Starting phenix.real_space_refine (version: dev) on Fri May 13 01:05:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/05_2022/6pmj_20395_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/05_2022/6pmj_20395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/05_2022/6pmj_20395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/05_2022/6pmj_20395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/05_2022/6pmj_20395_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pmj_20395/05_2022/6pmj_20395_trim_updated.pdb" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.020 sd= 0.289 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 57984 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3599 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 220, 'PCIS': 1} Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3556 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 8, 'TRANS': 218, 'PCIS': 1} Chain: "C" Number of atoms: 21152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 21152 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1283} Chain: "D" Number of atoms: 21010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1337, 21010 Classifications: {'peptide': 1337} Link IDs: {'PTRANS': 54, 'TRANS': 1281, 'PCIS': 1} Chain breaks: 2 Chain: "E" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1261 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3871 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain: "1" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1712 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "2" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1724 Classifications: {'DNA': 54} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 53} Chain: "3" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 96 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1, 'RNA': 2} Modifications used: {'rna3p_pyr': 1, 'rna3p_pur': 1, '3*END': 1} Link IDs: {None: 1, 'rna3p': 1} Not linked: pdbres="ATP 3 1 " pdbres=" A 3 2 " Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 29207 SG CYS D 70 76.218 120.159 81.133 1.00 20.00 S ATOM 29466 SG CYS D 85 79.796 121.605 79.994 1.00 20.00 S ATOM 41046 SG CYS D 814 102.032 70.512 133.648 1.00 20.00 S ATOM 42183 SG CYS D 888 99.178 70.554 131.686 1.00 20.00 S ATOM 42274 SG CYS D 895 103.449 69.053 130.838 1.00 20.00 S Time building chain proxies: 20.31, per 1000 atoms: 0.35 Number of scatterers: 57984 At special positions: 0 Unit cell: (171, 149.4, 180.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 110 16.00 P 113 15.00 Mg 1 11.99 O 5889 8.00 N 5218 7.00 C 18042 6.00 H 28609 1.00 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: 37.01 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 110 helices and 29 sheets defined 33.6% alpha, 9.1% beta 31 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 19.53 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 78 through 87 removed outlier: 4.160A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 213 through 232 removed outlier: 3.686A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 78 through 85 Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'C' and resid 5 through 8 No H-bonds generated for 'chain 'C' and resid 5 through 8' Processing helix chain 'C' and resid 29 through 39 Processing helix chain 'C' and resid 49 through 55 Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 217 through 224 Processing helix chain 'C' and resid 271 through 279 Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 359 through 370 Processing helix chain 'C' and resid 378 through 390 removed outlier: 3.751A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 422 through 437 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 479 removed outlier: 4.280A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 492 removed outlier: 3.760A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 489 through 492' Processing helix chain 'C' and resid 496 through 508 removed outlier: 3.560A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 527 Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 610 through 612 No H-bonds generated for 'chain 'C' and resid 610 through 612' Processing helix chain 'C' and resid 663 through 666 No H-bonds generated for 'chain 'C' and resid 663 through 666' Processing helix chain 'C' and resid 671 through 673 No H-bonds generated for 'chain 'C' and resid 671 through 673' Processing helix chain 'C' and resid 676 through 686 Processing helix chain 'C' and resid 705 through 711 Processing helix chain 'C' and resid 821 through 825 Processing helix chain 'C' and resid 859 through 864 removed outlier: 4.509A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 906 Processing helix chain 'C' and resid 943 through 980 removed outlier: 4.147A pdb=" N ARG C 974 " --> pdb=" O GLY C 970 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU C 979 " --> pdb=" O ILE C 975 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 1008 through 1037 Processing helix chain 'C' and resid 1100 through 1102 No H-bonds generated for 'chain 'C' and resid 1100 through 1102' Processing helix chain 'C' and resid 1110 through 1134 removed outlier: 3.524A pdb=" N ALA C1121 " --> pdb=" O LEU C1117 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY C1123 " --> pdb=" O MET C1119 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1149 Processing helix chain 'C' and resid 1166 through 1178 removed outlier: 5.425A pdb=" N LYS C1178 " --> pdb=" O GLU C1174 " (cutoff:3.500A) Processing helix chain 'C' and resid 1192 through 1201 Processing helix chain 'C' and resid 1262 through 1264 No H-bonds generated for 'chain 'C' and resid 1262 through 1264' Processing helix chain 'C' and resid 1272 through 1281 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1298 through 1309 Processing helix chain 'C' and resid 1321 through 1333 removed outlier: 3.679A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 59 through 62 No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 125 through 128 No H-bonds generated for 'chain 'D' and resid 125 through 128' Processing helix chain 'D' and resid 132 through 139 Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 182 through 191 Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.964A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 229 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 264 through 285 Processing helix chain 'D' and resid 290 through 307 Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 394 through 403 Processing helix chain 'D' and resid 406 through 416 Processing helix chain 'D' and resid 431 through 433 No H-bonds generated for 'chain 'D' and resid 431 through 433' Processing helix chain 'D' and resid 451 through 454 Processing helix chain 'D' and resid 475 through 482 Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 530 through 537 Processing helix chain 'D' and resid 574 through 582 removed outlier: 3.661A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 592 No H-bonds generated for 'chain 'D' and resid 590 through 592' Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 615 through 634 Processing helix chain 'D' and resid 651 through 670 Processing helix chain 'D' and resid 676 through 701 Processing helix chain 'D' and resid 721 through 728 Processing helix chain 'D' and resid 734 through 741 Processing helix chain 'D' and resid 769 through 787 removed outlier: 4.472A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 806 removed outlier: 5.712A pdb=" N ASP D 806 " --> pdb=" O ASP D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 839 Processing helix chain 'D' and resid 866 through 873 Processing helix chain 'D' and resid 916 through 929 Proline residue: D 926 - end of helix removed outlier: 4.587A pdb=" N GLN D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1145 Processing helix chain 'D' and resid 1217 through 1223 Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 4.049A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1260 removed outlier: 3.789A pdb=" N VAL D1255 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D1256 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1287 Processing helix chain 'D' and resid 1309 through 1314 removed outlier: 3.666A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1322 through 1324 No H-bonds generated for 'chain 'D' and resid 1322 through 1324' Processing helix chain 'D' and resid 1328 through 1338 removed outlier: 4.152A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 removed outlier: 3.713A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1363 through 1374 Processing helix chain 'E' and resid 8 through 13 removed outlier: 3.582A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 31 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 61 through 79 Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.016A pdb=" N LYS F 13 " --> pdb=" O GLY F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 30 removed outlier: 4.600A pdb=" N ARG F 30 " --> pdb=" O HIS F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 40 No H-bonds generated for 'chain 'F' and resid 37 through 40' Processing helix chain 'F' and resid 42 through 58 removed outlier: 3.505A pdb=" N ARG F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 86 removed outlier: 4.285A pdb=" N GLN F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG F 74 " --> pdb=" O TYR F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 111 Processing helix chain 'F' and resid 117 through 123 removed outlier: 3.741A pdb=" N ARG F 123 " --> pdb=" O VAL F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 138 removed outlier: 4.242A pdb=" N LEU F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 188 removed outlier: 3.536A pdb=" N LEU F 173 " --> pdb=" O PRO F 169 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 Processing helix chain 'F' and resid 208 through 214 Processing helix chain 'F' and resid 220 through 232 Processing sheet with id= A, first strand: chain 'A' and resid 24 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 90 through 92 Processing sheet with id= C, first strand: chain 'A' and resid 97 through 105 removed outlier: 5.669A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 108 through 110 Processing sheet with id= E, first strand: chain 'B' and resid 23 through 26 removed outlier: 4.124A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 170 through 172 removed outlier: 6.538A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= H, first strand: chain 'C' and resid 116 through 123 removed outlier: 4.066A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 148 through 151 Processing sheet with id= J, first strand: chain 'C' and resid 154 through 161 Processing sheet with id= K, first strand: chain 'C' and resid 332 through 336 removed outlier: 5.119A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 236 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 579 through 581 Processing sheet with id= M, first strand: chain 'C' and resid 634 through 638 Processing sheet with id= N, first strand: chain 'C' and resid 750 through 752 removed outlier: 6.044A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 798 through 803 Processing sheet with id= P, first strand: chain 'C' and resid 830 through 832 Processing sheet with id= Q, first strand: chain 'C' and resid 876 through 878 Processing sheet with id= R, first strand: chain 'C' and resid 887 through 889 Processing sheet with id= S, first strand: chain 'C' and resid 931 through 935 removed outlier: 6.692A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 816 through 818 removed outlier: 8.313A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 103 through 106 Processing sheet with id= V, first strand: chain 'D' and resid 351 through 354 Processing sheet with id= W, first strand: chain 'D' and resid 548 through 552 Processing sheet with id= X, first strand: chain 'D' and resid 820 through 822 Processing sheet with id= Y, first strand: chain 'D' and resid 957 through 959 removed outlier: 3.784A pdb=" N LYS D 959 " --> pdb=" O LYS D 983 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 965 through 967 Processing sheet with id= AA, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 4.012A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 1162 through 1165 Processing sheet with id= AC, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.695A pdb=" N VAL D 952 " --> pdb=" O THR D1016 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR D1016 " --> pdb=" O VAL D 952 " (cutoff:3.500A) 881 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 75 stacking parallelities Total time for adding SS restraints: 18.40 Time building geometry restraints manager: 38.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 28585 1.01 - 1.21: 27 1.21 - 1.41: 12044 1.41 - 1.61: 17793 1.61 - 1.81: 205 Bond restraints: 58654 Sorted by residual: bond pdb=" CA VAL D 997 " pdb=" C VAL D 997 " ideal model delta sigma weight residual 1.522 1.589 -0.067 7.10e-03 1.98e+04 8.97e+01 bond pdb=" CA PRO D 584 " pdb=" CB PRO D 584 " ideal model delta sigma weight residual 1.531 1.628 -0.097 1.22e-02 6.72e+03 6.27e+01 bond pdb=" C4 ATP 3 1 " pdb=" C5 ATP 3 1 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.06e+01 bond pdb=" C5 ATP 3 1 " pdb=" C6 ATP 3 1 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.63e+01 bond pdb=" C5 ATP 3 1 " pdb=" N7 ATP 3 1 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.94e+01 ... (remaining 58649 not shown) Histogram of bond angle deviations from ideal: 96.74 - 104.73: 1026 104.73 - 112.72: 68678 112.72 - 120.71: 21296 120.71 - 128.70: 15062 128.70 - 136.69: 306 Bond angle restraints: 106368 Sorted by residual: angle pdb=" PB ATP 3 1 " pdb=" O3B ATP 3 1 " pdb=" PG ATP 3 1 " ideal model delta sigma weight residual 139.87 117.42 22.45 1.00e+00 1.00e+00 5.04e+02 angle pdb=" PA ATP 3 1 " pdb=" O3A ATP 3 1 " pdb=" PB ATP 3 1 " ideal model delta sigma weight residual 136.83 118.77 18.06 1.00e+00 1.00e+00 3.26e+02 angle pdb=" C5 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N3 ATP 3 1 " ideal model delta sigma weight residual 126.80 116.96 9.84 1.00e+00 1.00e+00 9.68e+01 angle pdb=" N3 ATP 3 1 " pdb=" C4 ATP 3 1 " pdb=" N9 ATP 3 1 " ideal model delta sigma weight residual 127.04 136.69 -9.65 1.15e+00 7.59e-01 7.07e+01 angle pdb=" C LEU F 31 " pdb=" N GLN F 32 " pdb=" CA GLN F 32 " ideal model delta sigma weight residual 123.04 131.24 -8.20 1.08e+00 8.57e-01 5.76e+01 ... (remaining 106363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 22132 35.91 - 71.82: 736 71.82 - 107.73: 17 107.73 - 143.64: 1 143.64 - 179.56: 9 Dihedral angle restraints: 22895 sinusoidal: 11899 harmonic: 10996 Sorted by residual: dihedral pdb=" CA ASP D 67 " pdb=" C ASP D 67 " pdb=" N TYR D 68 " pdb=" CA TYR D 68 " ideal model delta harmonic sigma weight residual -180.00 -114.16 -65.84 0 5.00e+00 4.00e-02 1.73e+02 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual -180.00 -128.50 -51.50 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA GLU F 151 " pdb=" C GLU F 151 " pdb=" N GLU F 152 " pdb=" CA GLU F 152 " ideal model delta harmonic sigma weight residual -180.00 -130.72 -49.28 0 5.00e+00 4.00e-02 9.71e+01 ... (remaining 22892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 3736 0.076 - 0.151: 851 0.151 - 0.227: 84 0.227 - 0.303: 3 0.303 - 0.378: 1 Chirality restraints: 4675 Sorted by residual: chirality pdb=" CB VAL D 65 " pdb=" CA VAL D 65 " pdb=" CG1 VAL D 65 " pdb=" CG2 VAL D 65 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CG LEU C 971 " pdb=" CB LEU C 971 " pdb=" CD1 LEU C 971 " pdb=" CD2 LEU C 971 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU F 80 " pdb=" CB LEU F 80 " pdb=" CD1 LEU F 80 " pdb=" CD2 LEU F 80 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 4672 not shown) Planarity restraints: 8383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 68 " -0.018 2.00e-02 2.50e+03 3.71e-02 4.14e+01 pdb=" CG TYR D 68 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 68 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 68 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 68 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 68 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 68 " -0.080 2.00e-02 2.50e+03 pdb=" OH TYR D 68 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 TYR D 68 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR D 68 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR D 68 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR D 68 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 1 47 " 0.034 2.00e-02 2.50e+03 1.92e-02 1.10e+01 pdb=" N1 DT 1 47 " -0.038 2.00e-02 2.50e+03 pdb=" C2 DT 1 47 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT 1 47 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT 1 47 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT 1 47 " 0.023 2.00e-02 2.50e+03 pdb=" O4 DT 1 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DT 1 47 " 0.025 2.00e-02 2.50e+03 pdb=" C7 DT 1 47 " -0.023 2.00e-02 2.50e+03 pdb=" C6 DT 1 47 " -0.002 2.00e-02 2.50e+03 pdb=" H3 DT 1 47 " -0.001 2.00e-02 2.50e+03 pdb=" H6 DT 1 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 795 " -0.001 2.00e-02 2.50e+03 1.89e-02 1.07e+01 pdb=" CG TYR D 795 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR D 795 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR D 795 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR D 795 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 795 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D 795 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 795 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR D 795 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR D 795 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR D 795 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR D 795 " 0.001 2.00e-02 2.50e+03 ... (remaining 8380 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 2538 2.14 - 2.76: 114005 2.76 - 3.37: 162681 3.37 - 3.99: 205581 3.99 - 4.60: 315120 Nonbonded interactions: 799925 Sorted by model distance: nonbonded pdb=" HB3 LYS D 87 " pdb=" HZ3 LYS D 87 " model vdw 1.528 2.270 nonbonded pdb=" O GLU C 985 " pdb=" H LEU C 989 " model vdw 1.592 1.850 nonbonded pdb=" O ALA C 399 " pdb=" H MET C 403 " model vdw 1.600 1.850 nonbonded pdb=" O SER F 219 " pdb=" HG SER F 222 " model vdw 1.615 1.850 nonbonded pdb=" OE2 GLU A 214 " pdb=" HE ARG A 218 " model vdw 1.619 1.850 ... (remaining 799920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 113 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 18042 2.51 5 N 5218 2.21 5 O 5889 1.98 5 H 28609 0.53 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.920 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: 0.690 Extract box with map and model: 10.380 Check model and map are aligned: 0.660 Convert atoms to be neutral: 0.370 Process input model: 159.350 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4297 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 : 0.011 0.097 30045 Z= 0.701 Angle : 1.211 22.446 41067 Z= 0.709 Chirality : 0.061 0.378 4675 Planarity : 0.007 0.080 4992 Dihedral : 15.817 179.555 11671 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.36 % Favored : 89.29 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.30 % 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: -4.41 (0.11), residues: 3437 helix: -2.49 (0.11), residues: 1202 sheet: -3.35 (0.21), residues: 344 loop : -3.23 (0.12), residues: 1891 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 557 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 9 outliers final: 3 residues processed: 564 average time/residue: 0.9628 time to fit residues: 794.5890 Evaluate side-chains 375 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 372 time to evaluate : 3.395 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.1502 time to fit residues: 9.0531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 275 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 205 optimal weight: 0.7980 chunk 319 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 137 ASN A 186 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D 560 ASN ** E 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4328 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 30045 Z= 0.220 Angle : 0.723 9.454 41067 Z= 0.396 Chirality : 0.044 0.173 4675 Planarity : 0.005 0.066 4992 Dihedral : 18.351 176.113 4889 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.88 % Favored : 91.94 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.18 % 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: -3.41 (0.12), residues: 3437 helix: -1.34 (0.13), residues: 1223 sheet: -3.03 (0.22), residues: 346 loop : -2.83 (0.12), residues: 1868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 408 time to evaluate : 3.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 42 outliers final: 29 residues processed: 430 average time/residue: 0.9646 time to fit residues: 598.0782 Evaluate side-chains 387 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 358 time to evaluate : 3.426 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.5349 time to fit residues: 31.5887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 0.7980 chunk 99 optimal weight: 20.0000 chunk 266 optimal weight: 8.9990 chunk 217 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 320 optimal weight: 6.9990 chunk 345 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 317 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 256 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4501 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 30045 Z= 0.275 Angle : 0.707 9.169 41067 Z= 0.390 Chirality : 0.043 0.159 4675 Planarity : 0.005 0.062 4992 Dihedral : 18.116 175.571 4889 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.43 % Favored : 90.43 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.18 % 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: -3.08 (0.13), residues: 3437 helix: -1.02 (0.14), residues: 1241 sheet: -2.54 (0.23), residues: 375 loop : -2.74 (0.13), residues: 1821 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 355 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 39 outliers final: 30 residues processed: 377 average time/residue: 0.9875 time to fit residues: 537.7361 Evaluate side-chains 357 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 327 time to evaluate : 3.431 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5753 time to fit residues: 33.9177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 30.0000 chunk 240 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 152 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 321 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 304 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 725 GLN ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN D 665 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 GLN F 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4564 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 30045 Z= 0.242 Angle : 0.677 8.887 41067 Z= 0.371 Chirality : 0.043 0.149 4675 Planarity : 0.005 0.117 4992 Dihedral : 18.053 174.681 4889 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.32 % Favored : 91.53 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.18 % 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: -2.78 (0.13), residues: 3437 helix: -0.75 (0.14), residues: 1243 sheet: -2.21 (0.25), residues: 366 loop : -2.63 (0.13), residues: 1828 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 332 time to evaluate : 3.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 34 outliers final: 23 residues processed: 355 average time/residue: 0.9510 time to fit residues: 494.2541 Evaluate side-chains 336 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 313 time to evaluate : 3.419 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5648 time to fit residues: 26.7803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 253 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 305 optimal weight: 20.0000 chunk 85 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4683 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 30045 Z= 0.277 Angle : 0.693 10.144 41067 Z= 0.381 Chirality : 0.043 0.170 4675 Planarity : 0.005 0.062 4992 Dihedral : 18.029 176.028 4889 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.98 % Favored : 89.85 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.12 % 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: -2.79 (0.13), residues: 3437 helix: -0.72 (0.14), residues: 1229 sheet: -2.24 (0.24), residues: 384 loop : -2.64 (0.13), residues: 1824 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 320 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 34 residues processed: 356 average time/residue: 0.9189 time to fit residues: 480.4811 Evaluate side-chains 327 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 293 time to evaluate : 3.412 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 4 residues processed: 34 average time/residue: 0.5702 time to fit residues: 37.6685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 0.9990 chunk 306 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 340 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4688 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 30045 Z= 0.238 Angle : 0.661 8.093 41067 Z= 0.360 Chirality : 0.042 0.151 4675 Planarity : 0.005 0.064 4992 Dihedral : 17.933 175.593 4889 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.02 % Favored : 90.84 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % 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: -2.65 (0.13), residues: 3437 helix: -0.67 (0.14), residues: 1255 sheet: -2.02 (0.25), residues: 380 loop : -2.57 (0.13), residues: 1802 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 309 time to evaluate : 3.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 35 outliers final: 26 residues processed: 329 average time/residue: 0.9709 time to fit residues: 464.7745 Evaluate side-chains 318 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 292 time to evaluate : 3.436 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 5 residues processed: 26 average time/residue: 0.6614 time to fit residues: 32.3484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 194 optimal weight: 0.1980 chunk 248 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 286 optimal weight: 10.0000 chunk 190 optimal weight: 0.6980 chunk 339 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 206 optimal weight: 1.9990 chunk 156 optimal weight: 9.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4634 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 30045 Z= 0.183 Angle : 0.616 7.922 41067 Z= 0.334 Chirality : 0.042 0.160 4675 Planarity : 0.004 0.072 4992 Dihedral : 17.813 175.205 4889 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.77 % Favored : 92.09 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.09 % 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: -2.28 (0.14), residues: 3437 helix: -0.28 (0.15), residues: 1247 sheet: -1.88 (0.25), residues: 391 loop : -2.40 (0.13), residues: 1799 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 301 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 23 outliers final: 19 residues processed: 314 average time/residue: 0.9642 time to fit residues: 445.2413 Evaluate side-chains 307 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 288 time to evaluate : 4.230 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 19 average time/residue: 0.6058 time to fit residues: 24.2649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 209 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 202 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 266 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.125 30045 Z= 0.267 Angle : 0.671 11.881 41067 Z= 0.368 Chirality : 0.042 0.174 4675 Planarity : 0.005 0.076 4992 Dihedral : 17.812 176.551 4889 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 23.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.27 % Favored : 89.58 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % 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: -2.47 (0.13), residues: 3437 helix: -0.55 (0.14), residues: 1248 sheet: -1.85 (0.26), residues: 377 loop : -2.45 (0.13), residues: 1812 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 284 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 33 outliers final: 24 residues processed: 297 average time/residue: 0.9359 time to fit residues: 409.0017 Evaluate side-chains 299 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 275 time to evaluate : 3.427 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 5 residues processed: 24 average time/residue: 0.5625 time to fit residues: 27.8064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 308 optimal weight: 8.9990 chunk 325 optimal weight: 3.9990 chunk 296 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 137 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 299 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1099 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4739 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 30045 Z= 0.219 Angle : 0.637 9.260 41067 Z= 0.346 Chirality : 0.042 0.152 4675 Planarity : 0.005 0.060 4992 Dihedral : 17.782 175.438 4889 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.64 % Favored : 91.24 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.47 % Twisted General : 0.09 % 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: -2.34 (0.13), residues: 3437 helix: -0.47 (0.14), residues: 1265 sheet: -1.79 (0.26), residues: 378 loop : -2.36 (0.13), residues: 1794 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 279 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 17 outliers final: 15 residues processed: 290 average time/residue: 0.9663 time to fit residues: 412.3096 Evaluate side-chains 291 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 276 time to evaluate : 3.413 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 15 average time/residue: 0.6219 time to fit residues: 20.0020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 158 optimal weight: 0.7980 chunk 232 optimal weight: 8.9990 chunk 350 optimal weight: 8.9990 chunk 322 optimal weight: 0.3980 chunk 279 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4664 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.163 30045 Z= 0.189 Angle : 0.616 9.603 41067 Z= 0.332 Chirality : 0.042 0.174 4675 Planarity : 0.004 0.089 4992 Dihedral : 17.690 175.068 4889 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.51 % Favored : 92.38 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % 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: -1.98 (0.14), residues: 3437 helix: -0.04 (0.15), residues: 1251 sheet: -1.67 (0.25), residues: 391 loop : -2.23 (0.14), residues: 1795 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 294 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 10 outliers final: 10 residues processed: 298 average time/residue: 0.9788 time to fit residues: 428.5467 Evaluate side-chains 288 residues out of total 2944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 278 time to evaluate : 3.414 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 10 average time/residue: 0.6605 time to fit residues: 15.2093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 171 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 257 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.069818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.053211 restraints weight = 794594.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.055342 restraints weight = 476542.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.056808 restraints weight = 333296.949| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.128 30045 Z= 0.231 Angle : 0.634 11.501 41067 Z= 0.346 Chirality : 0.042 0.192 4675 Planarity : 0.005 0.100 4992 Dihedral : 17.700 175.903 4889 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.19 % Favored : 90.69 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.09 % 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: -2.17 (0.14), residues: 3437 helix: -0.29 (0.14), residues: 1273 sheet: -1.75 (0.25), residues: 393 loop : -2.29 (0.14), residues: 1771 =============================================================================== Job complete usr+sys time: 10544.77 seconds wall clock time: 183 minutes 42.64 seconds (11022.64 seconds total)