue 182 ILE Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 254 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 780 optimal weight: 10.0000 chunk 821 optimal weight: 30.0000 chunk 749 optimal weight: 7.9990 chunk 799 optimal weight: 9.9990 chunk 481 optimal weight: 1.9990 chunk 348 optimal weight: 3.9990 chunk 627 optimal weight: 10.0000 chunk 245 optimal weight: 0.6980 chunk 722 optimal weight: 5.9990 chunk 756 optimal weight: 8.9990 chunk 796 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 66 HIS 0 614 HIS 0 664 GLN 1 493 ASN 1 516 HIS ** 2 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN 6 314 ASN 6 445 HIS 7 366 GLN 7 426 GLN A 118 HIS ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN A 760 GLN A1378 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN G 131 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 120 ASN W 165 ASN ** W 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 220 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.151 75459 Z= 0.581 Angle : 0.684 11.559 102389 Z= 0.351 Chirality : 0.048 0.262 11570 Planarity : 0.005 0.086 12699 Dihedral : 12.020 84.977 11078 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.80 % Allowed : 14.65 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.06 (0.09), residues: 8769 helix: 0.85 (0.09), residues: 3520 sheet: -0.14 (0.14), residues: 1324 loop : -0.56 (0.10), residues: 3925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1304 HIS 0.016 0.002 HIS A 451 PHE 0.048 0.003 PHE A 219 TYR 0.030 0.002 TYR 4 115 ARG 0.019 0.001 ARG 4 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1298 time to evaluate : 6.151 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: 0 132 LYS cc_start: 0.7541 (mttt) cc_final: 0.7332 (mmmt) REVERT: 0 197 ARG cc_start: 0.7478 (mtp85) cc_final: 0.7273 (mtp85) REVERT: 0 225 GLU cc_start: 0.6535 (mm-30) cc_final: 0.5675 (mm-30) REVERT: 0 270 ARG cc_start: 0.7769 (tpt170) cc_final: 0.7492 (tpt170) REVERT: 1 11 LYS cc_start: 0.8599 (mttm) cc_final: 0.8320 (ptpp) REVERT: 1 177 ASN cc_start: 0.7130 (t0) cc_final: 0.6756 (t0) REVERT: 1 184 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7870 (pt) REVERT: 1 440 ASN cc_start: 0.7616 (p0) cc_final: 0.7331 (p0) REVERT: 2 17 ILE cc_start: 0.9120 (mm) cc_final: 0.8680 (mm) REVERT: 2 205 LEU cc_start: 0.8519 (tp) cc_final: 0.8293 (mm) REVERT: 2 249 MET cc_start: 0.8144 (tpt) cc_final: 0.7873 (tpt) REVERT: 2 270 TYR cc_start: 0.7374 (m-80) cc_final: 0.7001 (m-80) REVERT: 2 409 ARG cc_start: 0.7816 (ttm110) cc_final: 0.7446 (mtt90) REVERT: 2 446 LEU cc_start: 0.8089 (mm) cc_final: 0.7788 (tp) REVERT: 3 31 ASN cc_start: 0.8771 (t0) cc_final: 0.8376 (t0) REVERT: 3 112 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7421 (mt-10) REVERT: 3 114 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7688 (tm-30) REVERT: 3 115 ASP cc_start: 0.7170 (t0) cc_final: 0.6776 (t0) REVERT: 3 116 ILE cc_start: 0.8131 (mt) cc_final: 0.7807 (mt) REVERT: 4 210 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.6609 (mt) REVERT: 4 323 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8541 (mtmm) REVERT: 6 148 MET cc_start: 0.7468 (ttm) cc_final: 0.7242 (ttm) REVERT: 6 164 ASN cc_start: 0.8246 (m110) cc_final: 0.7856 (m-40) REVERT: 6 180 GLN cc_start: 0.7508 (tp40) cc_final: 0.7292 (mm-40) REVERT: 6 298 LYS cc_start: 0.7707 (tttt) cc_final: 0.7428 (ttpp) REVERT: 6 341 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7827 (tttm) REVERT: 6 351 ASN cc_start: 0.8336 (t0) cc_final: 0.7781 (t0) REVERT: 6 441 ASP cc_start: 0.8052 (t0) cc_final: 0.7851 (t0) REVERT: 7 231 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7080 (ptt-90) REVERT: 7 367 GLU cc_start: 0.7962 (tt0) cc_final: 0.7333 (tp30) REVERT: 7 392 LYS cc_start: 0.7250 (pttt) cc_final: 0.6966 (pttt) REVERT: 7 613 TYR cc_start: 0.7824 (t80) cc_final: 0.7408 (t80) REVERT: 7 637 MET cc_start: 0.8266 (tpp) cc_final: 0.7943 (mmm) REVERT: 7 677 TYR cc_start: 0.7136 (m-10) cc_final: 0.6837 (m-10) REVERT: 7 738 HIS cc_start: 0.7293 (OUTLIER) cc_final: 0.6951 (p-80) REVERT: A 133 LYS cc_start: 0.8333 (mtmt) cc_final: 0.7922 (mttp) REVERT: A 141 LEU cc_start: 0.8567 (mm) cc_final: 0.8278 (mp) REVERT: A 389 THR cc_start: 0.8805 (m) cc_final: 0.8520 (m) REVERT: A 501 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8511 (mt) REVERT: A 545 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: A 609 ASP cc_start: 0.7936 (t70) cc_final: 0.7609 (t70) REVERT: A 702 LEU cc_start: 0.8635 (tp) cc_final: 0.8400 (tp) REVERT: A 740 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8732 (pp) REVERT: A 838 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7902 (tm-30) REVERT: A 898 ARG cc_start: 0.7926 (tpt170) cc_final: 0.7700 (tpt90) REVERT: A 985 ASP cc_start: 0.6961 (t0) cc_final: 0.6594 (t70) REVERT: A 1036 ARG cc_start: 0.7924 (mtp85) cc_final: 0.7712 (mtp85) REVERT: A 1040 GLN cc_start: 0.7439 (tt0) cc_final: 0.6983 (pt0) REVERT: A 1373 ASP cc_start: 0.7459 (m-30) cc_final: 0.6864 (m-30) REVERT: A 1454 MET cc_start: 0.7180 (tpp) cc_final: 0.6774 (ttt) REVERT: B 22 SER cc_start: 0.8419 (p) cc_final: 0.8094 (t) REVERT: B 65 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7165 (mm-30) REVERT: B 227 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7997 (ttmt) REVERT: B 312 GLU cc_start: 0.7784 (tp30) cc_final: 0.7460 (tp30) REVERT: B 358 LYS cc_start: 0.7845 (ptpt) cc_final: 0.7337 (pttt) REVERT: B 592 ASN cc_start: 0.8397 (t0) cc_final: 0.8144 (t0) REVERT: B 662 MET cc_start: 0.8294 (mtp) cc_final: 0.7927 (mmm) REVERT: B 665 GLU cc_start: 0.7050 (tt0) cc_final: 0.6714 (tp30) REVERT: B 894 ASP cc_start: 0.7685 (m-30) cc_final: 0.6905 (m-30) REVERT: B 906 SER cc_start: 0.8801 (p) cc_final: 0.8418 (t) REVERT: B 1104 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8193 (p90) REVERT: B 1129 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8153 (ttt-90) REVERT: E 20 LYS cc_start: 0.8552 (mmtm) cc_final: 0.8235 (mmtt) REVERT: F 104 ASN cc_start: 0.8430 (t0) cc_final: 0.7979 (t0) REVERT: F 137 TYR cc_start: 0.9045 (m-80) cc_final: 0.8844 (m-80) REVERT: G 115 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7852 (mtt) REVERT: I 17 ARG cc_start: 0.7546 (tpp80) cc_final: 0.7108 (tpp80) REVERT: I 25 LEU cc_start: 0.8432 (tp) cc_final: 0.8193 (tp) REVERT: I 48 LEU cc_start: 0.8930 (mm) cc_final: 0.8707 (mm) REVERT: I 80 SER cc_start: 0.7555 (m) cc_final: 0.7217 (m) REVERT: I 98 VAL cc_start: 0.8520 (p) cc_final: 0.8239 (t) REVERT: L 27 LEU cc_start: 0.7265 (mt) cc_final: 0.6666 (mp) REVERT: L 36 SER cc_start: 0.8518 (t) cc_final: 0.8127 (m) REVERT: L 37 LYS cc_start: 0.8499 (tttt) cc_final: 0.8180 (tttt) REVERT: L 47 ARG cc_start: 0.8429 (ptm-80) cc_final: 0.8158 (ptm160) REVERT: M 108 LYS cc_start: 0.7833 (mmtt) cc_final: 0.7624 (mmtt) REVERT: M 182 ARG cc_start: 0.7098 (tmt170) cc_final: 0.6816 (tmt170) REVERT: M 208 ASN cc_start: 0.7956 (t0) cc_final: 0.7663 (t0) REVERT: M 261 LYS cc_start: 0.7853 (tttt) cc_final: 0.7124 (ttpp) REVERT: M 320 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7907 (mtm-85) REVERT: R 266 THR cc_start: 0.9118 (m) cc_final: 0.8846 (p) REVERT: R 348 LYS cc_start: 0.4009 (tttt) cc_final: 0.3787 (mmtp) REVERT: W 74 GLU cc_start: 0.6852 (tt0) cc_final: 0.6530 (mt-10) REVERT: W 96 ASP cc_start: 0.7546 (t0) cc_final: 0.7249 (t0) REVERT: W 111 ASP cc_start: 0.7925 (m-30) cc_final: 0.7484 (m-30) REVERT: W 179 ILE cc_start: 0.7992 (tt) cc_final: 0.7771 (tt) REVERT: X 210 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8386 (mp) REVERT: X 214 TRP cc_start: 0.7972 (t60) cc_final: 0.7194 (t60) outliers start: 223 outliers final: 183 residues processed: 1423 average time/residue: 0.6960 time to fit residues: 1683.4173 Evaluate side-chains 1456 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1261 time to evaluate : 7.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 75 THR Chi-restraints excluded: chain 0 residue 80 GLU Chi-restraints excluded: chain 0 residue 171 LEU Chi-restraints excluded: chain 0 residue 195 ILE Chi-restraints excluded: chain 0 residue 284 ASP Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 316 LEU Chi-restraints excluded: chain 0 residue 385 VAL Chi-restraints excluded: chain 0 residue 395 ASP Chi-restraints excluded: chain 0 residue 455 SER Chi-restraints excluded: chain 0 residue 478 VAL Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 580 SER Chi-restraints excluded: chain 0 residue 630 THR Chi-restraints excluded: chain 0 residue 632 SER Chi-restraints excluded: chain 0 residue 691 SER Chi-restraints excluded: chain 0 residue 701 LEU Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 248 ASN Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 286 ARG Chi-restraints excluded: chain 1 residue 289 SER Chi-restraints excluded: chain 1 residue 306 ARG Chi-restraints excluded: chain 1 residue 367 ASN Chi-restraints excluded: chain 1 residue 493 ASN Chi-restraints excluded: chain 1 residue 504 ILE Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 231 GLU Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 410 PHE Chi-restraints excluded: chain 6 residue 439 ASP Chi-restraints excluded: chain 6 residue 456 SER Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 231 ARG Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 455 SER Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 539 ASN Chi-restraints excluded: chain 7 residue 586 THR Chi-restraints excluded: chain 7 residue 588 PHE Chi-restraints excluded: chain 7 residue 646 ASN Chi-restraints excluded: chain 7 residue 647 ASP Chi-restraints excluded: chain 7 residue 675 SER Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 545 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1138 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1387 HIS Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain A residue 1449 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1104 HIS Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 198 LEU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 47 CYS Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 38 PHE Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 206 THR Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 281 SER Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain M residue 305 THR Chi-restraints excluded: chain O residue 66 THR Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 188 GLU Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 254 THR Chi-restraints excluded: chain R residue 256 ASP Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 36 SER Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 120 ASN Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 140 LEU Chi-restraints excluded: chain W residue 194 ILE Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 218 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 254 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 524 optimal weight: 0.0970 chunk 845 optimal weight: 0.7980 chunk 515 optimal weight: 0.9980 chunk 401 optimal weight: 0.7980 chunk 587 optimal weight: 0.9990 chunk 886 optimal weight: 0.8980 chunk 816 optimal weight: 20.0000 chunk 706 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 545 optimal weight: 0.8980 chunk 432 optimal weight: 9.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 66 HIS ** 0 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 664 GLN 1 516 HIS ** 2 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN ** 6 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 445 HIS ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 118 HIS ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN B 957 ASN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN G 131 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 232 ASN W 165 ASN W 178 GLN W 220 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 75459 Z= 0.174 Angle : 0.537 14.135 102389 Z= 0.276 Chirality : 0.041 0.222 11570 Planarity : 0.004 0.051 12699 Dihedral : 11.885 81.388 11078 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.84 % Allowed : 16.05 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.45 (0.09), residues: 8769 helix: 1.23 (0.09), residues: 3536 sheet: 0.02 (0.14), residues: 1336 loop : -0.37 (0.10), residues: 3897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 0 696 HIS 0.007 0.001 HIS M 197 PHE 0.035 0.001 PHE 2 269 TYR 0.028 0.001 TYR 7 581 ARG 0.010 0.000 ARG 4 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17538 Ramachandran restraints generated. 8769 Oldfield, 0 Emsley, 8769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1284 time to evaluate : 6.168 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: 0 132 LYS cc_start: 0.7410 (mttt) cc_final: 0.7097 (mmmt) REVERT: 0 197 ARG cc_start: 0.7387 (mtp85) cc_final: 0.7180 (mtp85) REVERT: 0 225 GLU cc_start: 0.6518 (mm-30) cc_final: 0.5615 (mm-30) REVERT: 0 270 ARG cc_start: 0.7625 (tpt170) cc_final: 0.7354 (tpt170) REVERT: 0 712 MET cc_start: 0.6894 (mtm) cc_final: 0.6655 (mtm) REVERT: 1 11 LYS cc_start: 0.8589 (mttm) cc_final: 0.8259 (ptpp) REVERT: 1 37 VAL cc_start: 0.8584 (t) cc_final: 0.8380 (p) REVERT: 1 177 ASN cc_start: 0.7049 (t0) cc_final: 0.6660 (t0) REVERT: 1 184 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7721 (pt) REVERT: 1 440 ASN cc_start: 0.7306 (p0) cc_final: 0.6926 (p0) REVERT: 2 17 ILE cc_start: 0.9103 (mm) cc_final: 0.8771 (mt) REVERT: 2 184 ILE cc_start: 0.8471 (mp) cc_final: 0.8203 (mt) REVERT: 2 205 LEU cc_start: 0.8556 (tp) cc_final: 0.8343 (mm) REVERT: 2 249 MET cc_start: 0.8098 (tpt) cc_final: 0.7835 (tpt) REVERT: 2 270 TYR cc_start: 0.7344 (m-80) cc_final: 0.6975 (m-80) REVERT: 2 277 MET cc_start: 0.7022 (tpp) cc_final: 0.6657 (tpp) REVERT: 2 363 PHE cc_start: 0.7227 (p90) cc_final: 0.6932 (p90) REVERT: 2 373 MET cc_start: 0.6758 (tmm) cc_final: 0.6340 (tmm) REVERT: 2 409 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7189 (mtm-85) REVERT: 2 446 LEU cc_start: 0.7969 (mm) cc_final: 0.7693 (tp) REVERT: 3 11 ASP cc_start: 0.8154 (t0) cc_final: 0.7865 (t0) REVERT: 3 31 ASN cc_start: 0.8677 (t0) cc_final: 0.8286 (t0) REVERT: 3 115 ASP cc_start: 0.7124 (t0) cc_final: 0.6852 (t0) REVERT: 3 116 ILE cc_start: 0.8071 (mt) cc_final: 0.7751 (mt) REVERT: 4 190 ILE cc_start: 0.7894 (mm) cc_final: 0.7519 (mt) REVERT: 4 210 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6280 (mt) REVERT: 4 323 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8485 (mtmm) REVERT: 6 148 MET cc_start: 0.7227 (ttm) cc_final: 0.7021 (ttm) REVERT: 6 180 GLN cc_start: 0.7433 (tp40) cc_final: 0.7224 (mm-40) REVERT: 6 296 HIS cc_start: 0.7321 (t-90) cc_final: 0.7000 (t-170) REVERT: 6 298 LYS cc_start: 0.7622 (tttt) cc_final: 0.7354 (ttpp) REVERT: 6 341 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7752 (tttm) REVERT: 6 351 ASN cc_start: 0.8292 (t0) cc_final: 0.7759 (t0) REVERT: 6 447 ILE cc_start: 0.8057 (mm) cc_final: 0.7801 (mm) REVERT: 7 164 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7569 (pt) REVERT: 7 231 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7017 (ptt-90) REVERT: 7 367 GLU cc_start: 0.7925 (tt0) cc_final: 0.7279 (tp30) REVERT: 7 392 LYS cc_start: 0.7028 (pttt) cc_final: 0.6747 (pttt) REVERT: 7 613 TYR cc_start: 0.7704 (t80) cc_final: 0.7349 (t80) REVERT: 7 637 MET cc_start: 0.8263 (tpp) cc_final: 0.7941 (mmm) REVERT: 7 677 TYR cc_start: 0.6968 (m-10) cc_final: 0.6664 (m-10) REVERT: 7 738 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6920 (p-80) REVERT: 7 833 ILE cc_start: 0.7355 (mp) cc_final: 0.7068 (tp) REVERT: A 133 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7898 (mttp) REVERT: A 545 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: A 609 ASP cc_start: 0.7819 (t70) cc_final: 0.7479 (t70) REVERT: A 676 MET cc_start: 0.6713 (mmm) cc_final: 0.6181 (mmm) REVERT: A 702 LEU cc_start: 0.8511 (tp) cc_final: 0.8287 (tp) REVERT: A 740 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8721 (pp) REVERT: A 838 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8070 (tp-100) REVERT: A 898 ARG cc_start: 0.7851 (tpt170) cc_final: 0.7617 (tpt90) REVERT: A 934 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7873 (ptmm) REVERT: A 985 ASP cc_start: 0.6851 (t0) cc_final: 0.6486 (t70) REVERT: A 1029 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7610 (tpp80) REVERT: A 1040 GLN cc_start: 0.7227 (tt0) cc_final: 0.6897 (pt0) REVERT: A 1240 CYS cc_start: 0.7340 (m) cc_final: 0.7044 (t) REVERT: A 1287 TYR cc_start: 0.7872 (m-10) cc_final: 0.7619 (m-10) REVERT: A 1373 ASP cc_start: 0.7499 (m-30) cc_final: 0.6892 (m-30) REVERT: A 1454 MET cc_start: 0.7104 (tpp) cc_final: 0.6800 (ttt) REVERT: B 22 SER cc_start: 0.8305 (p) cc_final: 0.7983 (t) REVERT: B 65 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6952 (mm-30) REVERT: B 115 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7846 (tm-30) REVERT: B 227 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7983 (ttmt) REVERT: B 312 GLU cc_start: 0.7663 (tp30) cc_final: 0.7355 (tp30) REVERT: B 353 LYS cc_start: 0.7495 (ttmm) cc_final: 0.7064 (mttm) REVERT: B 358 LYS cc_start: 0.7834 (ptpt) cc_final: 0.7420 (pttt) REVERT: B 592 ASN cc_start: 0.8382 (t0) cc_final: 0.8164 (t0) REVERT: B 662 MET cc_start: 0.8139 (mtp) cc_final: 0.7647 (mmm) REVERT: B 665 GLU cc_start: 0.6931 (tt0) cc_final: 0.6663 (tp30) REVERT: B 863 GLU cc_start: 0.6630 (mt-10) cc_final: 0.6398 (mt-10) REVERT: B 906 SER cc_start: 0.8787 (p) cc_final: 0.8372 (t) REVERT: B 1072 MET cc_start: 0.8845 (mtp) cc_final: 0.8582 (mtm) REVERT: C 252 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: C 260 LEU cc_start: 0.8712 (tt) cc_final: 0.8399 (tp) REVERT: D 71 LYS cc_start: 0.6931 (mmmm) cc_final: 0.6643 (mmmm) REVERT: E 20 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8251 (mmtt) REVERT: E 60 PHE cc_start: 0.7210 (p90) cc_final: 0.6862 (p90) REVERT: E 171 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7754 (mttt) REVERT: F 104 ASN cc_start: 0.8329 (t0) cc_final: 0.8091 (t0) REVERT: F 127 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6618 (mt-10) REVERT: F 128 LYS cc_start: 0.7722 (mtpt) cc_final: 0.7520 (mtpt) REVERT: F 137 TYR cc_start: 0.8950 (m-80) cc_final: 0.8128 (m-80) REVERT: G 41 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7796 (mtpp) REVERT: G 115 MET cc_start: 0.8206 (mtm) cc_final: 0.7900 (mtt) REVERT: G 137 ILE cc_start: 0.8487 (mm) cc_final: 0.8287 (mm) REVERT: I 17 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7179 (tpp80) REVERT: I 25 LEU cc_start: 0.8406 (tp) cc_final: 0.8191 (tp) REVERT: I 48 LEU cc_start: 0.8909 (mm) cc_final: 0.8700 (mm) REVERT: I 80 SER cc_start: 0.7497 (m) cc_final: 0.7161 (m) REVERT: I 98 VAL cc_start: 0.8490 (p) cc_final: 0.8193 (t) REVERT: L 36 SER cc_start: 0.8528 (t) cc_final: 0.8258 (m) REVERT: L 37 LYS cc_start: 0.8393 (tttt) cc_final: 0.8128 (tttt) REVERT: L 47 ARG cc_start: 0.8388 (ptm-80) cc_final: 0.8119 (ptm160) REVERT: M 101 THR cc_start: 0.7701 (OUTLIER) cc_final: 0.7191 (p) REVERT: M 108 LYS cc_start: 0.7709 (mmtt) cc_final: 0.7410 (mtpt) REVERT: M 119 MET cc_start: 0.4303 (ppp) cc_final: 0.2958 (ptm) REVERT: M 152 GLU cc_start: 0.7252 (tt0) cc_final: 0.6703 (pp20) REVERT: M 208 ASN cc_start: 0.7912 (t0) cc_final: 0.7632 (t0) REVERT: M 261 LYS cc_start: 0.7722 (tttt) cc_final: 0.6997 (ttpp) REVERT: O 67 LEU cc_start: 0.8389 (tt) cc_final: 0.8065 (pp) REVERT: O 106 ILE cc_start: 0.8203 (mp) cc_final: 0.7886 (tp) REVERT: O 121 MET cc_start: 0.4613 (ppp) cc_final: 0.4017 (ttp) REVERT: Q 333 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8177 (mmmm) REVERT: R 266 THR cc_start: 0.9036 (m) cc_final: 0.8796 (p) REVERT: R 348 LYS cc_start: 0.3912 (tttt) cc_final: 0.3689 (mmtp) REVERT: W 96 ASP cc_start: 0.7590 (t0) cc_final: 0.7178 (t0) REVERT: W 179 ILE cc_start: 0.7745 (tt) cc_final: 0.7536 (tt) REVERT: W 193 ARG cc_start: 0.7534 (tpp-160) cc_final: 0.7132 (mmt180) REVERT: W 195 GLU cc_start: 0.6718 (tp30) cc_final: 0.6458 (tm-30) REVERT: X 210 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8367 (mp) REVERT: X 214 TRP cc_start: 0.7772 (t60) cc_final: 0.6989 (t60) outliers start: 146 outliers final: 115 residues processed: 1370 average time/residue: 0.7311 time to fit residues: 1714.7952 Evaluate side-chains 1382 residues out of total 7958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1256 time to evaluate : 6.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 75 THR Chi-restraints excluded: chain 0 residue 171 LEU Chi-restraints excluded: chain 0 residue 195 ILE Chi-restraints excluded: chain 0 residue 309 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 580 SER Chi-restraints excluded: chain 0 residue 701 LEU Chi-restraints excluded: chain 1 residue 48 LEU Chi-restraints excluded: chain 1 residue 59 MET Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 248 ASN Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 286 ARG Chi-restraints excluded: chain 1 residue 289 SER Chi-restraints excluded: chain 1 residue 306 ARG Chi-restraints excluded: chain 1 residue 367 ASN Chi-restraints excluded: chain 1 residue 504 ILE Chi-restraints excluded: chain 2 residue 61 ASP Chi-restraints excluded: chain 2 residue 87 LEU Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 4 residue 110 ILE Chi-restraints excluded: chain 4 residue 210 ILE Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 231 GLU Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 292 LEU Chi-restraints excluded: chain 6 residue 308 LEU Chi-restraints excluded: chain 6 residue 410 PHE Chi-restraints excluded: chain 6 residue 439 ASP Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 231 ARG Chi-restraints excluded: chain 7 residue 412 THR Chi-restraints excluded: chain 7 residue 442 ASN Chi-restraints excluded: chain 7 residue 452 LEU Chi-restraints excluded: chain 7 residue 455 SER Chi-restraints excluded: chain 7 residue 493 VAL Chi-restraints excluded: chain 7 residue 539 ASN Chi-restraints excluded: chain 7 residue 586 THR Chi-restraints excluded: chain 7 residue 588 PHE Chi-restraints excluded: chain 7 residue 646 ASN Chi-restraints excluded: chain 7 residue 675 SER Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 545 GLN Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 713 SER Chi-restraints excluded: chain A residue 740 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1038 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1305 VAL Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1442 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 393 LYS Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 544 CYS Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 606 LYS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 955 THR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain B residue 1160 VAL Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 252 GLN Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 97 ARG Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 281 SER Chi-restraints excluded: chain M residue 293 ILE Chi-restraints excluded: chain O residue 103 ILE Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 123 SER Chi-restraints excluded: chain Q residue 152 THR Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 215 VAL Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain U residue 51 VAL Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 132 THR Chi-restraints excluded: chain W residue 140 LEU Chi-restraints excluded: chain W residue 182 ILE Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 218 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 254 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 560 optimal weight: 0.8980 chunk 752 optimal weight: 9.9990 chunk 216 optimal weight: 30.0000 chunk 651 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 196 optimal weight: 0.7980 chunk 707 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 726 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 130 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 664 GLN ** 1 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 516 HIS ** 2 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 395 GLN ** 4 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN G 131 GLN ** M 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 120 ASN W 165 ASN W 220 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.222849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.160260 restraints weight = 85891.286| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.63 r_work: 0.3254 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 75459 Z= 0.181 Angle : 0.524 11.743 102389 Z= 0.269 Chirality : 0.041 0.234 11570 Planarity : 0.004 0.053 12699 Dihedral : 11.824 72.273 11078 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.68 % Allowed : 16.33 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.09), residues: 8769 helix: 1.32 (0.09), residues: 3556 sheet: 0.10 (0.14), residues: 1322 loop : -0.33 (0.10), residues: 3891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 7 133 HIS 0.008 0.001 HIS X 316 PHE 0.034 0.001 PHE 2 269 TYR 0.025 0.001 TYR 7 581 ARG 0.007 0.000 ARG B 879 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24684.29 seconds wall clock time: 428 minutes 7.19 seconds (25687.19 seconds total)