Starting phenix.real_space_refine on Fri Mar 22 18:44:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/03_2024/7o4k_12721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/03_2024/7o4k_12721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/03_2024/7o4k_12721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/03_2024/7o4k_12721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/03_2024/7o4k_12721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/03_2024/7o4k_12721_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.027 sd= 0.977 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 10 6.06 5 P 22 5.49 5 Mg 1 5.21 5 S 202 5.16 5 Be 1 3.05 5 C 21697 2.51 5 N 5849 2.21 5 O 6475 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 ARG 67": "NH1" <-> "NH2" Residue "0 GLU 80": "OE1" <-> "OE2" Residue "0 ARG 104": "NH1" <-> "NH2" Residue "0 GLU 147": "OE1" <-> "OE2" Residue "0 GLU 160": "OE1" <-> "OE2" Residue "0 GLU 186": "OE1" <-> "OE2" Residue "0 ARG 197": "NH1" <-> "NH2" Residue "0 GLU 225": "OE1" <-> "OE2" Residue "0 GLU 246": "OE1" <-> "OE2" Residue "0 ARG 259": "NH1" <-> "NH2" Residue "0 ARG 270": "NH1" <-> "NH2" Residue "0 GLU 285": "OE1" <-> "OE2" Residue "0 GLU 287": "OE1" <-> "OE2" Residue "0 GLU 319": "OE1" <-> "OE2" Residue "0 ARG 375": "NH1" <-> "NH2" Residue "0 ARG 380": "NH1" <-> "NH2" Residue "0 GLU 392": "OE1" <-> "OE2" Residue "0 GLU 424": "OE1" <-> "OE2" Residue "0 GLU 451": "OE1" <-> "OE2" Residue "0 ARG 509": "NH1" <-> "NH2" Residue "0 ARG 520": "NH1" <-> "NH2" Residue "0 ARG 594": "NH1" <-> "NH2" Residue "0 GLU 608": "OE1" <-> "OE2" Residue "0 ARG 638": "NH1" <-> "NH2" Residue "0 GLU 650": "OE1" <-> "OE2" Residue "0 ARG 671": "NH1" <-> "NH2" Residue "0 ARG 685": "NH1" <-> "NH2" Residue "0 ARG 688": "NH1" <-> "NH2" Residue "0 ARG 722": "NH1" <-> "NH2" Residue "0 ARG 751": "NH1" <-> "NH2" Residue "1 ARG 30": "NH1" <-> "NH2" Residue "1 ARG 86": "NH1" <-> "NH2" Residue "1 ARG 110": "NH1" <-> "NH2" Residue "1 ARG 121": "NH1" <-> "NH2" Residue "1 ARG 253": "NH1" <-> "NH2" Residue "1 GLU 254": "OE1" <-> "OE2" Residue "1 TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 286": "NH1" <-> "NH2" Residue "1 GLU 320": "OE1" <-> "OE2" Residue "1 ARG 416": "NH1" <-> "NH2" Residue "1 ARG 502": "NH1" <-> "NH2" Residue "2 GLU 15": "OE1" <-> "OE2" Residue "2 GLU 16": "OE1" <-> "OE2" Residue "2 ARG 24": "NH1" <-> "NH2" Residue "2 ARG 37": "NH1" <-> "NH2" Residue "2 GLU 127": "OE1" <-> "OE2" Residue "2 GLU 144": "OE1" <-> "OE2" Residue "2 PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 212": "OE1" <-> "OE2" Residue "2 GLU 232": "OE1" <-> "OE2" Residue "2 TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 247": "NH1" <-> "NH2" Residue "2 ARG 254": "NH1" <-> "NH2" Residue "2 GLU 342": "OE1" <-> "OE2" Residue "2 PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 369": "NH1" <-> "NH2" Residue "2 ARG 384": "NH1" <-> "NH2" Residue "2 ARG 385": "NH1" <-> "NH2" Residue "2 GLU 401": "OE1" <-> "OE2" Residue "2 GLU 447": "OE1" <-> "OE2" Residue "2 ARG 450": "NH1" <-> "NH2" Residue "2 GLU 467": "OE1" <-> "OE2" Residue "2 PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 40": "OE1" <-> "OE2" Residue "3 GLU 105": "OE1" <-> "OE2" Residue "3 GLU 111": "OE1" <-> "OE2" Residue "4 GLU 42": "OE1" <-> "OE2" Residue "4 ARG 119": "NH1" <-> "NH2" Residue "4 GLU 123": "OE1" <-> "OE2" Residue "4 GLU 128": "OE1" <-> "OE2" Residue "4 ARG 146": "NH1" <-> "NH2" Residue "4 TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 162": "NH1" <-> "NH2" Residue "4 ARG 175": "NH1" <-> "NH2" Residue "4 GLU 242": "OE1" <-> "OE2" Residue "4 ARG 281": "NH1" <-> "NH2" Residue "4 ARG 328": "NH1" <-> "NH2" Residue "5 GLU 48": "OE1" <-> "OE2" Residue "6 GLU 104": "OE1" <-> "OE2" Residue "6 ARG 142": "NH1" <-> "NH2" Residue "6 GLU 275": "OE1" <-> "OE2" Residue "6 GLU 285": "OE1" <-> "OE2" Residue "6 GLU 303": "OE1" <-> "OE2" Residue "6 ARG 327": "NH1" <-> "NH2" Residue "6 TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 409": "NH1" <-> "NH2" Residue "6 ARG 426": "NH1" <-> "NH2" Residue "6 ARG 428": "NH1" <-> "NH2" Residue "6 PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 455": "OE1" <-> "OE2" Residue "7 ARG 114": "NH1" <-> "NH2" Residue "7 ARG 122": "NH1" <-> "NH2" Residue "7 ARG 124": "NH1" <-> "NH2" Residue "7 ARG 140": "NH1" <-> "NH2" Residue "7 GLU 162": "OE1" <-> "OE2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 GLU 317": "OE1" <-> "OE2" Residue "7 ARG 329": "NH1" <-> "NH2" Residue "7 GLU 332": "OE1" <-> "OE2" Residue "7 ARG 344": "NH1" <-> "NH2" Residue "7 GLU 367": "OE1" <-> "OE2" Residue "7 ARG 378": "NH1" <-> "NH2" Residue "7 ARG 421": "NH1" <-> "NH2" Residue "7 GLU 433": "OE1" <-> "OE2" Residue "7 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 449": "OE1" <-> "OE2" Residue "7 PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 480": "NH1" <-> "NH2" Residue "7 ARG 500": "NH1" <-> "NH2" Residue "7 ARG 519": "NH1" <-> "NH2" Residue "7 GLU 537": "OE1" <-> "OE2" Residue "7 PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 571": "NH1" <-> "NH2" Residue "7 ARG 577": "NH1" <-> "NH2" Residue "7 TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 686": "NH1" <-> "NH2" Residue "7 ARG 692": "NH1" <-> "NH2" Residue "7 ARG 696": "NH1" <-> "NH2" Residue "7 GLU 743": "OE1" <-> "OE2" Residue "7 GLU 762": "OE1" <-> "OE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "B GLU 1206": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "W ASP 2": "OD1" <-> "OD2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W GLU 83": "OE1" <-> "OE2" Residue "W ARG 108": "NH1" <-> "NH2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "W GLU 196": "OE1" <-> "OE2" Residue "W GLU 200": "OE1" <-> "OE2" Residue "W ARG 205": "NH1" <-> "NH2" Residue "W GLU 270": "OE1" <-> "OE2" Residue "W ARG 274": "NH1" <-> "NH2" Residue "W GLU 292": "OE1" <-> "OE2" Residue "W GLU 349": "OE1" <-> "OE2" Residue "W ARG 351": "NH1" <-> "NH2" Residue "X ARG 197": "NH1" <-> "NH2" Residue "X ARG 234": "NH1" <-> "NH2" Residue "X GLU 264": "OE1" <-> "OE2" Residue "X ARG 295": "NH1" <-> "NH2" Residue "X TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34264 Number of models: 1 Model: "" Number of chains: 25 Chain: "0" Number of atoms: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6091 Classifications: {'peptide': 752} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 719} Chain: "1" Number of atoms: 4214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4214 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 503} Chain breaks: 6 Chain: "2" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3597 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain breaks: 4 Chain: "3" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1081 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "4" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2267 Classifications: {'peptide': 292} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 278} 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: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2786 Classifications: {'peptide': 355} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 333} Chain breaks: 1 Chain: "7" Number of atoms: 4889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4889 Classifications: {'peptide': 608} Link IDs: {'PTRANS': 24, 'TRANS': 583} Chain breaks: 1 Chain: "A" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1298 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain breaks: 10 Chain: "B" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 569 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain breaks: 1 Chain: "D" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1305 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 2, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 228 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain breaks: 2 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: "N" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 204 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1094 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain breaks: 1 Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} 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: "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 52.255 89.308 110.935 1.00 61.92 S ATOM 1265 SG CYS 0 156 46.922 88.513 114.660 1.00 71.41 S ATOM 1080 SG CYS 0 133 48.713 94.417 112.999 1.00 66.77 S ATOM 1566 SG CYS 0 191 51.804 91.445 117.238 1.00 62.83 S ATOM 13933 SG CYS 3 13 37.561 119.989 65.296 1.00106.17 S ATOM 13954 SG CYS 3 16 38.737 119.365 61.697 1.00104.70 S ATOM 14149 SG CYS 3 39 40.214 122.232 63.705 1.00104.87 S ATOM 14170 SG CYS 3 42 36.665 122.440 62.505 1.00105.96 S ATOM 14102 SG CYS 3 34 30.897 125.475 74.362 1.00104.99 S ATOM 14260 SG CYS 3 54 30.224 124.304 70.752 1.00107.16 S ATOM 14298 SG CYS 3 59 27.402 124.114 73.377 1.00117.67 S ATOM 16955 SG CYS 4 289 101.195 49.137 131.691 1.00 82.91 S ATOM 16974 SG CYS 4 292 104.736 49.595 133.037 1.00 81.75 S ATOM 17066 SG CYS 4 305 102.205 47.646 135.039 1.00101.46 S ATOM 17084 SG CYS 4 308 101.815 51.406 134.692 1.00100.16 S ATOM 19751 SG CYS 6 349 105.282 32.142 117.946 1.00 87.94 S ATOM 19772 SG CYS 6 352 103.282 29.826 115.662 1.00101.87 S ATOM 19851 SG CYS 6 363 104.164 33.311 114.520 1.00 85.86 S ATOM 19870 SG CYS 6 366 101.610 32.826 117.324 1.00 94.45 S ATOM 20172 SG CYS 6 403 132.009 67.799 129.976 1.00 95.69 S ATOM 20195 SG CYS 6 406 133.976 66.777 126.889 1.00 83.95 S ATOM 20381 SG CYS 6 437 131.232 69.390 126.603 1.00 94.08 S ATOM 20402 SG CYS 6 440 130.338 65.759 127.215 1.00 85.29 S ATOM 20314 SG CYS 6 429 121.660 65.384 136.585 1.00100.90 S ATOM 20337 SG CYS 6 432 124.991 64.128 137.960 1.00 98.91 S ATOM 20495 SG CYS 6 451 123.986 63.219 134.454 1.00 80.80 S ATOM 20512 SG CYS 6 454 122.074 61.726 137.419 1.00 86.05 S ATOM 19650 SG CYS 6 336 109.055 33.158 104.173 1.00107.56 S ATOM 19662 SG CYS 6 338 107.878 36.008 106.476 1.00100.79 S ATOM 19810 SG CYS 6 357 111.611 35.360 105.974 1.00 87.54 S ATOM 25753 SG CYS A 107 76.965 112.371 38.449 1.00 81.89 S ATOM 25777 SG CYS A 110 75.910 114.160 41.628 1.00 78.01 S ATOM 25866 SG CYS A 148 79.490 112.825 41.236 1.00 93.14 S ATOM 26004 SG CYS A 167 76.470 110.452 41.663 1.00 92.18 S ATOM 26843 SG CYS B1163 52.410 143.197 35.667 1.00 52.45 S ATOM 26861 SG CYS B1166 54.003 140.347 33.461 1.00 51.55 S ATOM 26986 SG CYS B1182 50.255 140.533 34.173 1.00 45.94 S ATOM 27005 SG CYS B1185 52.756 139.651 36.915 1.00 55.21 S ATOM 31598 SG CYS W 124 25.685 136.816 32.775 1.00 99.73 S ATOM 31619 SG CYS W 127 28.867 135.876 31.091 1.00100.42 S ATOM 31804 SG CYS W 149 28.166 139.570 32.102 1.00 90.79 S ATOM 31824 SG CYS W 152 26.368 137.920 29.154 1.00 96.55 S Time building chain proxies: 18.18, per 1000 atoms: 0.53 Number of scatterers: 34264 At special positions: 0 Unit cell: (190.05, 197.4, 165.9, 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 10 29.99 Fe 4 26.01 S 202 16.00 P 22 15.00 Mg 1 11.99 F 3 9.00 O 6475 8.00 N 5849 7.00 C 21697 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: 13.92 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="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 34 " pdb="ZN ZN 3 402 " - pdb=" SG CYS 3 59 " pdb=" ZN 4 401 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 305 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 308 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 292 " pdb="ZN ZN 4 401 " - pdb=" SG CYS 4 289 " pdb=" ZN 6 501 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 349 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 352 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 363 " pdb="ZN ZN 6 501 " - pdb=" SG CYS 6 366 " pdb=" ZN 6 502 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 406 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 440 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 437 " pdb="ZN ZN 6 502 " - pdb=" SG CYS 6 403 " pdb=" ZN 6 503 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 432 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 454 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 429 " pdb="ZN ZN 6 503 " - pdb=" SG CYS 6 451 " 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 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 127 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 149 " Number of angles added : 54 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8070 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 177 helices and 29 sheets defined 43.8% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain '0' and resid 19 through 34 Processing helix chain '0' and resid 49 through 62 Processing helix chain '0' and resid 76 through 97 Processing helix chain '0' and resid 111 through 113 No H-bonds generated for 'chain '0' and resid 111 through 113' Processing helix chain '0' and resid 126 through 137 Processing helix chain '0' and resid 140 through 147 Processing helix chain '0' and resid 157 through 164 removed outlier: 3.765A pdb=" N LEU 0 162 " --> pdb=" O TYR 0 158 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR 0 163 " --> pdb=" O HIS 0 159 " (cutoff:3.500A) removed outlier: 4.244A 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 197 Processing helix chain '0' and resid 210 through 214 removed outlier: 4.154A pdb=" N LEU 0 214 " --> pdb=" O HIS 0 211 " (cutoff:3.500A) Processing helix chain '0' and resid 216 through 223 removed outlier: 3.699A pdb=" N GLU 0 220 " --> pdb=" O PRO 0 216 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N ARG 0 221 " --> pdb=" O LYS 0 217 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL 0 222 " --> pdb=" O ILE 0 218 " (cutoff:3.500A) Processing helix chain '0' and resid 240 through 248 removed outlier: 4.471A pdb=" N LEU 0 248 " --> pdb=" O CYS 0 244 " (cutoff:3.500A) Processing helix chain '0' and resid 254 through 277 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 323 through 325 No H-bonds generated for 'chain '0' and resid 323 through 325' Processing helix chain '0' and resid 328 through 344 Processing helix chain '0' and resid 356 through 366 Processing helix chain '0' and resid 371 through 387 removed outlier: 5.290A pdb=" N SER 0 378 " --> pdb=" O LEU 0 374 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU 0 379 " --> pdb=" O ARG 0 375 " (cutoff:3.500A) Processing helix chain '0' and resid 395 through 409 removed outlier: 4.157A pdb=" N ALA 0 398 " --> pdb=" O ASP 0 395 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE 0 409 " --> pdb=" O ALA 0 406 " (cutoff:3.500A) Processing helix chain '0' and resid 447 through 452 Processing helix chain '0' and resid 467 through 472 removed outlier: 3.558A pdb=" N ARG 0 471 " --> pdb=" O ASP 0 467 " (cutoff:3.500A) 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: 3.767A 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 564 Processing helix chain '0' and resid 576 through 591 Processing helix chain '0' and resid 614 through 616 No H-bonds generated for 'chain '0' and resid 614 through 616' Processing helix chain '0' and resid 633 through 645 Processing helix chain '0' and resid 650 through 668 removed outlier: 3.519A pdb=" N HIS 0 661 " --> pdb=" O ASP 0 657 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG 0 668 " --> pdb=" O GLN 0 664 " (cutoff:3.500A) Processing helix chain '0' and resid 687 through 692 removed outlier: 4.123A pdb=" N ARG 0 690 " --> pdb=" O SER 0 687 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER 0 691 " --> pdb=" O ARG 0 688 " (cutoff:3.500A) Processing helix chain '0' and resid 695 through 698 No H-bonds generated for 'chain '0' and resid 695 through 698' Processing helix chain '0' and resid 703 through 705 No H-bonds generated for 'chain '0' and resid 703 through 705' Processing helix chain '0' and resid 710 through 724 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: 3.536A pdb=" N LEU 1 185 " --> pdb=" O GLN 1 181 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY 1 187 " --> pdb=" O SER 1 183 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 199 Processing helix chain '1' and resid 206 through 209 No H-bonds generated for 'chain '1' and resid 206 through 209' Processing helix chain '1' and resid 211 through 224 removed outlier: 4.089A pdb=" N ILE 1 214 " --> pdb=" O SER 1 211 " (cutoff:3.500A) Proline residue: 1 215 - end of helix removed outlier: 3.508A pdb=" N SER 1 223 " --> pdb=" O PHE 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 233 through 236 No H-bonds generated for 'chain '1' and resid 233 through 236' Processing helix chain '1' and resid 253 through 262 Processing helix chain '1' and resid 264 through 271 Processing helix chain '1' and resid 280 through 289 Processing helix chain '1' and resid 291 through 296 Processing helix chain '1' and resid 309 through 329 removed outlier: 3.775A pdb=" N ARG 1 313 " --> pdb=" O VAL 1 309 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR 1 314 " --> pdb=" O ILE 1 310 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU 1 315 " --> pdb=" O ILE 1 311 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N THR 1 316 " --> pdb=" O ASP 1 312 " (cutoff:3.500A) removed outlier: 4.505A 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: 3.690A 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 Processing helix chain '1' and resid 414 through 418 removed outlier: 3.704A pdb=" N GLU 1 418 " --> pdb=" O ASP 1 414 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 414 through 418' Processing helix chain '1' and resid 466 through 482 Processing helix chain '1' and resid 487 through 489 No H-bonds generated for 'chain '1' and resid 487 through 489' Processing helix chain '1' and resid 496 through 516 removed outlier: 3.511A pdb=" N ILE 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS 1 516 " --> pdb=" O LYS 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 544 through 568 Processing helix chain '1' and resid 573 through 604 removed outlier: 3.616A pdb=" N SER 1 577 " --> pdb=" O LYS 1 574 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN 1 602 " --> pdb=" O ASP 1 599 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP 1 604 " --> pdb=" O LEU 1 601 " (cutoff:3.500A) Processing helix chain '1' and resid 609 through 615 Processing helix chain '1' and resid 617 through 637 Processing helix chain '2' and resid 6 through 16 Processing helix chain '2' and resid 19 through 25 removed outlier: 3.765A pdb=" N ARG 2 24 " --> pdb=" O GLN 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 38 removed outlier: 3.603A pdb=" N ARG 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE 2 38 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 41 through 51 Processing helix chain '2' and resid 59 through 65 Processing helix chain '2' and resid 69 through 83 removed outlier: 4.523A pdb=" N LEU 2 72 " --> pdb=" O ASN 2 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE 2 78 " --> pdb=" O GLN 2 75 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER 2 80 " --> pdb=" O ALA 2 77 " (cutoff:3.500A) Processing helix chain '2' and resid 102 through 113 Processing helix chain '2' and resid 135 through 151 Processing helix chain '2' and resid 161 through 169 Processing helix chain '2' and resid 186 through 193 removed outlier: 3.746A pdb=" N GLN 2 190 " --> pdb=" O ASN 2 186 " (cutoff:3.500A) Processing helix chain '2' and resid 196 through 210 removed outlier: 4.108A pdb=" N LEU 2 203 " --> pdb=" O GLN 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 218 through 230 removed outlier: 3.520A pdb=" N MET 2 227 " --> pdb=" O HIS 2 223 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY 2 229 " --> pdb=" O ILE 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 244 through 256 removed outlier: 3.924A pdb=" N ILE 2 248 " --> pdb=" O GLU 2 244 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP 2 255 " --> pdb=" O GLN 2 251 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR 2 256 " --> pdb=" O ASP 2 252 " (cutoff:3.500A) Processing helix chain '2' and resid 273 through 279 removed outlier: 4.183A pdb=" N THR 2 279 " --> pdb=" O ALA 2 275 " (cutoff:3.500A) Processing helix chain '2' and resid 354 through 362 removed outlier: 3.713A pdb=" N LEU 2 362 " --> pdb=" O ALA 2 358 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 389 removed outlier: 3.700A pdb=" N ASN 2 389 " --> pdb=" O ARG 2 385 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 402 Processing helix chain '2' and resid 406 through 420 Processing helix chain '2' and resid 435 through 448 Processing helix chain '2' and resid 465 through 477 Processing helix chain '2' and resid 498 through 506 Processing helix chain '3' and resid 40 through 47 Processing helix chain '3' and resid 65 through 67 No H-bonds generated for 'chain '3' and resid 65 through 67' Processing helix chain '3' and resid 76 through 89 Processing helix chain '3' and resid 96 through 99 Processing helix chain '3' and resid 103 through 122 Processing helix chain '3' and resid 126 through 138 removed outlier: 3.557A pdb=" N GLU 3 138 " --> pdb=" O ARG 3 134 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 43 removed outlier: 3.787A pdb=" N THR 4 39 " --> pdb=" O LYS 4 35 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 67 Processing helix chain '4' and resid 116 through 138 removed outlier: 4.138A pdb=" N THR 4 124 " --> pdb=" O ASN 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 149 through 165 Processing helix chain '4' and resid 190 through 205 removed outlier: 4.387A pdb=" N ILE 4 194 " --> pdb=" O PHE 4 191 " (cutoff:3.500A) Proline residue: 4 195 - end of helix removed outlier: 3.529A pdb=" N ILE 4 200 " --> pdb=" O MET 4 197 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE 4 201 " --> pdb=" O ASN 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 231 removed outlier: 3.649A pdb=" N GLN 4 226 " --> pdb=" O THR 4 222 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 250 Processing helix chain '4' and resid 256 through 261 removed outlier: 3.714A pdb=" N ARG 4 259 " --> pdb=" O PRO 4 256 " (cutoff:3.500A) Proline residue: 4 260 - end of helix No H-bonds generated for 'chain '4' and resid 256 through 261' 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: 3.576A pdb=" N LEU 4 320 " --> pdb=" O VAL 4 316 " (cutoff:3.500A) Processing helix chain '5' and resid 14 through 26 Processing helix chain '5' and resid 28 through 30 No H-bonds generated for 'chain '5' and resid 28 through 30' Processing helix chain '5' and resid 44 through 60 removed outlier: 4.571A pdb=" N GLU 5 48 " --> pdb=" O PRO 5 44 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE 5 49 " --> pdb=" O SER 5 45 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG 5 56 " --> pdb=" O HIS 5 52 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 113 removed outlier: 3.676A pdb=" N ALA 6 111 " --> pdb=" O LYS 6 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS 6 112 " --> pdb=" O LYS 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 134 through 137 Processing helix chain '6' and resid 145 through 163 Processing helix chain '6' and resid 189 through 199 Processing helix chain '6' and resid 210 through 220 Processing helix chain '6' and resid 247 through 256 Processing helix chain '6' and resid 271 through 280 Processing helix chain '6' and resid 294 through 305 Processing helix chain '6' and resid 373 through 382 removed outlier: 4.398A pdb=" N SER 6 379 " --> pdb=" O HIS 6 375 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR 6 380 " --> pdb=" O LEU 6 376 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N HIS 6 381 " --> pdb=" O ALA 6 377 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS 6 382 " --> pdb=" O ARG 6 378 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 446 removed outlier: 3.602A pdb=" N VAL 6 442 " --> pdb=" O VAL 6 438 " (cutoff:3.500A) 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 150 through 160 removed outlier: 3.838A pdb=" N ASP 7 155 " --> pdb=" O GLU 7 151 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE 7 156 " --> pdb=" O GLN 7 152 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL 7 158 " --> pdb=" O GLN 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 177 through 187 Processing helix chain '7' and resid 190 through 200 Processing helix chain '7' and resid 207 through 215 Processing helix chain '7' and resid 239 through 245 Processing helix chain '7' and resid 321 through 332 removed outlier: 3.920A pdb=" N GLU 7 324 " --> pdb=" O GLU 7 321 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS 7 327 " --> pdb=" O GLU 7 324 " (cutoff:3.500A) Processing helix chain '7' and resid 364 through 371 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 459 No H-bonds generated for 'chain '7' and resid 457 through 459' Processing helix chain '7' and resid 468 through 479 removed outlier: 3.893A pdb=" N LYS 7 472 " --> pdb=" O HIS 7 468 " (cutoff:3.500A) removed outlier: 4.037A 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 removed outlier: 4.198A pdb=" N THR 7 504 " --> pdb=" O VAL 7 501 " (cutoff:3.500A) Processing helix chain '7' and resid 523 through 529 Processing helix chain '7' and resid 540 through 545 Processing helix chain '7' and resid 563 through 571 removed outlier: 4.199A pdb=" N GLU 7 568 " --> pdb=" O GLU 7 564 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU 7 570 " --> pdb=" O TYR 7 566 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG 7 571 " --> pdb=" O GLN 7 567 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 581 removed outlier: 3.736A pdb=" N MET 7 578 " --> pdb=" O ALA 7 574 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU 7 579 " --> pdb=" O ARG 7 575 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU 7 580 " --> pdb=" O LYS 7 576 " (cutoff:3.500A) Processing helix chain '7' and resid 585 through 600 Processing helix chain '7' and resid 612 through 622 Processing helix chain '7' and resid 633 through 645 Processing helix chain '7' and resid 656 through 659 Processing helix chain '7' and resid 680 through 690 removed outlier: 3.843A pdb=" N ARG 7 689 " --> pdb=" O GLN 7 685 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE 7 690 " --> pdb=" O ARG 7 686 " (cutoff:3.500A) Processing helix chain '7' and resid 714 through 722 Processing helix chain '7' and resid 726 through 729 No H-bonds generated for 'chain '7' and resid 726 through 729' Processing helix chain '7' and resid 753 through 766 removed outlier: 3.901A pdb=" N LYS 7 766 " --> pdb=" O GLU 7 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 100 through 103 No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 286 through 289 No H-bonds generated for 'chain 'A' and resid 286 through 289' Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 3.976A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1148 No H-bonds generated for 'chain 'B' and resid 1145 through 1148' Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'D' and resid 52 through 72 removed outlier: 3.507A pdb=" N GLU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 133 removed outlier: 3.512A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 157 through 169 removed outlier: 4.047A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (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 216 Processing helix chain 'F' and resid 93 through 102 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 'W' and resid 4 through 20 Processing helix chain 'W' and resid 24 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: 4.049A pdb=" N GLN W 138 " --> pdb=" O LEU W 134 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) Processing helix chain 'W' and resid 167 through 178 Processing helix chain 'W' and resid 180 through 191 removed outlier: 3.502A pdb=" N LYS W 188 " --> pdb=" O ASP W 184 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 205 removed outlier: 3.857A pdb=" N ALA W 204 " --> pdb=" O GLU W 200 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG W 205 " --> pdb=" O ILE W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 287 Processing helix chain 'W' and resid 292 through 295 No H-bonds generated for 'chain 'W' and resid 292 through 295' Processing helix chain 'W' and resid 350 through 368 Processing helix chain 'X' and resid 189 through 197 Processing helix chain 'X' and resid 207 through 211 Processing helix chain 'X' and resid 218 through 226 Processing helix chain 'X' and resid 257 through 265 removed outlier: 3.998A pdb=" N MET X 262 " --> pdb=" O GLU X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 271 through 280 Proline residue: X 275 - end of helix Processing helix chain 'X' and resid 290 through 292 No H-bonds generated for 'chain 'X' and resid 290 through 292' Processing sheet with id= A, first strand: chain '0' and resid 2 through 4 Processing sheet with id= B, first strand: chain '0' and resid 174 through 176 removed outlier: 4.227A pdb=" N GLY 0 107 " --> pdb=" O PHE 0 176 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE 0 205 " --> pdb=" O LEU 0 106 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE 0 69 " --> pdb=" O ILE 0 206 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N TYR 0 208 " --> pdb=" O ILE 0 69 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR 0 71 " --> pdb=" O TYR 0 208 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE 0 231 " --> pdb=" O ILE 0 70 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N CYS 0 72 " --> pdb=" O ILE 0 231 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE 0 233 " --> pdb=" O CYS 0 72 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 478 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN 0 480 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLU 0 41 " --> pdb=" O GLN 0 480 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER 0 482 " --> pdb=" O GLU 0 41 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '0' and resid 250 through 253 Processing sheet with id= D, first strand: chain '0' and resid 492 through 497 removed outlier: 7.589A pdb=" N GLY 0 677 " --> pdb=" O LEU 0 493 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N MET 0 495 " --> pdb=" O GLY 0 677 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET 0 679 " --> pdb=" O MET 0 495 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE 0 497 " --> pdb=" O MET 0 679 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU 0 681 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLY 0 536 " --> pdb=" O THR 0 619 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N LEU 0 621 " --> pdb=" O GLY 0 536 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL 0 538 " --> pdb=" O LEU 0 621 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE 0 623 " --> pdb=" O VAL 0 538 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE 0 540 " --> pdb=" O ILE 0 623 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA 0 596 " --> pdb=" O MET 0 537 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL 0 539 " --> pdb=" O ALA 0 596 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU 0 598 " --> pdb=" O VAL 0 539 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N PHE 0 541 " --> pdb=" O LEU 0 598 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER 0 600 " --> pdb=" O PHE 0 541 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU 0 568 " --> pdb=" O ILE 0 597 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU 0 599 " --> pdb=" O LEU 0 568 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU 0 570 " --> pdb=" O LEU 0 599 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N VAL 0 601 " --> pdb=" O LEU 0 570 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '1' and resid 4 through 9 Processing sheet with id= F, first strand: chain '1' and resid 86 through 90 removed outlier: 3.578A pdb=" N LYS 1 47 " --> pdb=" O ILE 1 63 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '2' and resid 87 through 92 Processing sheet with id= H, first strand: chain '2' and resid 174 through 176 Processing sheet with id= I, first strand: chain '2' and resid 236 through 238 removed outlier: 3.654A pdb=" N TYR 2 237 " --> pdb=" O PHE 2 269 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE 2 269 " --> pdb=" O TYR 2 237 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '2' and resid 339 through 341 removed outlier: 6.332A pdb=" N GLN 2 377 " --> pdb=" O LEU 2 366 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LEU 2 366 " --> pdb=" O GLN 2 377 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '2' and resid 456 through 459 removed outlier: 6.301A pdb=" N SER 2 494 " --> pdb=" O LEU 2 481 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU 2 481 " --> pdb=" O SER 2 494 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '4' and resid 82 through 87 removed outlier: 6.446A pdb=" N VAL 4 75 " --> pdb=" O LEU 4 86 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ALA 4 74 " --> pdb=" O SER 4 24 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU 4 26 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ILE 4 76 " --> pdb=" O LEU 4 26 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL 4 28 " --> pdb=" O ILE 4 76 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA 4 78 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE 4 30 " --> pdb=" O ALA 4 78 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS 4 173 " --> pdb=" O LEU 4 25 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR 4 27 " --> pdb=" O LYS 4 173 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG 4 175 " --> pdb=" O THR 4 27 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE 4 29 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU 4 177 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLU 4 31 " --> pdb=" O LEU 4 177 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU 4 179 " --> pdb=" O GLU 4 31 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '5' and resid 8 through 11 Processing sheet with id= N, first strand: chain '6' and resid 178 through 183 removed outlier: 6.341A pdb=" N ILE 6 171 " --> pdb=" O VAL 6 182 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR 6 229 " --> pdb=" O SER 6 125 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE 6 127 " --> pdb=" O THR 6 229 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU 6 231 " --> pdb=" O ILE 6 127 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR 6 129 " --> pdb=" O GLU 6 231 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU 6 233 " --> pdb=" O THR 6 129 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ASP 6 131 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL 6 235 " --> pdb=" O ASP 6 131 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain '6' and resid 326 through 329 removed outlier: 3.747A pdb=" N THR 6 326 " --> pdb=" O PHE 6 348 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE 6 348 " --> pdb=" O THR 6 326 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE 6 328 " --> pdb=" O GLY 6 346 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY 6 346 " --> pdb=" O ILE 6 328 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain '7' and resid 132 through 134 removed outlier: 6.123A pdb=" N LYS 7 174 " --> pdb=" O PRO 7 163 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '7' and resid 223 through 228 Processing sheet with id= R, first strand: chain '7' and resid 435 through 438 removed outlier: 6.029A pdb=" N LEU 7 452 " --> pdb=" O ALA 7 436 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE 7 438 " --> pdb=" O LEU 7 452 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL 7 454 " --> pdb=" O PHE 7 438 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL 7 407 " --> pdb=" O VAL 7 453 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N SER 7 455 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL 7 409 " --> pdb=" O SER 7 455 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE 7 484 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU 7 410 " --> pdb=" O PHE 7 484 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE 7 486 " --> pdb=" O LEU 7 410 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA 7 509 " --> pdb=" O ILE 7 485 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU 7 487 " --> pdb=" O ALA 7 509 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU 7 511 " --> pdb=" O LEU 7 487 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLY 7 382 " --> pdb=" O GLY 7 512 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR 7 514 " --> pdb=" O GLY 7 382 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE 7 384 " --> pdb=" O THR 7 514 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL 7 385 " --> pdb=" O PRO 7 533 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU 7 535 " --> pdb=" O VAL 7 385 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain '7' and resid 734 through 736 removed outlier: 3.966A pdb=" N LYS 7 734 " --> pdb=" O CYS 7 554 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA 7 703 " --> pdb=" O GLN 7 553 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ALA 7 555 " --> pdb=" O ALA 7 703 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE 7 705 " --> pdb=" O ALA 7 555 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL 7 557 " --> pdb=" O PHE 7 705 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N SER 7 707 " --> pdb=" O VAL 7 557 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS 7 559 " --> pdb=" O SER 7 707 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL 7 709 " --> pdb=" O CYS 7 559 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= U, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.563A pdb=" N SER A 184 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= W, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id= X, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= Y, first strand: chain 'G' and resid 2 through 13 removed outlier: 4.163A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS G 47 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 142 through 146 removed outlier: 3.525A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ILE G 157 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N PHE G 109 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ALA G 159 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N THR G 111 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLY G 161 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= AB, first strand: chain 'W' and resid 68 through 74 Processing sheet with id= AC, first strand: chain 'X' and resid 230 through 232 1274 hydrogen bonds defined for protein. 3492 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.98 Time building geometry restraints manager: 14.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 14189 1.43 - 1.64: 20396 1.64 - 1.85: 305 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 34902 Sorted by residual: bond pdb=" C4 ADP 7 903 " pdb=" C5 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" BE BEF 7 901 " pdb=" F2 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C5 ADP 7 903 " pdb=" C6 ADP 7 903 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" BE BEF 7 901 " pdb=" F3 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.543 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" BE BEF 7 901 " pdb=" F1 BEF 7 901 " ideal model delta sigma weight residual 1.476 1.531 -0.055 2.00e-02 2.50e+03 7.65e+00 ... (remaining 34897 not shown) Histogram of bond angle deviations from ideal: 73.69 - 85.75: 12 85.75 - 97.81: 0 97.81 - 109.87: 4139 109.87 - 121.93: 36007 121.93 - 133.99: 7021 Bond angle restraints: 47179 Sorted by residual: angle pdb=" N VAL 1 495 " pdb=" CA VAL 1 495 " pdb=" C VAL 1 495 " ideal model delta sigma weight residual 112.96 108.60 4.36 1.00e+00 1.00e+00 1.90e+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 98.62 12.38 3.00e+00 1.11e-01 1.70e+01 angle pdb=" N VAL 0 736 " pdb=" CA VAL 0 736 " pdb=" C VAL 0 736 " ideal model delta sigma weight residual 112.96 109.52 3.44 1.00e+00 1.00e+00 1.18e+01 angle pdb=" PA ADP 7 903 " pdb=" O3A ADP 7 903 " pdb=" PB ADP 7 903 " ideal model delta sigma weight residual 120.50 130.78 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" N VAL 7 460 " pdb=" CA VAL 7 460 " pdb=" C VAL 7 460 " ideal model delta sigma weight residual 113.53 110.21 3.32 9.80e-01 1.04e+00 1.15e+01 ... (remaining 47174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 21005 35.57 - 71.15: 368 71.15 - 106.72: 41 106.72 - 142.29: 2 142.29 - 177.86: 1 Dihedral angle restraints: 21417 sinusoidal: 9037 harmonic: 12380 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 -60.00 117.86 -177.86 1 2.00e+01 2.50e-03 4.80e+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 63.94 -123.94 1 2.00e+01 2.50e-03 3.74e+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 -169.82 109.82 1 2.00e+01 2.50e-03 3.21e+01 ... (remaining 21414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 4418 0.042 - 0.084: 613 0.084 - 0.127: 337 0.127 - 0.169: 9 0.169 - 0.211: 1 Chirality restraints: 5378 Sorted by residual: chirality pdb=" C3' ADP 7 903 " pdb=" C2' ADP 7 903 " pdb=" C4' ADP 7 903 " pdb=" O3' ADP 7 903 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE 7 745 " pdb=" N ILE 7 745 " pdb=" C ILE 7 745 " pdb=" CB ILE 7 745 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE 0 5 " pdb=" N ILE 0 5 " pdb=" C ILE 0 5 " pdb=" CB ILE 0 5 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 5375 not shown) Planarity restraints: 5947 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS 0 614 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C HIS 0 614 " 0.048 2.00e-02 2.50e+03 pdb=" O HIS 0 614 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN 0 615 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP 5 13 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO 5 14 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO 5 14 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO 5 14 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN 3 31 " 0.024 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO 3 32 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO 3 32 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 3 32 " 0.021 5.00e-02 4.00e+02 ... (remaining 5944 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 231 2.58 - 3.16: 28919 3.16 - 3.74: 50906 3.74 - 4.32: 72365 4.32 - 4.90: 119742 Nonbonded interactions: 272163 Sorted by model distance: nonbonded pdb="MG MG 7 902 " pdb=" O3B ADP 7 903 " model vdw 2.001 2.170 nonbonded pdb=" F1 BEF 7 901 " pdb="MG MG 7 902 " model vdw 2.001 2.120 nonbonded pdb=" O ARG 7 130 " pdb=" NZ LYS 7 202 " model vdw 2.162 2.520 nonbonded pdb=" OH TYR W 21 " pdb=" OD2 ASP W 64 " model vdw 2.166 2.440 nonbonded pdb=" OG1 THR X 235 " pdb=" O ASP X 238 " model vdw 2.166 2.440 ... (remaining 272158 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 13.450 Check model and map are aligned: 0.530 Set scattering table: 0.440 Process input model: 98.020 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.110 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 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 0.110 34902 Z= 0.150 Angle : 0.458 12.379 47179 Z= 0.264 Chirality : 0.038 0.211 5378 Planarity : 0.002 0.050 5947 Dihedral : 14.038 177.863 13347 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 1.05 (0.14), residues: 4122 helix: 1.91 (0.13), residues: 1879 sheet: -0.38 (0.23), residues: 550 loop : -0.24 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 7 420 HIS 0.003 0.000 HIS D 173 PHE 0.009 0.001 PHE A 22 TYR 0.009 0.001 TYR 7 581 ARG 0.002 0.000 ARG W 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 929 time to evaluate : 3.905 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: 0 34 VAL cc_start: 0.8645 (p) cc_final: 0.8219 (m) REVERT: 0 71 TYR cc_start: 0.8110 (t80) cc_final: 0.7769 (t80) REVERT: 0 90 MET cc_start: 0.7859 (mmm) cc_final: 0.7471 (mmp) REVERT: 0 91 ASP cc_start: 0.6794 (m-30) cc_final: 0.6577 (m-30) REVERT: 0 131 GLU cc_start: 0.5088 (tp30) cc_final: 0.4831 (pt0) REVERT: 0 135 ARG cc_start: 0.7237 (mtp85) cc_final: 0.6966 (mmm-85) REVERT: 0 136 MET cc_start: 0.8157 (mtm) cc_final: 0.7528 (mtt) REVERT: 0 142 LYS cc_start: 0.7870 (tttt) cc_final: 0.7431 (tttp) REVERT: 0 183 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7497 (mtpp) REVERT: 0 218 ILE cc_start: 0.8495 (pt) cc_final: 0.8222 (pt) REVERT: 0 236 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6553 (mt-10) REVERT: 0 259 ARG cc_start: 0.7406 (mtp85) cc_final: 0.7022 (mtm-85) REVERT: 0 365 GLN cc_start: 0.6526 (tt0) cc_final: 0.6213 (mt0) REVERT: 0 547 MET cc_start: 0.8309 (ttp) cc_final: 0.8079 (ttm) REVERT: 0 553 MET cc_start: 0.6281 (mmm) cc_final: 0.5776 (mtp) REVERT: 0 622 MET cc_start: 0.8460 (tpt) cc_final: 0.8186 (mmm) REVERT: 0 640 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7055 (mm-30) REVERT: 0 643 ARG cc_start: 0.7324 (ttp80) cc_final: 0.6964 (ttp80) REVERT: 0 675 ASP cc_start: 0.8219 (t0) cc_final: 0.7964 (t0) REVERT: 0 718 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7501 (mtpp) REVERT: 1 19 ASN cc_start: 0.7647 (t0) cc_final: 0.7399 (t0) REVERT: 1 29 TRP cc_start: 0.8617 (t60) cc_final: 0.8151 (t60) REVERT: 1 58 MET cc_start: 0.7121 (mtt) cc_final: 0.6840 (mtm) REVERT: 1 61 ARG cc_start: 0.6881 (ttp-110) cc_final: 0.6588 (ptm160) REVERT: 1 88 MET cc_start: 0.5175 (ttp) cc_final: 0.4657 (mtt) REVERT: 1 178 LEU cc_start: 0.8198 (mt) cc_final: 0.7926 (tp) REVERT: 1 238 LYS cc_start: 0.7537 (mttt) cc_final: 0.7284 (mmtm) REVERT: 1 299 GLU cc_start: 0.7467 (tt0) cc_final: 0.6609 (tt0) REVERT: 1 313 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6898 (mtm-85) REVERT: 1 318 ASP cc_start: 0.7018 (t0) cc_final: 0.6741 (t0) REVERT: 1 321 PHE cc_start: 0.7836 (m-10) cc_final: 0.7528 (m-80) REVERT: 1 364 ILE cc_start: 0.8062 (mm) cc_final: 0.7559 (mm) REVERT: 1 373 ASP cc_start: 0.6891 (t0) cc_final: 0.6508 (m-30) REVERT: 1 552 MET cc_start: 0.8482 (ttt) cc_final: 0.7811 (tpp) REVERT: 1 563 HIS cc_start: 0.8191 (m-70) cc_final: 0.7878 (m-70) REVERT: 1 581 LYS cc_start: 0.8574 (mttt) cc_final: 0.7733 (mptt) REVERT: 1 585 HIS cc_start: 0.8160 (m170) cc_final: 0.7895 (m90) REVERT: 1 597 PHE cc_start: 0.7638 (m-10) cc_final: 0.7166 (m-80) REVERT: 1 628 HIS cc_start: 0.8533 (t-90) cc_final: 0.8231 (t-90) REVERT: 2 13 TYR cc_start: 0.8324 (t80) cc_final: 0.8071 (t80) REVERT: 2 66 VAL cc_start: 0.9107 (t) cc_final: 0.8879 (p) REVERT: 2 81 MET cc_start: 0.7784 (mtp) cc_final: 0.7424 (mtm) REVERT: 2 97 MET cc_start: 0.6451 (mmm) cc_final: 0.6160 (tpp) REVERT: 2 138 TYR cc_start: 0.8030 (t80) cc_final: 0.7787 (t80) REVERT: 2 200 LEU cc_start: 0.7849 (mt) cc_final: 0.7604 (mt) REVERT: 2 277 MET cc_start: 0.7396 (tpp) cc_final: 0.6517 (tmm) REVERT: 2 344 ASN cc_start: 0.6915 (t0) cc_final: 0.6691 (t0) REVERT: 3 11 ASP cc_start: 0.8122 (t0) cc_final: 0.6803 (t0) REVERT: 3 20 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8066 (ttp80) REVERT: 3 33 GLU cc_start: 0.7135 (tp30) cc_final: 0.6620 (tm-30) REVERT: 3 35 TYR cc_start: 0.7514 (m-80) cc_final: 0.6947 (m-10) REVERT: 3 129 THR cc_start: 0.8474 (m) cc_final: 0.7998 (t) REVERT: 3 130 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6581 (mt-10) REVERT: 4 39 THR cc_start: 0.8671 (m) cc_final: 0.8386 (p) REVERT: 4 232 ASN cc_start: 0.8334 (t0) cc_final: 0.8082 (t0) REVERT: 4 323 LYS cc_start: 0.8792 (ptmt) cc_final: 0.8445 (ptmt) REVERT: 6 139 LYS cc_start: 0.8404 (mmtp) cc_final: 0.8021 (mmmm) REVERT: 6 294 GLU cc_start: 0.7208 (tt0) cc_final: 0.6841 (tt0) REVERT: 6 450 ASN cc_start: 0.8666 (p0) cc_final: 0.8353 (p0) REVERT: 7 138 ASP cc_start: 0.6850 (m-30) cc_final: 0.6418 (p0) REVERT: 7 568 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6866 (tp30) REVERT: 7 621 LYS cc_start: 0.8317 (tptp) cc_final: 0.7964 (mmmt) REVERT: 7 663 ASP cc_start: 0.7070 (t0) cc_final: 0.6816 (t0) REVERT: 7 694 LYS cc_start: 0.7986 (tmtt) cc_final: 0.7677 (tppt) REVERT: 7 748 LEU cc_start: 0.8743 (mt) cc_final: 0.8532 (mt) REVERT: 7 762 GLU cc_start: 0.7571 (tp30) cc_final: 0.7237 (tp30) REVERT: A 112 LYS cc_start: 0.7606 (tttm) cc_final: 0.6941 (mtpp) REVERT: A 169 ASN cc_start: 0.8550 (m-40) cc_final: 0.7899 (m110) REVERT: A 175 ARG cc_start: 0.6853 (ptt90) cc_final: 0.6561 (ttp-110) REVERT: A 1444 MET cc_start: 0.7528 (mmm) cc_final: 0.7314 (mmm) REVERT: A 1454 MET cc_start: 0.5660 (tpp) cc_final: 0.5312 (mmm) REVERT: D 34 GLN cc_start: 0.7283 (mt0) cc_final: 0.6921 (pt0) REVERT: F 101 ILE cc_start: 0.7115 (mt) cc_final: 0.6740 (mm) REVERT: G 53 ASN cc_start: 0.7434 (m110) cc_final: 0.7156 (t0) REVERT: G 140 LYS cc_start: 0.7794 (ttpp) cc_final: 0.7381 (ttmm) REVERT: W 81 SER cc_start: 0.6931 (p) cc_final: 0.6249 (m) REVERT: W 106 VAL cc_start: 0.7766 (t) cc_final: 0.7529 (m) REVERT: W 114 ASP cc_start: 0.7905 (m-30) cc_final: 0.7693 (t0) REVERT: W 135 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7098 (mm-30) REVERT: W 145 THR cc_start: 0.6913 (p) cc_final: 0.5778 (t) REVERT: W 156 LEU cc_start: 0.8513 (mm) cc_final: 0.8276 (mt) REVERT: W 180 GLN cc_start: 0.7384 (tp40) cc_final: 0.6880 (tp40) REVERT: W 181 PRO cc_start: 0.8689 (Cg_exo) cc_final: 0.8402 (Cg_endo) REVERT: W 193 ARG cc_start: 0.6613 (tpp80) cc_final: 0.6392 (tpp-160) REVERT: W 211 ASN cc_start: 0.6470 (m110) cc_final: 0.6046 (m110) REVERT: W 263 ASN cc_start: 0.7424 (t0) cc_final: 0.7123 (m110) REVERT: X 194 LYS cc_start: 0.7908 (ptmt) cc_final: 0.7671 (ptmm) REVERT: X 203 LYS cc_start: 0.7731 (tptm) cc_final: 0.7384 (tptt) REVERT: X 239 LYS cc_start: 0.8553 (mmtp) cc_final: 0.8180 (mmmt) REVERT: X 284 LYS cc_start: 0.8324 (tttt) cc_final: 0.8071 (tmtt) outliers start: 0 outliers final: 0 residues processed: 929 average time/residue: 0.4779 time to fit residues: 705.5924 Evaluate side-chains 686 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 686 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 0.6980 chunk 316 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 108 optimal weight: 0.0050 chunk 213 optimal weight: 20.0000 chunk 169 optimal weight: 50.0000 chunk 327 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 379 optimal weight: 1.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 352 ASN ** 1 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 563 HIS 2 85 HIS 2 206 GLN ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 225 GLN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 345 ASN ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 548 HIS ** 7 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 672 GLN 7 738 HIS A 109 HIS A 282 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN F 100 GLN G 97 HIS G 113 HIS W 133 GLN W 169 GLN W 178 GLN X 267 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34902 Z= 0.271 Angle : 0.552 10.995 47179 Z= 0.282 Chirality : 0.042 0.186 5378 Planarity : 0.004 0.051 5947 Dihedral : 8.269 141.136 4758 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 8.51 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.63 (0.13), residues: 4122 helix: 1.42 (0.12), residues: 1872 sheet: -0.50 (0.22), residues: 532 loop : -0.31 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 214 HIS 0.012 0.001 HIS 6 449 PHE 0.019 0.002 PHE A 22 TYR 0.021 0.002 TYR 4 79 ARG 0.006 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 724 time to evaluate : 3.771 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: 0 34 VAL cc_start: 0.8706 (p) cc_final: 0.8345 (m) REVERT: 0 90 MET cc_start: 0.8056 (mmm) cc_final: 0.7605 (mmp) REVERT: 0 96 GLU cc_start: 0.6250 (mm-30) cc_final: 0.5975 (mp0) REVERT: 0 108 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8018 (tp) REVERT: 0 131 GLU cc_start: 0.5201 (tp30) cc_final: 0.4934 (pt0) REVERT: 0 136 MET cc_start: 0.8156 (mtm) cc_final: 0.7788 (mtt) REVERT: 0 142 LYS cc_start: 0.7861 (tttt) cc_final: 0.7365 (tttp) REVERT: 0 183 LYS cc_start: 0.7606 (ttmt) cc_final: 0.7281 (mtpp) REVERT: 0 236 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6715 (mt-10) REVERT: 0 259 ARG cc_start: 0.7381 (mtp85) cc_final: 0.7013 (mtm110) REVERT: 0 357 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7208 (ttpp) REVERT: 0 365 GLN cc_start: 0.6556 (tt0) cc_final: 0.6174 (mt0) REVERT: 0 553 MET cc_start: 0.6100 (mmm) cc_final: 0.5879 (mtp) REVERT: 0 622 MET cc_start: 0.8625 (tpt) cc_final: 0.8176 (mmm) REVERT: 0 643 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7200 (ttp80) REVERT: 0 650 GLU cc_start: 0.7415 (mp0) cc_final: 0.7141 (mt-10) REVERT: 0 675 ASP cc_start: 0.8344 (t0) cc_final: 0.8116 (t0) REVERT: 1 9 PHE cc_start: 0.7022 (t80) cc_final: 0.6677 (t80) REVERT: 1 19 ASN cc_start: 0.7638 (t0) cc_final: 0.7374 (t0) REVERT: 1 29 TRP cc_start: 0.8639 (t60) cc_final: 0.8152 (t60) REVERT: 1 88 MET cc_start: 0.4979 (ttp) cc_final: 0.4591 (ttm) REVERT: 1 102 MET cc_start: 0.6689 (mmm) cc_final: 0.6391 (mmm) REVERT: 1 173 LYS cc_start: 0.6999 (mmtp) cc_final: 0.6349 (mtpt) REVERT: 1 178 LEU cc_start: 0.8297 (mt) cc_final: 0.8016 (tp) REVERT: 1 192 MET cc_start: 0.7874 (tpt) cc_final: 0.7542 (tpt) REVERT: 1 238 LYS cc_start: 0.7636 (mttt) cc_final: 0.7408 (mmtm) REVERT: 1 299 GLU cc_start: 0.7476 (tt0) cc_final: 0.7257 (tt0) REVERT: 1 318 ASP cc_start: 0.6820 (t0) cc_final: 0.6552 (t0) REVERT: 1 321 PHE cc_start: 0.7812 (m-10) cc_final: 0.7569 (m-80) REVERT: 1 346 ASP cc_start: 0.7786 (t0) cc_final: 0.7356 (t70) REVERT: 1 373 ASP cc_start: 0.6873 (t0) cc_final: 0.6414 (m-30) REVERT: 1 560 PHE cc_start: 0.8812 (m-80) cc_final: 0.8516 (m-80) REVERT: 1 581 LYS cc_start: 0.8726 (mttt) cc_final: 0.8343 (mptt) REVERT: 1 609 SER cc_start: 0.8368 (t) cc_final: 0.8094 (m) REVERT: 1 628 HIS cc_start: 0.8528 (t-90) cc_final: 0.8208 (t-90) REVERT: 2 66 VAL cc_start: 0.8936 (t) cc_final: 0.8698 (p) REVERT: 2 87 LEU cc_start: 0.8234 (mp) cc_final: 0.7900 (mp) REVERT: 2 97 MET cc_start: 0.6693 (mmm) cc_final: 0.6354 (tpp) REVERT: 2 200 LEU cc_start: 0.7846 (mt) cc_final: 0.7605 (mt) REVERT: 2 222 LEU cc_start: 0.8931 (mt) cc_final: 0.8655 (mp) REVERT: 2 224 PHE cc_start: 0.7602 (t80) cc_final: 0.6910 (t80) REVERT: 2 247 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8386 (mtt-85) REVERT: 2 251 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7500 (mm-40) REVERT: 2 277 MET cc_start: 0.7593 (tpp) cc_final: 0.7255 (tpt) REVERT: 2 344 ASN cc_start: 0.7042 (t0) cc_final: 0.6770 (t0) REVERT: 3 20 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.8062 (ttp80) REVERT: 3 35 TYR cc_start: 0.7649 (m-80) cc_final: 0.7305 (m-10) REVERT: 3 69 LYS cc_start: 0.8096 (tppt) cc_final: 0.7862 (tppt) REVERT: 3 115 ASP cc_start: 0.6546 (t0) cc_final: 0.6284 (t0) REVERT: 3 129 THR cc_start: 0.8445 (m) cc_final: 0.7984 (t) REVERT: 3 130 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6456 (mt-10) REVERT: 4 232 ASN cc_start: 0.8288 (t0) cc_final: 0.8068 (t0) REVERT: 4 281 ARG cc_start: 0.7873 (mtm-85) cc_final: 0.7631 (mtm-85) REVERT: 6 134 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6980 (mm-30) REVERT: 6 139 LYS cc_start: 0.8450 (mmtp) cc_final: 0.8121 (mmmm) REVERT: 6 215 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6808 (mt-10) REVERT: 6 252 ASP cc_start: 0.6722 (t0) cc_final: 0.6374 (t0) REVERT: 6 303 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7465 (tm-30) REVERT: 6 450 ASN cc_start: 0.8753 (p0) cc_final: 0.8452 (p0) REVERT: 7 138 ASP cc_start: 0.6809 (m-30) cc_final: 0.6579 (p0) REVERT: 7 162 GLU cc_start: 0.8072 (pt0) cc_final: 0.7625 (pt0) REVERT: 7 174 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7821 (ptmt) REVERT: 7 235 GLU cc_start: 0.6299 (tt0) cc_final: 0.5990 (tm-30) REVERT: 7 236 THR cc_start: 0.7883 (p) cc_final: 0.7428 (t) REVERT: 7 546 LYS cc_start: 0.7768 (mttt) cc_final: 0.7516 (mttm) REVERT: 7 621 LYS cc_start: 0.8234 (tptp) cc_final: 0.7921 (mmtp) REVERT: 7 694 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7794 (tppt) REVERT: A 112 LYS cc_start: 0.7667 (tttm) cc_final: 0.7023 (mtpp) REVERT: A 169 ASN cc_start: 0.8634 (m-40) cc_final: 0.7909 (m-40) REVERT: A 199 LEU cc_start: 0.8153 (tt) cc_final: 0.7806 (pp) REVERT: D 145 MET cc_start: 0.7912 (mmm) cc_final: 0.7404 (mmm) REVERT: D 180 LEU cc_start: 0.7574 (mt) cc_final: 0.7314 (mt) REVERT: F 101 ILE cc_start: 0.7186 (mt) cc_final: 0.6893 (mm) REVERT: F 103 MET cc_start: 0.6661 (mtp) cc_final: 0.5926 (mtp) REVERT: G 140 LYS cc_start: 0.7740 (ttpp) cc_final: 0.7356 (ttmm) REVERT: W 81 SER cc_start: 0.6480 (p) cc_final: 0.5876 (m) REVERT: W 106 VAL cc_start: 0.7867 (t) cc_final: 0.7575 (m) REVERT: W 114 ASP cc_start: 0.8040 (m-30) cc_final: 0.7665 (t0) REVERT: W 130 LYS cc_start: 0.6894 (mttp) cc_final: 0.6543 (mttm) REVERT: W 135 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7138 (mm-30) REVERT: W 148 LEU cc_start: 0.6595 (mm) cc_final: 0.5948 (pp) REVERT: W 180 GLN cc_start: 0.7517 (tp40) cc_final: 0.6764 (tp40) REVERT: W 195 GLU cc_start: 0.6911 (pt0) cc_final: 0.6646 (pt0) REVERT: W 211 ASN cc_start: 0.6424 (m110) cc_final: 0.6154 (m110) REVERT: W 223 LYS cc_start: 0.8566 (tppt) cc_final: 0.7942 (tptp) REVERT: W 263 ASN cc_start: 0.7393 (t0) cc_final: 0.7004 (m-40) REVERT: X 194 LYS cc_start: 0.8015 (ptmt) cc_final: 0.7507 (tppt) REVERT: X 196 LEU cc_start: 0.8523 (mt) cc_final: 0.8133 (mt) REVERT: X 239 LYS cc_start: 0.8515 (mmtp) cc_final: 0.8139 (mmmt) REVERT: X 284 LYS cc_start: 0.8221 (tttt) cc_final: 0.8015 (tmtt) REVERT: X 322 LYS cc_start: 0.8198 (tttp) cc_final: 0.7996 (pttp) outliers start: 69 outliers final: 46 residues processed: 748 average time/residue: 0.4863 time to fit residues: 585.1249 Evaluate side-chains 714 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 666 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 301 ILE Chi-restraints excluded: chain 1 residue 328 MET Chi-restraints excluded: chain 1 residue 365 ASN Chi-restraints excluded: chain 1 residue 387 MET Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 50 MET Chi-restraints excluded: chain 2 residue 432 VAL Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 97 ASP Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 354 SER Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 174 LYS Chi-restraints excluded: chain 7 residue 244 MET Chi-restraints excluded: chain 7 residue 330 CYS Chi-restraints excluded: chain 7 residue 345 ASN Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 755 GLU Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 254 CYS Chi-restraints excluded: chain X residue 262 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 210 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 315 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 104 optimal weight: 0.0020 chunk 380 optimal weight: 0.8980 chunk 410 optimal weight: 6.9990 chunk 338 optimal weight: 0.0270 chunk 377 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 305 optimal weight: 2.9990 overall best weight: 0.9448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 692 GLN 1 468 GLN ** 1 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 85 HIS 4 311 GLN 6 269 GLN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 491 HIS 7 592 GLN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS W 169 GLN W 178 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34902 Z= 0.258 Angle : 0.531 9.018 47179 Z= 0.270 Chirality : 0.042 0.220 5378 Planarity : 0.004 0.053 5947 Dihedral : 8.163 122.769 4758 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.23 % Allowed : 10.71 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.46 (0.13), residues: 4122 helix: 1.24 (0.12), residues: 1889 sheet: -0.52 (0.22), residues: 532 loop : -0.37 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 284 HIS 0.010 0.001 HIS 6 449 PHE 0.022 0.001 PHE 7 316 TYR 0.022 0.001 TYR 4 79 ARG 0.005 0.000 ARG 6 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 698 time to evaluate : 3.975 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: 0 34 VAL cc_start: 0.8689 (p) cc_final: 0.8265 (m) REVERT: 0 79 ILE cc_start: 0.8112 (mt) cc_final: 0.7831 (mp) REVERT: 0 90 MET cc_start: 0.8094 (mmm) cc_final: 0.7540 (mmp) REVERT: 0 108 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7937 (tp) REVERT: 0 135 ARG cc_start: 0.7438 (mmm-85) cc_final: 0.7194 (ttm170) REVERT: 0 136 MET cc_start: 0.8003 (mtm) cc_final: 0.7609 (mtt) REVERT: 0 142 LYS cc_start: 0.7910 (tttt) cc_final: 0.7399 (tttp) REVERT: 0 183 LYS cc_start: 0.7621 (ttmt) cc_final: 0.7298 (mtpp) REVERT: 0 218 ILE cc_start: 0.8649 (pt) cc_final: 0.8449 (pt) REVERT: 0 236 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6790 (mt-10) REVERT: 0 259 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7061 (mtm110) REVERT: 0 262 ARG cc_start: 0.7306 (mtm110) cc_final: 0.7071 (ttm110) REVERT: 0 357 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7242 (ttpp) REVERT: 0 365 GLN cc_start: 0.6484 (tt0) cc_final: 0.6078 (mt0) REVERT: 0 525 MET cc_start: 0.8362 (ttm) cc_final: 0.8060 (ttm) REVERT: 0 531 LYS cc_start: 0.8263 (mttt) cc_final: 0.7836 (mttt) REVERT: 0 553 MET cc_start: 0.6086 (mmm) cc_final: 0.5805 (mtp) REVERT: 0 622 MET cc_start: 0.8669 (tpt) cc_final: 0.8166 (mmm) REVERT: 0 650 GLU cc_start: 0.7443 (mp0) cc_final: 0.7138 (mt-10) REVERT: 0 659 MET cc_start: 0.8470 (mmt) cc_final: 0.8230 (mmt) REVERT: 0 675 ASP cc_start: 0.8509 (t0) cc_final: 0.8287 (t0) REVERT: 1 19 ASN cc_start: 0.7628 (t0) cc_final: 0.7340 (t0) REVERT: 1 61 ARG cc_start: 0.7319 (ptm160) cc_final: 0.7050 (ptm-80) REVERT: 1 173 LYS cc_start: 0.6994 (mmtp) cc_final: 0.6473 (mmtt) REVERT: 1 178 LEU cc_start: 0.8336 (mt) cc_final: 0.8030 (tp) REVERT: 1 299 GLU cc_start: 0.7512 (tt0) cc_final: 0.7291 (tt0) REVERT: 1 318 ASP cc_start: 0.7028 (t0) cc_final: 0.6694 (t0) REVERT: 1 321 PHE cc_start: 0.7870 (m-10) cc_final: 0.7647 (m-80) REVERT: 1 346 ASP cc_start: 0.7937 (t0) cc_final: 0.7565 (t70) REVERT: 1 373 ASP cc_start: 0.6891 (t0) cc_final: 0.6405 (m-30) REVERT: 1 581 LYS cc_start: 0.8731 (mttt) cc_final: 0.8334 (mptt) REVERT: 1 609 SER cc_start: 0.8407 (t) cc_final: 0.8124 (m) REVERT: 1 616 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8941 (pt) REVERT: 1 628 HIS cc_start: 0.8522 (t-90) cc_final: 0.8165 (t-90) REVERT: 1 630 TYR cc_start: 0.8554 (t80) cc_final: 0.8320 (t80) REVERT: 2 97 MET cc_start: 0.6865 (mmm) cc_final: 0.6503 (tpp) REVERT: 2 199 GLN cc_start: 0.8073 (tt0) cc_final: 0.7724 (tp40) REVERT: 2 200 LEU cc_start: 0.7869 (mt) cc_final: 0.7648 (mt) REVERT: 2 222 LEU cc_start: 0.8877 (mt) cc_final: 0.8671 (mp) REVERT: 2 224 PHE cc_start: 0.7653 (t80) cc_final: 0.6981 (t80) REVERT: 2 247 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.8299 (mtt-85) REVERT: 2 277 MET cc_start: 0.7679 (tpp) cc_final: 0.7029 (tpt) REVERT: 2 344 ASN cc_start: 0.7178 (t0) cc_final: 0.6891 (t0) REVERT: 2 362 LEU cc_start: 0.8537 (mt) cc_final: 0.8223 (mp) REVERT: 2 419 LYS cc_start: 0.7702 (ttmt) cc_final: 0.7449 (tppt) REVERT: 2 428 GLU cc_start: 0.7174 (mp0) cc_final: 0.6842 (mp0) REVERT: 3 20 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7988 (ttp80) REVERT: 3 35 TYR cc_start: 0.7697 (m-80) cc_final: 0.7387 (m-10) REVERT: 3 69 LYS cc_start: 0.8113 (tppt) cc_final: 0.7894 (tppt) REVERT: 3 115 ASP cc_start: 0.6597 (t0) cc_final: 0.6240 (t0) REVERT: 3 129 THR cc_start: 0.8451 (m) cc_final: 0.8052 (t) REVERT: 3 130 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6405 (mt-10) REVERT: 4 207 LYS cc_start: 0.7872 (mmmt) cc_final: 0.7563 (tptp) REVERT: 4 235 TYR cc_start: 0.8821 (t80) cc_final: 0.8414 (t80) REVERT: 6 134 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7078 (mm-30) REVERT: 6 215 GLU cc_start: 0.7675 (mm-30) cc_final: 0.6912 (mt-10) REVERT: 6 252 ASP cc_start: 0.6801 (t0) cc_final: 0.6453 (t0) REVERT: 6 303 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7456 (tm-30) REVERT: 6 434 GLN cc_start: 0.8253 (mm-40) cc_final: 0.8013 (mm-40) REVERT: 6 450 ASN cc_start: 0.8823 (p0) cc_final: 0.8535 (p0) REVERT: 7 138 ASP cc_start: 0.6919 (m-30) cc_final: 0.6639 (p0) REVERT: 7 235 GLU cc_start: 0.6352 (tt0) cc_final: 0.6016 (tm-30) REVERT: 7 236 THR cc_start: 0.7900 (p) cc_final: 0.7438 (t) REVERT: 7 313 VAL cc_start: 0.7041 (OUTLIER) cc_final: 0.6546 (t) REVERT: 7 454 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8923 (m) REVERT: 7 546 LYS cc_start: 0.7792 (mttt) cc_final: 0.7506 (mttm) REVERT: 7 576 LYS cc_start: 0.8080 (mttt) cc_final: 0.7689 (mtmm) REVERT: 7 694 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7696 (tppt) REVERT: 7 742 MET cc_start: 0.8853 (ttt) cc_final: 0.7784 (ttp) REVERT: A 112 LYS cc_start: 0.7800 (tttm) cc_final: 0.7141 (mtpp) REVERT: A 169 ASN cc_start: 0.8654 (m-40) cc_final: 0.8053 (m110) REVERT: A 199 LEU cc_start: 0.8168 (tt) cc_final: 0.7830 (pp) REVERT: D 145 MET cc_start: 0.7978 (mmm) cc_final: 0.7486 (mmm) REVERT: D 180 LEU cc_start: 0.7580 (mt) cc_final: 0.7282 (mt) REVERT: D 199 ASN cc_start: 0.6418 (p0) cc_final: 0.6104 (m-40) REVERT: F 101 ILE cc_start: 0.7135 (mt) cc_final: 0.6832 (mm) REVERT: F 103 MET cc_start: 0.6842 (mtp) cc_final: 0.6072 (mtt) REVERT: G 32 GLU cc_start: 0.6952 (tp30) cc_final: 0.6728 (tp30) REVERT: G 140 LYS cc_start: 0.7729 (ttpp) cc_final: 0.7352 (ttmm) REVERT: W 106 VAL cc_start: 0.7843 (t) cc_final: 0.7555 (m) REVERT: W 114 ASP cc_start: 0.8047 (m-30) cc_final: 0.7728 (t0) REVERT: W 130 LYS cc_start: 0.6895 (mttp) cc_final: 0.6554 (mttm) REVERT: W 135 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7181 (mm-30) REVERT: W 148 LEU cc_start: 0.6756 (mm) cc_final: 0.6152 (pp) REVERT: W 180 GLN cc_start: 0.7263 (tp40) cc_final: 0.6566 (tp40) REVERT: W 195 GLU cc_start: 0.6895 (pt0) cc_final: 0.6649 (pt0) REVERT: W 211 ASN cc_start: 0.6521 (m110) cc_final: 0.6236 (m110) REVERT: W 223 LYS cc_start: 0.8637 (tppt) cc_final: 0.8082 (tptp) REVERT: W 263 ASN cc_start: 0.7388 (t0) cc_final: 0.6926 (m-40) REVERT: X 194 LYS cc_start: 0.8034 (ptmt) cc_final: 0.7535 (tppt) REVERT: X 239 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8137 (mmmt) REVERT: X 322 LYS cc_start: 0.8215 (tttp) cc_final: 0.7997 (tttt) outliers start: 85 outliers final: 56 residues processed: 731 average time/residue: 0.4674 time to fit residues: 544.7861 Evaluate side-chains 727 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 667 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 365 ASN Chi-restraints excluded: chain 1 residue 378 MET Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 1 residue 570 SER Chi-restraints excluded: chain 1 residue 616 LEU Chi-restraints excluded: chain 2 residue 432 VAL Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 2 residue 451 VAL Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 97 ASP Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 4 residue 117 ARG Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 296 LEU Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 306 THR Chi-restraints excluded: chain 6 residue 354 SER Chi-restraints excluded: chain 7 residue 122 ARG Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 313 VAL Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 345 ASN Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 755 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 254 CYS Chi-restraints excluded: chain X residue 255 ILE Chi-restraints excluded: chain X residue 262 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 375 optimal weight: 0.0770 chunk 285 optimal weight: 0.5980 chunk 197 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 381 optimal weight: 5.9990 chunk 404 optimal weight: 0.3980 chunk 199 optimal weight: 4.9990 chunk 361 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 85 HIS 3 36 HIS 6 281 ASN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 331 GLN 7 345 ASN ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 740 HIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS W 169 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34902 Z= 0.191 Angle : 0.494 7.408 47179 Z= 0.251 Chirality : 0.040 0.179 5378 Planarity : 0.003 0.054 5947 Dihedral : 8.077 118.049 4758 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.12 % Allowed : 12.15 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.55 (0.13), residues: 4122 helix: 1.29 (0.12), residues: 1892 sheet: -0.46 (0.23), residues: 512 loop : -0.32 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 1 284 HIS 0.009 0.001 HIS 4 237 PHE 0.024 0.001 PHE 7 316 TYR 0.024 0.001 TYR 4 79 ARG 0.008 0.000 ARG 0 643 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 690 time to evaluate : 3.866 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: 0 34 VAL cc_start: 0.8651 (p) cc_final: 0.8226 (m) REVERT: 0 79 ILE cc_start: 0.8100 (mt) cc_final: 0.7808 (mp) REVERT: 0 108 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7900 (tp) REVERT: 0 136 MET cc_start: 0.8003 (mtm) cc_final: 0.7739 (mtt) REVERT: 0 142 LYS cc_start: 0.7918 (tttt) cc_final: 0.7396 (tttp) REVERT: 0 183 LYS cc_start: 0.7628 (ttmt) cc_final: 0.7299 (mtpp) REVERT: 0 218 ILE cc_start: 0.8660 (pt) cc_final: 0.8422 (pt) REVERT: 0 236 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6756 (mt-10) REVERT: 0 259 ARG cc_start: 0.7505 (mtp85) cc_final: 0.7059 (mtm110) REVERT: 0 262 ARG cc_start: 0.7323 (mtm110) cc_final: 0.7059 (ttm110) REVERT: 0 357 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7236 (ttpp) REVERT: 0 365 GLN cc_start: 0.6422 (tt0) cc_final: 0.6028 (mt0) REVERT: 0 525 MET cc_start: 0.8354 (ttm) cc_final: 0.8052 (ttm) REVERT: 0 531 LYS cc_start: 0.8259 (mttt) cc_final: 0.7784 (mttt) REVERT: 0 553 MET cc_start: 0.6031 (mmm) cc_final: 0.5777 (mtp) REVERT: 0 622 MET cc_start: 0.8679 (tpt) cc_final: 0.8207 (mmm) REVERT: 0 659 MET cc_start: 0.8510 (mmt) cc_final: 0.8191 (mmt) REVERT: 1 19 ASN cc_start: 0.7605 (t0) cc_final: 0.7285 (t0) REVERT: 1 61 ARG cc_start: 0.7156 (ptm160) cc_final: 0.6888 (ptm-80) REVERT: 1 173 LYS cc_start: 0.6924 (mmtp) cc_final: 0.6436 (mmtt) REVERT: 1 178 LEU cc_start: 0.8326 (mt) cc_final: 0.8047 (tp) REVERT: 1 192 MET cc_start: 0.7941 (tpt) cc_final: 0.7702 (tpt) REVERT: 1 261 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6308 (tm-30) REVERT: 1 299 GLU cc_start: 0.7464 (tt0) cc_final: 0.7246 (tt0) REVERT: 1 318 ASP cc_start: 0.7058 (t0) cc_final: 0.6685 (t0) REVERT: 1 321 PHE cc_start: 0.7922 (m-10) cc_final: 0.7663 (m-80) REVERT: 1 346 ASP cc_start: 0.7924 (t0) cc_final: 0.7572 (t70) REVERT: 1 373 ASP cc_start: 0.6847 (t0) cc_final: 0.6310 (m-30) REVERT: 1 437 LEU cc_start: 0.8574 (tp) cc_final: 0.8311 (pp) REVERT: 1 560 PHE cc_start: 0.8821 (m-80) cc_final: 0.8529 (m-80) REVERT: 1 581 LYS cc_start: 0.8690 (mttt) cc_final: 0.8288 (mptt) REVERT: 1 609 SER cc_start: 0.8486 (t) cc_final: 0.8158 (m) REVERT: 1 628 HIS cc_start: 0.8519 (t-90) cc_final: 0.8106 (t-90) REVERT: 2 48 MET cc_start: 0.8904 (tpp) cc_final: 0.8639 (tpp) REVERT: 2 199 GLN cc_start: 0.8060 (tt0) cc_final: 0.7723 (tp40) REVERT: 2 200 LEU cc_start: 0.7844 (mt) cc_final: 0.7644 (mt) REVERT: 2 222 LEU cc_start: 0.8833 (mt) cc_final: 0.8614 (mp) REVERT: 2 227 MET cc_start: 0.7776 (ttp) cc_final: 0.7016 (ptt) REVERT: 2 247 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.8158 (mtt-85) REVERT: 2 277 MET cc_start: 0.7458 (tpp) cc_final: 0.6828 (tpt) REVERT: 2 339 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8252 (pp) REVERT: 2 344 ASN cc_start: 0.7074 (t0) cc_final: 0.6771 (t0) REVERT: 2 362 LEU cc_start: 0.8483 (mt) cc_final: 0.8167 (mp) REVERT: 2 419 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7470 (ttmt) REVERT: 2 428 GLU cc_start: 0.7081 (mp0) cc_final: 0.6757 (mp0) REVERT: 3 35 TYR cc_start: 0.7735 (m-80) cc_final: 0.7405 (m-10) REVERT: 3 69 LYS cc_start: 0.8040 (tppt) cc_final: 0.7802 (tppt) REVERT: 3 115 ASP cc_start: 0.6656 (t0) cc_final: 0.6267 (t0) REVERT: 4 115 TYR cc_start: 0.7874 (t80) cc_final: 0.7552 (t80) REVERT: 4 207 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7736 (tptp) REVERT: 4 235 TYR cc_start: 0.8868 (t80) cc_final: 0.8451 (t80) REVERT: 4 237 HIS cc_start: 0.7805 (t-170) cc_final: 0.7572 (t-90) REVERT: 4 281 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7524 (mtm-85) REVERT: 5 63 TYR cc_start: 0.8550 (t80) cc_final: 0.8297 (t80) REVERT: 6 134 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7062 (mm-30) REVERT: 6 215 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6905 (mt-10) REVERT: 6 252 ASP cc_start: 0.6816 (t0) cc_final: 0.6431 (t0) REVERT: 6 303 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7450 (tm-30) REVERT: 6 434 GLN cc_start: 0.8237 (mm-40) cc_final: 0.7968 (mm-40) REVERT: 6 450 ASN cc_start: 0.8728 (p0) cc_final: 0.8414 (p0) REVERT: 7 235 GLU cc_start: 0.6272 (tt0) cc_final: 0.5795 (mt-10) REVERT: 7 401 CYS cc_start: 0.7551 (m) cc_final: 0.7007 (m) REVERT: 7 404 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7666 (mmtm) REVERT: 7 546 LYS cc_start: 0.7762 (mttt) cc_final: 0.7473 (mttm) REVERT: 7 576 LYS cc_start: 0.8090 (mttt) cc_final: 0.7713 (mtmm) REVERT: 7 694 LYS cc_start: 0.8027 (tmtt) cc_final: 0.7689 (tppt) REVERT: 7 742 MET cc_start: 0.8747 (ttt) cc_final: 0.8181 (ttp) REVERT: A 112 LYS cc_start: 0.7823 (tttm) cc_final: 0.7171 (mtpp) REVERT: A 169 ASN cc_start: 0.8649 (m-40) cc_final: 0.8014 (m110) REVERT: A 199 LEU cc_start: 0.8169 (tt) cc_final: 0.7834 (pp) REVERT: D 180 LEU cc_start: 0.7492 (mt) cc_final: 0.7237 (mt) REVERT: F 101 ILE cc_start: 0.7111 (mt) cc_final: 0.6818 (mm) REVERT: F 103 MET cc_start: 0.6831 (mtp) cc_final: 0.6059 (mtt) REVERT: G 140 LYS cc_start: 0.7743 (ttpp) cc_final: 0.7375 (ttmm) REVERT: W 53 GLU cc_start: 0.6942 (tt0) cc_final: 0.6467 (mt-10) REVERT: W 114 ASP cc_start: 0.8114 (m-30) cc_final: 0.7712 (t0) REVERT: W 130 LYS cc_start: 0.6901 (mttp) cc_final: 0.6541 (mttm) REVERT: W 135 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7223 (mm-30) REVERT: W 148 LEU cc_start: 0.6755 (mm) cc_final: 0.6168 (pp) REVERT: W 180 GLN cc_start: 0.7280 (tp40) cc_final: 0.6606 (tp40) REVERT: W 211 ASN cc_start: 0.6562 (m110) cc_final: 0.6278 (m110) REVERT: W 223 LYS cc_start: 0.8641 (tppt) cc_final: 0.8076 (tptp) REVERT: X 194 LYS cc_start: 0.8024 (ptmt) cc_final: 0.7519 (tppt) outliers start: 81 outliers final: 59 residues processed: 723 average time/residue: 0.4696 time to fit residues: 542.3053 Evaluate side-chains 722 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 660 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 557 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 339 LEU Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 74 ASP Chi-restraints excluded: chain 3 residue 97 ASP Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 117 ARG Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 281 ARG Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 296 LEU Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 354 SER Chi-restraints excluded: chain 7 residue 122 ARG Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 337 VAL Chi-restraints excluded: chain 7 residue 347 HIS Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 450 SER Chi-restraints excluded: chain 7 residue 467 SER Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 740 HIS Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 228 SER Chi-restraints excluded: chain X residue 255 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 336 optimal weight: 0.5980 chunk 229 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 300 optimal weight: 2.9990 chunk 166 optimal weight: 40.0000 chunk 344 optimal weight: 4.9990 chunk 279 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 206 optimal weight: 6.9990 chunk 362 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 265 ASN ** 1 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 85 HIS 4 81 GLN 6 184 GLN 6 281 ASN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN W 169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34902 Z= 0.206 Angle : 0.503 7.927 47179 Z= 0.254 Chirality : 0.041 0.187 5378 Planarity : 0.003 0.052 5947 Dihedral : 8.033 115.549 4758 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.36 % Allowed : 13.67 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.57 (0.13), residues: 4122 helix: 1.32 (0.12), residues: 1894 sheet: -0.42 (0.23), residues: 511 loop : -0.33 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 1 29 HIS 0.025 0.001 HIS 3 36 PHE 0.025 0.001 PHE 7 316 TYR 0.055 0.001 TYR 1 583 ARG 0.009 0.000 ARG X 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 698 time to evaluate : 3.856 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 34 VAL cc_start: 0.8533 (p) cc_final: 0.8078 (m) REVERT: 0 79 ILE cc_start: 0.8091 (mt) cc_final: 0.7805 (mp) REVERT: 0 108 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7912 (tp) REVERT: 0 136 MET cc_start: 0.8073 (mtm) cc_final: 0.7737 (mtt) REVERT: 0 142 LYS cc_start: 0.7931 (tttt) cc_final: 0.7399 (tttp) REVERT: 0 183 LYS cc_start: 0.7518 (ttmt) cc_final: 0.7192 (mtpp) REVERT: 0 218 ILE cc_start: 0.8661 (pt) cc_final: 0.8420 (pt) REVERT: 0 236 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6761 (mt-10) REVERT: 0 259 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7114 (mtm110) REVERT: 0 262 ARG cc_start: 0.7353 (mtm110) cc_final: 0.7057 (ttm110) REVERT: 0 270 ARG cc_start: 0.7078 (tpt-90) cc_final: 0.6867 (mmm160) REVERT: 0 357 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7252 (ttpp) REVERT: 0 365 GLN cc_start: 0.6499 (tt0) cc_final: 0.6273 (mt0) REVERT: 0 531 LYS cc_start: 0.8259 (mttt) cc_final: 0.7778 (mttt) REVERT: 0 553 MET cc_start: 0.6040 (mmm) cc_final: 0.5766 (mtp) REVERT: 0 622 MET cc_start: 0.8658 (tpt) cc_final: 0.8183 (mmm) REVERT: 0 650 GLU cc_start: 0.7473 (mp0) cc_final: 0.7100 (mt-10) REVERT: 0 659 MET cc_start: 0.8531 (mmt) cc_final: 0.8135 (mmt) REVERT: 0 747 HIS cc_start: 0.7919 (t70) cc_final: 0.7678 (t-170) REVERT: 1 10 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7844 (pt0) REVERT: 1 19 ASN cc_start: 0.7644 (t0) cc_final: 0.7326 (t0) REVERT: 1 61 ARG cc_start: 0.7205 (ptm160) cc_final: 0.6882 (ptm-80) REVERT: 1 88 MET cc_start: 0.5228 (ttp) cc_final: 0.5000 (ttm) REVERT: 1 97 MET cc_start: 0.7103 (ttp) cc_final: 0.6756 (ttt) REVERT: 1 173 LYS cc_start: 0.6921 (mmtp) cc_final: 0.6425 (mmtt) REVERT: 1 178 LEU cc_start: 0.8353 (mt) cc_final: 0.8044 (tp) REVERT: 1 192 MET cc_start: 0.7895 (tpt) cc_final: 0.7641 (tpt) REVERT: 1 318 ASP cc_start: 0.7051 (t0) cc_final: 0.6684 (t0) REVERT: 1 321 PHE cc_start: 0.7940 (m-10) cc_final: 0.7684 (m-80) REVERT: 1 346 ASP cc_start: 0.7878 (t0) cc_final: 0.7481 (t70) REVERT: 1 373 ASP cc_start: 0.6880 (t0) cc_final: 0.6336 (m-30) REVERT: 1 437 LEU cc_start: 0.8642 (tp) cc_final: 0.8355 (pp) REVERT: 1 469 MET cc_start: 0.8014 (mtm) cc_final: 0.7745 (mtp) REVERT: 1 560 PHE cc_start: 0.8854 (m-80) cc_final: 0.8585 (m-80) REVERT: 1 581 LYS cc_start: 0.8697 (mttt) cc_final: 0.8290 (mptt) REVERT: 1 609 SER cc_start: 0.8498 (t) cc_final: 0.8141 (m) REVERT: 1 617 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8402 (ttmm) REVERT: 1 628 HIS cc_start: 0.8474 (t-90) cc_final: 0.8074 (t-90) REVERT: 1 633 TYR cc_start: 0.8369 (m-80) cc_final: 0.8058 (t80) REVERT: 2 48 MET cc_start: 0.8862 (tpp) cc_final: 0.8635 (tpp) REVERT: 2 97 MET cc_start: 0.7363 (mmp) cc_final: 0.6418 (tpp) REVERT: 2 199 GLN cc_start: 0.8074 (tt0) cc_final: 0.7742 (tp40) REVERT: 2 200 LEU cc_start: 0.7851 (mt) cc_final: 0.7647 (mt) REVERT: 2 222 LEU cc_start: 0.8796 (mt) cc_final: 0.8562 (mp) REVERT: 2 247 ARG cc_start: 0.8561 (mtm-85) cc_final: 0.8149 (mtt-85) REVERT: 2 253 MET cc_start: 0.7922 (tpp) cc_final: 0.7528 (mmp) REVERT: 2 277 MET cc_start: 0.7397 (tpp) cc_final: 0.6721 (tpt) REVERT: 2 362 LEU cc_start: 0.8487 (mt) cc_final: 0.8161 (mp) REVERT: 3 11 ASP cc_start: 0.7641 (t0) cc_final: 0.7374 (t0) REVERT: 3 37 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7362 (ttp80) REVERT: 3 69 LYS cc_start: 0.8008 (tppt) cc_final: 0.7802 (tppt) REVERT: 3 115 ASP cc_start: 0.6663 (t0) cc_final: 0.6262 (t0) REVERT: 4 115 TYR cc_start: 0.7827 (t80) cc_final: 0.7575 (t80) REVERT: 4 235 TYR cc_start: 0.8893 (t80) cc_final: 0.8462 (t80) REVERT: 4 281 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7561 (mtm-85) REVERT: 6 134 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7067 (mm-30) REVERT: 6 215 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6821 (mt-10) REVERT: 6 252 ASP cc_start: 0.6838 (t0) cc_final: 0.6545 (t0) REVERT: 6 303 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7443 (tm-30) REVERT: 6 434 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7953 (mm-40) REVERT: 6 450 ASN cc_start: 0.8782 (p0) cc_final: 0.8488 (p0) REVERT: 7 174 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7868 (ptmt) REVERT: 7 401 CYS cc_start: 0.7510 (m) cc_final: 0.7010 (m) REVERT: 7 454 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8908 (m) REVERT: 7 546 LYS cc_start: 0.7730 (mttt) cc_final: 0.7455 (mttm) REVERT: 7 576 LYS cc_start: 0.8120 (mttt) cc_final: 0.7749 (mtmm) REVERT: 7 694 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7686 (tppt) REVERT: A 112 LYS cc_start: 0.7847 (tttm) cc_final: 0.7194 (mtpp) REVERT: A 169 ASN cc_start: 0.8624 (m-40) cc_final: 0.7997 (m110) REVERT: A 199 LEU cc_start: 0.8184 (tt) cc_final: 0.7865 (pp) REVERT: D 65 GLU cc_start: 0.6373 (mt-10) cc_final: 0.6142 (mt-10) REVERT: D 145 MET cc_start: 0.7778 (mmm) cc_final: 0.7377 (mmm) REVERT: D 180 LEU cc_start: 0.7482 (mt) cc_final: 0.7231 (mt) REVERT: F 101 ILE cc_start: 0.7105 (mt) cc_final: 0.6807 (mm) REVERT: F 103 MET cc_start: 0.6896 (mtp) cc_final: 0.6092 (mtt) REVERT: G 140 LYS cc_start: 0.7730 (ttpp) cc_final: 0.7374 (ttmm) REVERT: W 53 GLU cc_start: 0.7002 (tt0) cc_final: 0.6564 (mt-10) REVERT: W 114 ASP cc_start: 0.8104 (m-30) cc_final: 0.7688 (t0) REVERT: W 135 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7241 (mm-30) REVERT: W 148 LEU cc_start: 0.6788 (mm) cc_final: 0.6251 (pp) REVERT: W 180 GLN cc_start: 0.7480 (tp40) cc_final: 0.6822 (tp40) REVERT: W 211 ASN cc_start: 0.6553 (m110) cc_final: 0.6242 (m110) REVERT: W 223 LYS cc_start: 0.8662 (tppt) cc_final: 0.8164 (tmtt) REVERT: X 194 LYS cc_start: 0.8010 (ptmt) cc_final: 0.7504 (tppt) REVERT: X 199 GLN cc_start: 0.7939 (mp10) cc_final: 0.7687 (mp10) REVERT: X 201 THR cc_start: 0.9056 (p) cc_final: 0.8740 (t) outliers start: 90 outliers final: 74 residues processed: 739 average time/residue: 0.4938 time to fit residues: 584.6570 Evaluate side-chains 740 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 662 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 557 MET Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 365 ASN Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 419 LYS Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 74 ASP Chi-restraints excluded: chain 3 residue 97 ASP Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 117 ARG Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 281 ARG Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 4 residue 296 LEU Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 354 SER Chi-restraints excluded: chain 7 residue 122 ARG Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 174 LYS Chi-restraints excluded: chain 7 residue 347 HIS Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 450 SER Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 467 SER Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 254 CYS Chi-restraints excluded: chain X residue 255 ILE Chi-restraints excluded: chain X residue 262 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 135 optimal weight: 8.9990 chunk 363 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 404 optimal weight: 5.9990 chunk 335 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 212 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 85 HIS 4 81 GLN 6 184 GLN 6 281 ASN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 738 HIS 7 740 HIS G 53 ASN W 169 GLN W 178 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34902 Z= 0.237 Angle : 0.521 11.921 47179 Z= 0.261 Chirality : 0.041 0.193 5378 Planarity : 0.003 0.051 5947 Dihedral : 8.037 113.074 4758 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.88 % Allowed : 13.90 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.57 (0.13), residues: 4122 helix: 1.32 (0.12), residues: 1888 sheet: -0.42 (0.23), residues: 510 loop : -0.34 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 1 29 HIS 0.016 0.001 HIS 3 36 PHE 0.026 0.001 PHE 7 316 TYR 0.048 0.001 TYR 1 583 ARG 0.008 0.000 ARG 6 142 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 686 time to evaluate : 4.030 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 34 VAL cc_start: 0.8538 (p) cc_final: 0.8083 (m) REVERT: 0 79 ILE cc_start: 0.8067 (mt) cc_final: 0.7786 (mp) REVERT: 0 90 MET cc_start: 0.8400 (mmp) cc_final: 0.7881 (mmm) REVERT: 0 136 MET cc_start: 0.8171 (mtm) cc_final: 0.7837 (mtt) REVERT: 0 183 LYS cc_start: 0.7530 (ttmt) cc_final: 0.7196 (mtpp) REVERT: 0 236 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6775 (mt-10) REVERT: 0 259 ARG cc_start: 0.7477 (mtp85) cc_final: 0.7047 (mtm110) REVERT: 0 262 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7097 (ttm110) REVERT: 0 270 ARG cc_start: 0.7191 (tpt-90) cc_final: 0.6893 (mmm160) REVERT: 0 293 LEU cc_start: 0.8013 (mt) cc_final: 0.7779 (mp) REVERT: 0 357 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7274 (ttpp) REVERT: 0 365 GLN cc_start: 0.6531 (tt0) cc_final: 0.6153 (mt0) REVERT: 0 525 MET cc_start: 0.8260 (ttm) cc_final: 0.8058 (ttm) REVERT: 0 531 LYS cc_start: 0.8249 (mttt) cc_final: 0.7759 (mttt) REVERT: 0 553 MET cc_start: 0.6035 (mmm) cc_final: 0.5822 (mtp) REVERT: 0 622 MET cc_start: 0.8675 (tpt) cc_final: 0.8207 (mmm) REVERT: 0 650 GLU cc_start: 0.7503 (mp0) cc_final: 0.7063 (mt-10) REVERT: 0 659 MET cc_start: 0.8497 (mmt) cc_final: 0.8141 (mmt) REVERT: 0 747 HIS cc_start: 0.7927 (t70) cc_final: 0.7704 (t-170) REVERT: 1 10 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7867 (pt0) REVERT: 1 19 ASN cc_start: 0.7631 (t0) cc_final: 0.7311 (t0) REVERT: 1 61 ARG cc_start: 0.7335 (ptm160) cc_final: 0.7017 (ptm-80) REVERT: 1 173 LYS cc_start: 0.6924 (mmtp) cc_final: 0.6425 (mmtt) REVERT: 1 178 LEU cc_start: 0.8394 (mt) cc_final: 0.8062 (tp) REVERT: 1 192 MET cc_start: 0.7886 (tpt) cc_final: 0.7598 (tpt) REVERT: 1 261 GLU cc_start: 0.6497 (tm-30) cc_final: 0.6228 (tm-30) REVERT: 1 318 ASP cc_start: 0.7093 (t0) cc_final: 0.6721 (t0) REVERT: 1 321 PHE cc_start: 0.7936 (m-10) cc_final: 0.7714 (m-80) REVERT: 1 373 ASP cc_start: 0.6892 (t0) cc_final: 0.6337 (m-30) REVERT: 1 437 LEU cc_start: 0.8620 (tp) cc_final: 0.8342 (pp) REVERT: 1 560 PHE cc_start: 0.8891 (m-80) cc_final: 0.8563 (m-80) REVERT: 1 581 LYS cc_start: 0.8690 (mttt) cc_final: 0.8297 (mptt) REVERT: 1 609 SER cc_start: 0.8530 (t) cc_final: 0.8166 (m) REVERT: 1 617 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8409 (ttmm) REVERT: 1 628 HIS cc_start: 0.8497 (t-90) cc_final: 0.8100 (t-90) REVERT: 2 48 MET cc_start: 0.8897 (tpp) cc_final: 0.8674 (tpp) REVERT: 2 75 GLN cc_start: 0.8306 (tp40) cc_final: 0.7749 (tm-30) REVERT: 2 97 MET cc_start: 0.7319 (mmp) cc_final: 0.6452 (tpp) REVERT: 2 200 LEU cc_start: 0.7897 (mt) cc_final: 0.7694 (mt) REVERT: 2 222 LEU cc_start: 0.8774 (mt) cc_final: 0.8571 (mt) REVERT: 2 247 ARG cc_start: 0.8570 (mtm-85) cc_final: 0.8119 (mtt-85) REVERT: 2 253 MET cc_start: 0.7940 (tpp) cc_final: 0.7519 (mmp) REVERT: 2 277 MET cc_start: 0.7380 (tpp) cc_final: 0.6701 (tpt) REVERT: 2 362 LEU cc_start: 0.8499 (mt) cc_final: 0.8174 (mp) REVERT: 2 419 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7378 (tppt) REVERT: 3 37 ARG cc_start: 0.7905 (mtp-110) cc_final: 0.7347 (ttp80) REVERT: 3 115 ASP cc_start: 0.6601 (t0) cc_final: 0.6186 (t0) REVERT: 4 115 TYR cc_start: 0.7814 (t80) cc_final: 0.7588 (t80) REVERT: 4 281 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7530 (mtm-85) REVERT: 6 134 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7122 (mm-30) REVERT: 6 139 LYS cc_start: 0.8482 (mmmm) cc_final: 0.8150 (mmmm) REVERT: 6 215 GLU cc_start: 0.7649 (mm-30) cc_final: 0.6930 (mt-10) REVERT: 6 252 ASP cc_start: 0.6853 (t0) cc_final: 0.6566 (t0) REVERT: 6 303 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7524 (tm-30) REVERT: 6 450 ASN cc_start: 0.8786 (p0) cc_final: 0.8495 (p0) REVERT: 7 124 ARG cc_start: 0.7376 (ttm-80) cc_final: 0.7034 (ttm-80) REVERT: 7 174 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7851 (ptmt) REVERT: 7 401 CYS cc_start: 0.7576 (m) cc_final: 0.7048 (m) REVERT: 7 454 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8920 (m) REVERT: 7 546 LYS cc_start: 0.7726 (mttt) cc_final: 0.7446 (mttm) REVERT: 7 694 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7732 (tppt) REVERT: A 112 LYS cc_start: 0.7886 (tttm) cc_final: 0.7213 (mtpp) REVERT: A 169 ASN cc_start: 0.8640 (m-40) cc_final: 0.8040 (m110) REVERT: A 199 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7915 (pp) REVERT: A 1454 MET cc_start: 0.5897 (mmm) cc_final: 0.5455 (mmm) REVERT: D 65 GLU cc_start: 0.6435 (mt-10) cc_final: 0.6117 (mt-10) REVERT: D 180 LEU cc_start: 0.7580 (mt) cc_final: 0.7337 (mt) REVERT: F 101 ILE cc_start: 0.7099 (mt) cc_final: 0.6794 (mm) REVERT: F 103 MET cc_start: 0.7002 (mtp) cc_final: 0.6121 (mtt) REVERT: G 140 LYS cc_start: 0.7742 (ttpp) cc_final: 0.7381 (ttmm) REVERT: W 53 GLU cc_start: 0.6995 (tt0) cc_final: 0.6576 (mt-10) REVERT: W 106 VAL cc_start: 0.7890 (t) cc_final: 0.7579 (m) REVERT: W 114 ASP cc_start: 0.8102 (m-30) cc_final: 0.7687 (t0) REVERT: W 116 ASN cc_start: 0.7392 (t0) cc_final: 0.7122 (t0) REVERT: W 135 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7257 (mm-30) REVERT: W 148 LEU cc_start: 0.6755 (mm) cc_final: 0.6176 (pp) REVERT: W 180 GLN cc_start: 0.7441 (tp40) cc_final: 0.6826 (tp40) REVERT: W 211 ASN cc_start: 0.6557 (m110) cc_final: 0.6227 (m110) REVERT: W 223 LYS cc_start: 0.8689 (tppt) cc_final: 0.8198 (tmtt) REVERT: W 229 ARG cc_start: 0.6654 (mtt90) cc_final: 0.6417 (mtt90) REVERT: X 194 LYS cc_start: 0.8105 (ptmt) cc_final: 0.7584 (tppt) REVERT: X 199 GLN cc_start: 0.7944 (mp10) cc_final: 0.7682 (mp10) REVERT: X 322 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7617 (ptpp) outliers start: 110 outliers final: 83 residues processed: 736 average time/residue: 0.5009 time to fit residues: 590.6336 Evaluate side-chains 750 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 661 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 707 ASN Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 365 ASN Chi-restraints excluded: chain 1 residue 387 MET Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 2 residue 419 LYS Chi-restraints excluded: chain 2 residue 433 LEU Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 36 HIS Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 74 ASP Chi-restraints excluded: chain 3 residue 97 ASP Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 117 ARG Chi-restraints excluded: chain 4 residue 120 ASN Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 281 ARG Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 354 SER Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 174 LYS Chi-restraints excluded: chain 7 residue 223 VAL Chi-restraints excluded: chain 7 residue 347 HIS Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 450 SER Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 467 SER Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 622 MET Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 737 THR Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain 7 residue 740 HIS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 254 CYS Chi-restraints excluded: chain X residue 255 ILE Chi-restraints excluded: chain X residue 262 MET Chi-restraints excluded: chain X residue 322 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 389 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 230 optimal weight: 0.3980 chunk 295 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 340 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 chunk 402 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 245 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 85 HIS 2 199 GLN 2 403 HIS 4 81 GLN ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 331 GLN 7 349 ASN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 738 HIS G 113 HIS W 169 GLN W 178 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34902 Z= 0.211 Angle : 0.519 14.125 47179 Z= 0.260 Chirality : 0.040 0.196 5378 Planarity : 0.003 0.051 5947 Dihedral : 8.025 111.963 4758 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.51 % Allowed : 14.98 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 (0.13), residues: 4122 helix: 1.35 (0.12), residues: 1889 sheet: -0.39 (0.23), residues: 511 loop : -0.35 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 1 29 HIS 0.017 0.001 HIS 3 36 PHE 0.029 0.001 PHE 7 316 TYR 0.025 0.001 TYR 4 79 ARG 0.007 0.000 ARG 0 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 671 time to evaluate : 3.784 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 34 VAL cc_start: 0.8525 (p) cc_final: 0.8071 (m) REVERT: 0 79 ILE cc_start: 0.8149 (mt) cc_final: 0.7848 (mp) REVERT: 0 101 GLU cc_start: 0.7526 (pt0) cc_final: 0.7184 (pm20) REVERT: 0 136 MET cc_start: 0.8171 (mtm) cc_final: 0.7838 (mtt) REVERT: 0 183 LYS cc_start: 0.7499 (ttmt) cc_final: 0.7152 (mtpp) REVERT: 0 236 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6749 (mt-10) REVERT: 0 259 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7018 (mtm110) REVERT: 0 262 ARG cc_start: 0.7425 (mtm110) cc_final: 0.7220 (ttm110) REVERT: 0 270 ARG cc_start: 0.7187 (tpt-90) cc_final: 0.6890 (mmm160) REVERT: 0 293 LEU cc_start: 0.7971 (mt) cc_final: 0.7727 (mp) REVERT: 0 357 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7266 (ttpp) REVERT: 0 365 GLN cc_start: 0.6483 (tt0) cc_final: 0.6227 (mt0) REVERT: 0 525 MET cc_start: 0.8258 (ttm) cc_final: 0.8046 (ttm) REVERT: 0 531 LYS cc_start: 0.8270 (mttt) cc_final: 0.7803 (mttt) REVERT: 0 553 MET cc_start: 0.6018 (mmm) cc_final: 0.5780 (mtp) REVERT: 0 650 GLU cc_start: 0.7524 (mp0) cc_final: 0.7105 (mt-10) REVERT: 0 659 MET cc_start: 0.8521 (mmt) cc_final: 0.8121 (mmt) REVERT: 0 747 HIS cc_start: 0.7918 (t70) cc_final: 0.7701 (t-170) REVERT: 1 19 ASN cc_start: 0.7569 (t0) cc_final: 0.7262 (t0) REVERT: 1 61 ARG cc_start: 0.7328 (ptm160) cc_final: 0.7022 (ptm-80) REVERT: 1 102 MET cc_start: 0.6443 (mmm) cc_final: 0.5861 (mmp) REVERT: 1 178 LEU cc_start: 0.8421 (mt) cc_final: 0.8080 (tp) REVERT: 1 192 MET cc_start: 0.7888 (tpt) cc_final: 0.7642 (tpt) REVERT: 1 238 LYS cc_start: 0.7945 (pttm) cc_final: 0.7618 (mmtm) REVERT: 1 261 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6309 (tm-30) REVERT: 1 318 ASP cc_start: 0.7124 (t0) cc_final: 0.6766 (t0) REVERT: 1 321 PHE cc_start: 0.7977 (m-10) cc_final: 0.7704 (m-80) REVERT: 1 346 ASP cc_start: 0.8021 (t0) cc_final: 0.7650 (t70) REVERT: 1 373 ASP cc_start: 0.6869 (t0) cc_final: 0.6330 (m-30) REVERT: 1 437 LEU cc_start: 0.8590 (tp) cc_final: 0.8270 (pp) REVERT: 1 560 PHE cc_start: 0.8891 (m-80) cc_final: 0.8560 (m-80) REVERT: 1 609 SER cc_start: 0.8545 (t) cc_final: 0.8184 (m) REVERT: 1 617 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8410 (ttmm) REVERT: 1 628 HIS cc_start: 0.8498 (t-90) cc_final: 0.8095 (t-90) REVERT: 2 13 TYR cc_start: 0.8518 (t80) cc_final: 0.8145 (t80) REVERT: 2 48 MET cc_start: 0.8894 (tpp) cc_final: 0.8675 (mmm) REVERT: 2 75 GLN cc_start: 0.8310 (tp40) cc_final: 0.7730 (tm-30) REVERT: 2 97 MET cc_start: 0.7300 (mmp) cc_final: 0.6425 (tpp) REVERT: 2 199 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7238 (tp-100) REVERT: 2 200 LEU cc_start: 0.7825 (mt) cc_final: 0.7601 (mt) REVERT: 2 222 LEU cc_start: 0.8678 (mt) cc_final: 0.8470 (mt) REVERT: 2 247 ARG cc_start: 0.8531 (mtm-85) cc_final: 0.8061 (ttp-110) REVERT: 2 277 MET cc_start: 0.7335 (tpp) cc_final: 0.6701 (tpt) REVERT: 3 37 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7375 (ttp80) REVERT: 3 115 ASP cc_start: 0.6747 (t0) cc_final: 0.6312 (t0) REVERT: 3 130 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6359 (mt-10) REVERT: 4 281 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.7377 (mtm-85) REVERT: 6 134 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7090 (mm-30) REVERT: 6 139 LYS cc_start: 0.8484 (mmmm) cc_final: 0.8162 (mmmm) REVERT: 6 215 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6656 (mt-10) REVERT: 6 252 ASP cc_start: 0.6857 (t0) cc_final: 0.6552 (t0) REVERT: 6 303 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7385 (tm-30) REVERT: 6 384 MET cc_start: 0.8018 (tpp) cc_final: 0.6990 (tpp) REVERT: 6 450 ASN cc_start: 0.8766 (p0) cc_final: 0.8432 (p0) REVERT: 7 118 PHE cc_start: 0.9108 (m-80) cc_final: 0.8863 (m-80) REVERT: 7 124 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.6971 (ttm110) REVERT: 7 174 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7806 (ptmt) REVERT: 7 401 CYS cc_start: 0.7536 (m) cc_final: 0.7042 (m) REVERT: 7 454 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8906 (m) REVERT: 7 546 LYS cc_start: 0.7729 (mttt) cc_final: 0.7484 (mttm) REVERT: 7 621 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8185 (mtpt) REVERT: 7 694 LYS cc_start: 0.8035 (tmtt) cc_final: 0.7722 (tppt) REVERT: 7 738 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.6826 (p-80) REVERT: A 112 LYS cc_start: 0.7867 (tttm) cc_final: 0.7196 (mtpp) REVERT: A 169 ASN cc_start: 0.8640 (m-40) cc_final: 0.8024 (m110) REVERT: A 199 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8013 (pp) REVERT: A 1454 MET cc_start: 0.5828 (mmm) cc_final: 0.5206 (mmp) REVERT: D 65 GLU cc_start: 0.6420 (mt-10) cc_final: 0.6127 (mt-10) REVERT: D 180 LEU cc_start: 0.7601 (mt) cc_final: 0.7365 (mt) REVERT: F 101 ILE cc_start: 0.7089 (mt) cc_final: 0.6789 (mm) REVERT: F 103 MET cc_start: 0.7018 (mtp) cc_final: 0.6108 (mtt) REVERT: G 140 LYS cc_start: 0.7757 (ttpp) cc_final: 0.7398 (ttmm) REVERT: W 53 GLU cc_start: 0.6919 (tt0) cc_final: 0.6555 (mt-10) REVERT: W 114 ASP cc_start: 0.8089 (m-30) cc_final: 0.7674 (t0) REVERT: W 116 ASN cc_start: 0.7379 (t0) cc_final: 0.7120 (t0) REVERT: W 130 LYS cc_start: 0.6651 (mmtp) cc_final: 0.6065 (mmtp) REVERT: W 135 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7255 (mm-30) REVERT: W 148 LEU cc_start: 0.6741 (mm) cc_final: 0.6145 (pp) REVERT: W 180 GLN cc_start: 0.7455 (tp40) cc_final: 0.6791 (tp40) REVERT: W 211 ASN cc_start: 0.6546 (m110) cc_final: 0.6209 (m110) REVERT: W 223 LYS cc_start: 0.8693 (tppt) cc_final: 0.8196 (tmtt) REVERT: W 229 ARG cc_start: 0.6666 (mtt90) cc_final: 0.6382 (mtt90) REVERT: X 194 LYS cc_start: 0.8053 (ptmt) cc_final: 0.7570 (tppt) REVERT: X 199 GLN cc_start: 0.7947 (mp10) cc_final: 0.7687 (mp10) REVERT: X 322 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7625 (ptpp) outliers start: 96 outliers final: 71 residues processed: 716 average time/residue: 0.4822 time to fit residues: 549.3730 Evaluate side-chains 731 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 652 time to evaluate : 3.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 707 ASN Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 365 ASN Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 199 GLN Chi-restraints excluded: chain 2 residue 419 LYS Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 74 ASP Chi-restraints excluded: chain 3 residue 97 ASP Chi-restraints excluded: chain 4 residue 117 ARG Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 281 ARG Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 354 SER Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 174 LYS Chi-restraints excluded: chain 7 residue 347 HIS Chi-restraints excluded: chain 7 residue 376 ASN Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 419 GLN Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 450 SER Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 467 SER Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 621 LYS Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 676 HIS Chi-restraints excluded: chain 7 residue 737 THR Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 254 CYS Chi-restraints excluded: chain X residue 255 ILE Chi-restraints excluded: chain X residue 322 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 249 optimal weight: 0.0030 chunk 160 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 199 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 316 optimal weight: 0.8980 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 199 GLN 4 81 GLN ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 281 ASN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 553 GLN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 738 HIS G 113 HIS W 169 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34902 Z= 0.295 Angle : 0.549 10.576 47179 Z= 0.276 Chirality : 0.042 0.199 5378 Planarity : 0.004 0.050 5947 Dihedral : 8.094 107.559 4758 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.44 % Allowed : 15.24 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.50 (0.13), residues: 4122 helix: 1.25 (0.12), residues: 1890 sheet: -0.44 (0.23), residues: 518 loop : -0.37 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 1 29 HIS 0.034 0.001 HIS 3 36 PHE 0.031 0.002 PHE 7 316 TYR 0.054 0.002 TYR 1 583 ARG 0.007 0.000 ARG X 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 665 time to evaluate : 3.858 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: 0 34 VAL cc_start: 0.8568 (p) cc_final: 0.8116 (m) REVERT: 0 136 MET cc_start: 0.8218 (mtm) cc_final: 0.7799 (mtt) REVERT: 0 183 LYS cc_start: 0.7484 (ttmt) cc_final: 0.7152 (mtpp) REVERT: 0 236 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6758 (mt-10) REVERT: 0 259 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7049 (mtm110) REVERT: 0 262 ARG cc_start: 0.7464 (mtm110) cc_final: 0.7253 (ttm110) REVERT: 0 270 ARG cc_start: 0.7208 (tpt-90) cc_final: 0.6625 (tpt90) REVERT: 0 293 LEU cc_start: 0.7963 (mt) cc_final: 0.7722 (mp) REVERT: 0 357 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7296 (ttpp) REVERT: 0 365 GLN cc_start: 0.6576 (tt0) cc_final: 0.6282 (mt0) REVERT: 0 553 MET cc_start: 0.6016 (mmm) cc_final: 0.5782 (mtp) REVERT: 0 650 GLU cc_start: 0.7563 (mp0) cc_final: 0.7178 (mt-10) REVERT: 0 659 MET cc_start: 0.8478 (mmt) cc_final: 0.8199 (mmt) REVERT: 0 747 HIS cc_start: 0.7978 (t70) cc_final: 0.7740 (t-170) REVERT: 1 19 ASN cc_start: 0.7547 (t0) cc_final: 0.7219 (t0) REVERT: 1 61 ARG cc_start: 0.7273 (ptm160) cc_final: 0.6945 (ptm-80) REVERT: 1 178 LEU cc_start: 0.8444 (mt) cc_final: 0.8098 (tp) REVERT: 1 192 MET cc_start: 0.7912 (tpt) cc_final: 0.7598 (tpt) REVERT: 1 238 LYS cc_start: 0.7942 (pttm) cc_final: 0.7639 (mmtm) REVERT: 1 318 ASP cc_start: 0.7153 (t0) cc_final: 0.6810 (t0) REVERT: 1 321 PHE cc_start: 0.7990 (m-10) cc_final: 0.7695 (m-80) REVERT: 1 346 ASP cc_start: 0.8093 (t0) cc_final: 0.7730 (t70) REVERT: 1 373 ASP cc_start: 0.6828 (t0) cc_final: 0.6331 (m-30) REVERT: 1 390 LYS cc_start: 0.7505 (tptt) cc_final: 0.6617 (mptt) REVERT: 1 437 LEU cc_start: 0.8580 (tp) cc_final: 0.8330 (pp) REVERT: 1 560 PHE cc_start: 0.8905 (m-80) cc_final: 0.8653 (m-80) REVERT: 1 581 LYS cc_start: 0.8659 (mttt) cc_final: 0.8236 (mptt) REVERT: 1 617 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8403 (ttmm) REVERT: 1 628 HIS cc_start: 0.8435 (t-90) cc_final: 0.8015 (t-90) REVERT: 1 634 PHE cc_start: 0.7513 (t80) cc_final: 0.7275 (t80) REVERT: 2 13 TYR cc_start: 0.8558 (t80) cc_final: 0.8193 (t80) REVERT: 2 48 MET cc_start: 0.8884 (tpp) cc_final: 0.8666 (mmm) REVERT: 2 75 GLN cc_start: 0.8279 (tp40) cc_final: 0.7724 (tm-30) REVERT: 2 97 MET cc_start: 0.7332 (mmp) cc_final: 0.6495 (tpp) REVERT: 2 165 ASN cc_start: 0.8301 (t0) cc_final: 0.8100 (t0) REVERT: 2 247 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8055 (ttp-110) REVERT: 2 277 MET cc_start: 0.7332 (tpp) cc_final: 0.6723 (tpt) REVERT: 2 362 LEU cc_start: 0.8572 (mt) cc_final: 0.8235 (mp) REVERT: 3 37 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7379 (ttp80) REVERT: 3 111 GLU cc_start: 0.7282 (tt0) cc_final: 0.7022 (tt0) REVERT: 3 115 ASP cc_start: 0.6621 (t0) cc_final: 0.6195 (t0) REVERT: 3 130 GLU cc_start: 0.6677 (mt-10) cc_final: 0.6363 (mt-10) REVERT: 4 165 LYS cc_start: 0.8674 (pptt) cc_final: 0.8447 (pttt) REVERT: 4 281 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7499 (mtm-85) REVERT: 6 134 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7121 (mm-30) REVERT: 6 139 LYS cc_start: 0.8536 (mmmm) cc_final: 0.8218 (mmmm) REVERT: 6 215 GLU cc_start: 0.7701 (mm-30) cc_final: 0.6902 (mt-10) REVERT: 6 252 ASP cc_start: 0.6860 (t0) cc_final: 0.6590 (t0) REVERT: 6 303 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7439 (tm-30) REVERT: 6 450 ASN cc_start: 0.8858 (p0) cc_final: 0.8570 (p0) REVERT: 7 118 PHE cc_start: 0.9139 (m-80) cc_final: 0.8888 (m-80) REVERT: 7 124 ARG cc_start: 0.7334 (ttm-80) cc_final: 0.6823 (ttm-80) REVERT: 7 174 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7863 (ptmt) REVERT: 7 235 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6136 (mt-10) REVERT: 7 401 CYS cc_start: 0.7524 (m) cc_final: 0.7040 (m) REVERT: 7 454 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8943 (m) REVERT: 7 529 PHE cc_start: 0.8086 (p90) cc_final: 0.7536 (p90) REVERT: 7 546 LYS cc_start: 0.7742 (mttt) cc_final: 0.7497 (mttm) REVERT: 7 621 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8108 (mtpt) REVERT: 7 694 LYS cc_start: 0.8142 (tmtt) cc_final: 0.7828 (tppt) REVERT: 7 738 HIS cc_start: 0.8620 (OUTLIER) cc_final: 0.6751 (p-80) REVERT: 7 740 HIS cc_start: 0.6958 (m-70) cc_final: 0.6331 (m-70) REVERT: A 112 LYS cc_start: 0.7926 (tttm) cc_final: 0.7300 (mtpp) REVERT: A 169 ASN cc_start: 0.8678 (m-40) cc_final: 0.8102 (m110) REVERT: A 199 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8030 (pp) REVERT: A 1454 MET cc_start: 0.5895 (mmm) cc_final: 0.4971 (mmt) REVERT: D 65 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6125 (mt-10) REVERT: D 145 MET cc_start: 0.7830 (mmm) cc_final: 0.7595 (mmm) REVERT: D 180 LEU cc_start: 0.7642 (mt) cc_final: 0.7394 (mt) REVERT: F 101 ILE cc_start: 0.7097 (mt) cc_final: 0.6782 (mm) REVERT: F 103 MET cc_start: 0.7137 (mtp) cc_final: 0.6179 (mtt) REVERT: F 104 ASN cc_start: 0.8297 (t0) cc_final: 0.7624 (t0) REVERT: G 140 LYS cc_start: 0.7755 (ttpp) cc_final: 0.7396 (ttmm) REVERT: W 53 GLU cc_start: 0.6891 (tt0) cc_final: 0.6523 (mt-10) REVERT: W 106 VAL cc_start: 0.7904 (t) cc_final: 0.7614 (m) REVERT: W 114 ASP cc_start: 0.8128 (m-30) cc_final: 0.7752 (t0) REVERT: W 116 ASN cc_start: 0.7396 (t0) cc_final: 0.7124 (t0) REVERT: W 123 MET cc_start: 0.6834 (ttp) cc_final: 0.6518 (ttm) REVERT: W 130 LYS cc_start: 0.6596 (mmtp) cc_final: 0.6073 (mmtp) REVERT: W 135 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7232 (mm-30) REVERT: W 148 LEU cc_start: 0.6725 (mm) cc_final: 0.6120 (pp) REVERT: W 180 GLN cc_start: 0.7533 (tp40) cc_final: 0.7092 (tp40) REVERT: W 211 ASN cc_start: 0.6543 (m110) cc_final: 0.6190 (m110) REVERT: W 223 LYS cc_start: 0.8688 (tppt) cc_final: 0.8211 (tmtt) REVERT: W 229 ARG cc_start: 0.6721 (mtt90) cc_final: 0.6482 (mtt90) REVERT: X 194 LYS cc_start: 0.8073 (ptmt) cc_final: 0.7583 (tppt) REVERT: X 199 GLN cc_start: 0.8039 (mp10) cc_final: 0.7756 (mp10) REVERT: X 322 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7677 (ptpp) outliers start: 93 outliers final: 76 residues processed: 710 average time/residue: 0.4863 time to fit residues: 545.9374 Evaluate side-chains 732 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 649 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 0 residue 108 LEU Chi-restraints excluded: chain 0 residue 353 SER Chi-restraints excluded: chain 0 residue 366 LEU Chi-restraints excluded: chain 0 residue 387 THR Chi-restraints excluded: chain 0 residue 473 LEU Chi-restraints excluded: chain 0 residue 486 THR Chi-restraints excluded: chain 0 residue 501 SER Chi-restraints excluded: chain 0 residue 507 SER Chi-restraints excluded: chain 0 residue 556 THR Chi-restraints excluded: chain 0 residue 573 THR Chi-restraints excluded: chain 0 residue 679 MET Chi-restraints excluded: chain 0 residue 680 VAL Chi-restraints excluded: chain 0 residue 707 ASN Chi-restraints excluded: chain 0 residue 736 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 184 LEU Chi-restraints excluded: chain 1 residue 249 VAL Chi-restraints excluded: chain 1 residue 274 VAL Chi-restraints excluded: chain 1 residue 365 ASN Chi-restraints excluded: chain 1 residue 422 ASP Chi-restraints excluded: chain 1 residue 509 ILE Chi-restraints excluded: chain 2 residue 98 ILE Chi-restraints excluded: chain 2 residue 373 MET Chi-restraints excluded: chain 2 residue 419 LYS Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 3 residue 66 ASN Chi-restraints excluded: chain 3 residue 74 ASP Chi-restraints excluded: chain 3 residue 97 ASP Chi-restraints excluded: chain 3 residue 133 LEU Chi-restraints excluded: chain 4 residue 24 SER Chi-restraints excluded: chain 4 residue 117 ARG Chi-restraints excluded: chain 4 residue 270 VAL Chi-restraints excluded: chain 4 residue 281 ARG Chi-restraints excluded: chain 4 residue 283 VAL Chi-restraints excluded: chain 4 residue 285 VAL Chi-restraints excluded: chain 6 residue 118 TYR Chi-restraints excluded: chain 6 residue 193 ILE Chi-restraints excluded: chain 6 residue 267 SER Chi-restraints excluded: chain 6 residue 354 SER Chi-restraints excluded: chain 7 residue 164 ILE Chi-restraints excluded: chain 7 residue 174 LYS Chi-restraints excluded: chain 7 residue 347 HIS Chi-restraints excluded: chain 7 residue 407 VAL Chi-restraints excluded: chain 7 residue 433 GLU Chi-restraints excluded: chain 7 residue 450 SER Chi-restraints excluded: chain 7 residue 454 VAL Chi-restraints excluded: chain 7 residue 467 SER Chi-restraints excluded: chain 7 residue 490 VAL Chi-restraints excluded: chain 7 residue 520 GLU Chi-restraints excluded: chain 7 residue 553 GLN Chi-restraints excluded: chain 7 residue 580 LEU Chi-restraints excluded: chain 7 residue 621 LYS Chi-restraints excluded: chain 7 residue 651 THR Chi-restraints excluded: chain 7 residue 657 VAL Chi-restraints excluded: chain 7 residue 664 LEU Chi-restraints excluded: chain 7 residue 670 LEU Chi-restraints excluded: chain 7 residue 737 THR Chi-restraints excluded: chain 7 residue 738 HIS Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain B residue 1219 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 111 THR Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain W residue 24 SER Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 69 ILE Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 198 THR Chi-restraints excluded: chain W residue 220 ASN Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 217 CYS Chi-restraints excluded: chain X residue 254 CYS Chi-restraints excluded: chain X residue 255 ILE Chi-restraints excluded: chain X residue 322 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.351 > 50: distance: 29 - 36: 14.170 distance: 36 - 37: 33.637 distance: 37 - 38: 16.768 distance: 37 - 40: 4.537 distance: 38 - 39: 9.310 distance: 38 - 44: 20.801 distance: 40 - 41: 14.084 distance: 41 - 42: 22.659 distance: 41 - 43: 11.562 distance: 44 - 45: 15.774 distance: 45 - 46: 13.399 distance: 45 - 48: 10.861 distance: 46 - 47: 12.622 distance: 46 - 52: 25.075 distance: 48 - 49: 19.243 distance: 49 - 50: 14.011 distance: 49 - 51: 7.071 distance: 52 - 53: 7.258 distance: 52 - 58: 29.610 distance: 53 - 54: 15.108 distance: 53 - 56: 34.839 distance: 54 - 55: 17.807 distance: 54 - 59: 13.708 distance: 56 - 57: 10.470 distance: 57 - 58: 3.992 distance: 59 - 60: 15.420 distance: 60 - 61: 13.365 distance: 60 - 63: 8.029 distance: 61 - 62: 15.573 distance: 61 - 67: 16.223 distance: 63 - 64: 13.461 distance: 64 - 65: 9.851 distance: 64 - 66: 4.849 distance: 68 - 69: 14.169 distance: 68 - 71: 4.171 distance: 69 - 70: 15.741 distance: 69 - 73: 15.159 distance: 71 - 72: 4.824 distance: 73 - 74: 10.671 distance: 74 - 75: 15.042 distance: 74 - 77: 4.031 distance: 75 - 76: 13.661 distance: 75 - 82: 12.303 distance: 77 - 78: 20.707 distance: 78 - 79: 10.449 distance: 79 - 80: 24.666 distance: 80 - 81: 21.047 distance: 82 - 83: 40.345 distance: 83 - 84: 19.129 distance: 83 - 86: 8.995 distance: 84 - 91: 22.928 distance: 86 - 87: 17.637 distance: 87 - 88: 8.569 distance: 88 - 89: 30.608 distance: 88 - 90: 11.229 distance: 91 - 92: 27.040 distance: 91 - 97: 39.469 distance: 92 - 93: 29.613 distance: 92 - 95: 6.550 distance: 93 - 94: 29.321 distance: 93 - 98: 18.972 distance: 95 - 96: 38.755 distance: 96 - 97: 10.399 distance: 98 - 99: 16.294 distance: 99 - 100: 12.487 distance: 99 - 102: 35.470 distance: 100 - 101: 9.880 distance: 100 - 106: 14.381 distance: 102 - 103: 7.454 distance: 103 - 104: 5.840 distance: 103 - 105: 31.434 distance: 106 - 107: 13.525 distance: 107 - 108: 7.797 distance: 107 - 110: 17.335 distance: 108 - 109: 6.524 distance: 108 - 115: 4.827 distance: 110 - 111: 8.527 distance: 111 - 112: 7.604 distance: 112 - 113: 8.543 distance: 112 - 114: 6.705