Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 02:42:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/10_2023/7o4k_12721_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/10_2023/7o4k_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_12721/10_2023/7o4k_12721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/10_2023/7o4k_12721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/10_2023/7o4k_12721_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o4k_12721/10_2023/7o4k_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 17.72, per 1000 atoms: 0.52 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: 14.02 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 801 " pdb="FE3 SF4 0 801 " - pdb=" SG CYS 0 133 " pdb="FE4 SF4 0 801 " - pdb=" SG CYS 0 191 " pdb="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: 5.93 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: 12.90 Time building geometry restraints manager: 14.95 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: 20979 35.57 - 71.15: 366 71.15 - 106.72: 41 106.72 - 142.29: 2 142.29 - 177.86: 1 Dihedral angle restraints: 21389 sinusoidal: 9009 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 21386 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.210 Check model and map are aligned: 0.470 Set scattering table: 0.320 Process input model: 99.140 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.010 ------------------------------------------------------------------------------- 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 : 14.015 177.863 13319 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 *********************** 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 : 3.913 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 outliers start: 0 outliers final: 0 residues processed: 929 average time/residue: 0.4799 time to fit residues: 705.5780 Evaluate side-chains 666 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 3.772 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4467 ------------------------------------------------------------------------------- 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: 4.9990 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: 1.9990 chunk 243 optimal weight: 10.0000 chunk 379 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 ASN 0 361 GLN 1 352 ASN 1 488 GLN ** 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 7 592 GLN ** 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 D 199 ASN F 100 GLN G 53 ASN G 97 HIS G 113 HIS W 133 GLN W 169 GLN W 178 GLN W 263 ASN X 267 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 34902 Z= 0.466 Angle : 0.648 10.176 47179 Z= 0.331 Chirality : 0.046 0.200 5378 Planarity : 0.005 0.062 5947 Dihedral : 8.306 135.210 4730 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.86 % Allowed : 9.61 % Favored : 88.53 % 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: 0.26 (0.13), residues: 4122 helix: 1.05 (0.12), residues: 1889 sheet: -0.64 (0.22), residues: 526 loop : -0.46 (0.15), residues: 1707 *********************** 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 799 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 728 time to evaluate : 3.648 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 outliers start: 71 outliers final: 49 residues processed: 751 average time/residue: 0.4705 time to fit residues: 563.3452 Evaluate side-chains 706 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 657 time to evaluate : 3.912 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3082 time to fit residues: 34.1690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 210 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 315 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 380 optimal weight: 0.9990 chunk 410 optimal weight: 0.2980 chunk 338 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 305 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 3 36 HIS 4 161 ASN 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 ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 ASN G 113 HIS W 169 GLN W 220 ASN ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34902 Z= 0.202 Angle : 0.523 7.255 47179 Z= 0.268 Chirality : 0.041 0.176 5378 Planarity : 0.004 0.053 5947 Dihedral : 8.087 120.905 4730 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.39 % Allowed : 11.99 % Favored : 86.62 % 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: 0.33 (0.13), residues: 4122 helix: 1.15 (0.12), residues: 1885 sheet: -0.70 (0.22), residues: 534 loop : -0.42 (0.15), residues: 1703 *********************** 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 739 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 686 time to evaluate : 3.841 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 outliers start: 53 outliers final: 28 residues processed: 706 average time/residue: 0.4654 time to fit residues: 525.4396 Evaluate side-chains 681 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 653 time to evaluate : 3.719 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3538 time to fit residues: 22.5759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 375 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 255 optimal weight: 5.9990 chunk 381 optimal weight: 5.9990 chunk 404 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 361 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 4 225 GLN 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** 7 553 GLN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 738 HIS 7 740 HIS A 282 ASN D 157 GLN D 199 ASN G 113 HIS W 169 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 34902 Z= 0.385 Angle : 0.582 8.835 47179 Z= 0.297 Chirality : 0.043 0.181 5378 Planarity : 0.004 0.050 5947 Dihedral : 8.156 118.139 4730 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.68 % Allowed : 13.90 % Favored : 84.42 % 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: 0.19 (0.13), residues: 4122 helix: 1.02 (0.12), residues: 1881 sheet: -0.75 (0.23), residues: 522 loop : -0.49 (0.15), residues: 1719 *********************** 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 740 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 676 time to evaluate : 3.722 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 outliers start: 64 outliers final: 41 residues processed: 706 average time/residue: 0.4883 time to fit residues: 550.3230 Evaluate side-chains 692 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 651 time to evaluate : 3.596 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.3228 time to fit residues: 30.1223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 5 optimal weight: 0.6980 chunk 300 optimal weight: 0.6980 chunk 166 optimal weight: 40.0000 chunk 344 optimal weight: 4.9990 chunk 279 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 362 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 66 ASN 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 199 ASN W 169 GLN ** W 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34902 Z= 0.198 Angle : 0.516 11.815 47179 Z= 0.263 Chirality : 0.041 0.186 5378 Planarity : 0.004 0.052 5947 Dihedral : 8.055 118.132 4730 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.34 % Allowed : 15.11 % Favored : 83.56 % 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: 0.39 (0.13), residues: 4122 helix: 1.23 (0.12), residues: 1874 sheet: -0.62 (0.23), residues: 523 loop : -0.44 (0.15), residues: 1725 *********************** 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 725 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 674 time to evaluate : 4.115 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 outliers start: 51 outliers final: 21 residues processed: 695 average time/residue: 0.4865 time to fit residues: 540.9686 Evaluate side-chains 661 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 640 time to evaluate : 3.989 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.3494 time to fit residues: 18.9089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 135 optimal weight: 0.7980 chunk 363 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 404 optimal weight: 0.9990 chunk 335 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 2 344 ASN 4 81 GLN 4 225 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** 7 331 GLN 7 345 ASN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 676 HIS W 169 GLN ** W 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34902 Z= 0.223 Angle : 0.537 12.756 47179 Z= 0.270 Chirality : 0.041 0.187 5378 Planarity : 0.003 0.051 5947 Dihedral : 8.007 116.120 4730 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.00 % Allowed : 16.26 % Favored : 82.74 % 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: 0.44 (0.13), residues: 4122 helix: 1.26 (0.12), residues: 1876 sheet: -0.58 (0.23), residues: 523 loop : -0.41 (0.15), residues: 1723 *********************** 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 683 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 645 time to evaluate : 3.802 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 outliers start: 38 outliers final: 24 residues processed: 654 average time/residue: 0.4927 time to fit residues: 515.1182 Evaluate side-chains 651 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 627 time to evaluate : 4.072 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3211 time to fit residues: 19.9373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 389 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 230 optimal weight: 0.0670 chunk 295 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 340 optimal weight: 1.9990 chunk 225 optimal weight: 0.2980 chunk 402 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 245 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 555 GLN ** 1 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 81 GLN 4 225 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** ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 738 HIS W 169 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34902 Z= 0.197 Angle : 0.521 8.577 47179 Z= 0.264 Chirality : 0.040 0.190 5378 Planarity : 0.003 0.051 5947 Dihedral : 7.969 115.245 4730 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.84 % Allowed : 16.68 % Favored : 82.48 % 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: 0.51 (0.13), residues: 4122 helix: 1.33 (0.12), residues: 1872 sheet: -0.47 (0.23), residues: 528 loop : -0.40 (0.15), residues: 1722 *********************** 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 680 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 648 time to evaluate : 4.232 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 outliers start: 32 outliers final: 16 residues processed: 660 average time/residue: 0.4884 time to fit residues: 514.3153 Evaluate side-chains 633 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 617 time to evaluate : 3.822 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.3609 time to fit residues: 15.6313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 249 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 240 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 274 optimal weight: 1.9990 chunk 199 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 316 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** ** 2 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 403 HIS ** 3 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** 7 345 ASN ** 7 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 GLN W 211 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34902 Z= 0.277 Angle : 0.560 12.672 47179 Z= 0.282 Chirality : 0.042 0.200 5378 Planarity : 0.004 0.049 5947 Dihedral : 8.020 114.003 4730 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.97 % Allowed : 17.26 % Favored : 81.78 % 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: 0.45 (0.13), residues: 4122 helix: 1.25 (0.12), residues: 1875 sheet: -0.50 (0.23), residues: 529 loop : -0.41 (0.15), residues: 1718 *********************** 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 675 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 638 time to evaluate : 4.010 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 outliers start: 37 outliers final: 21 residues processed: 650 average time/residue: 0.4827 time to fit residues: 503.2816 Evaluate side-chains 647 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 626 time to evaluate : 3.708 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.3086 time to fit residues: 17.8070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 366 optimal weight: 2.9990 chunk 385 optimal weight: 0.5980 chunk 352 optimal weight: 0.9990 chunk 375 optimal weight: 0.5980 chunk 225 optimal weight: 0.4980 chunk 163 optimal weight: 0.0370 chunk 294 optimal weight: 0.0870 chunk 115 optimal weight: 4.9990 chunk 339 optimal weight: 1.9990 chunk 355 optimal weight: 0.0980 chunk 374 optimal weight: 1.9990 overall best weight: 0.2636 ------------------------------------------------------------------------------- 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** 2 344 ASN 3 66 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** 7 642 ASN W 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34902 Z= 0.156 Angle : 0.541 13.402 47179 Z= 0.271 Chirality : 0.040 0.198 5378 Planarity : 0.003 0.049 5947 Dihedral : 7.938 113.421 4730 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.45 % Allowed : 18.20 % Favored : 81.36 % 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: 1.35 (0.12), residues: 1878 sheet: -0.41 (0.23), residues: 538 loop : -0.37 (0.15), residues: 1706 *********************** REFINEMENT MACRO_CYCLE 9 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 660 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 643 time to evaluate : 3.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 645 average time/residue: 0.4855 time to fit residues: 502.4893 Evaluate side-chains 614 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 608 time to evaluate : 3.703 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.3213 time to fit residues: 8.9793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 246 optimal weight: 5.9990 chunk 397 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 416 optimal weight: 0.7980 chunk 383 optimal weight: 0.9990 chunk 331 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 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** 2 344 ASN 4 81 GLN 4 161 ASN 4 311 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** 7 345 ASN W 169 GLN ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 34902 Z= 0.250 Angle : 0.570 13.491 47179 Z= 0.286 Chirality : 0.042 0.344 5378 Planarity : 0.004 0.049 5947 Dihedral : 7.935 103.699 4730 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.31 % Allowed : 19.27 % Favored : 80.41 % 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: 0.56 (0.13), residues: 4122 helix: 1.34 (0.12), residues: 1877 sheet: -0.35 (0.23), residues: 523 loop : -0.38 (0.15), residues: 1722 ********************** REFINEMENT MACRO_CYCLE 10 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 636 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 624 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 629 average time/residue: 0.4996 time to fit residues: 505.4004 Evaluate side-chains 618 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 613 time to evaluate : 3.860 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.3383 time to fit residues: 8.7051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 263 optimal weight: 0.4980 chunk 353 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 305 optimal weight: 1.9990 chunk 48 optimal weight: 0.0020 chunk 92 optimal weight: 0.0370 chunk 332 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 341 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.1844 ------------------------------------------------------------------------------- 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** 4 81 GLN ** 6 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 152 GLN ** 7 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 169 GLN ** X 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.190593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.125764 restraints weight = 40356.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.128506 restraints weight = 26337.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.129022 restraints weight = 19292.273| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 34902 Z= 0.151 Angle : 0.546 13.114 47179 Z= 0.273 Chirality : 0.040 0.211 5378 Planarity : 0.003 0.049 5947 Dihedral : 7.789 92.560 4730 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.37 % Allowed : 19.22 % Favored : 80.41 % 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: 0.67 (0.13), residues: 4122 helix: 1.44 (0.12), residues: 1873 sheet: -0.27 (0.23), residues: 537 loop : -0.35 (0.15), residues: 1712 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9211.57 seconds wall clock time: 166 minutes 34.11 seconds (9994.11 seconds total)