Starting phenix.real_space_refine on Wed Mar 4 11:43:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w01_32233/03_2026/7w01_32233.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w01_32233/03_2026/7w01_32233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w01_32233/03_2026/7w01_32233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w01_32233/03_2026/7w01_32233.map" model { file = "/net/cci-nas-00/data/ceres_data/7w01_32233/03_2026/7w01_32233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w01_32233/03_2026/7w01_32233.cif" } resolution = 3.3 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 8287 2.51 5 N 2114 2.21 5 O 2251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12724 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1598, 12556 Classifications: {'peptide': 1598} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 74, 'TRANS': 1523} Chain breaks: 5 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 168 Unusual residues: {'NAG': 2, 'POV': 3, 'PX4': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 2.78, per 1000 atoms: 0.22 Number of scatterers: 12724 At special positions: 0 Unit cell: (102.6, 142.56, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 P 2 15.00 O 2251 8.00 N 2114 7.00 C 8287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1274 " - pdb=" SG CYS A1284 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1801 " - " ASN A 124 " " NAG A1802 " - " ASN A 140 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 515.1 milliseconds 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2992 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 48.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 3.548A pdb=" N ALA A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 11 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 13 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.549A pdb=" N THR A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 122 removed outlier: 4.137A pdb=" N ARG A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 225 Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.560A pdb=" N GLN A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 272 removed outlier: 4.728A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Proline residue: A 264 - end of helix removed outlier: 3.663A pdb=" N SER A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.569A pdb=" N ARG A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 302 through 328 removed outlier: 3.560A pdb=" N LEU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 365 removed outlier: 3.673A pdb=" N VAL A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 379 through 385 removed outlier: 4.141A pdb=" N PHE A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 410 through 427 removed outlier: 3.610A pdb=" N ALA A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 474 removed outlier: 4.013A pdb=" N LEU A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 472 " --> pdb=" O TRP A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 Processing helix chain 'A' and resid 600 through 605 removed outlier: 3.657A pdb=" N ILE A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 removed outlier: 3.810A pdb=" N LEU A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 628 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 632 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 Processing helix chain 'A' and resid 669 through 679 removed outlier: 3.541A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 679 " --> pdb=" O ILE A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 710 removed outlier: 3.784A pdb=" N ILE A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 729 removed outlier: 3.531A pdb=" N LEU A 729 " --> pdb=" O GLU A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.695A pdb=" N LYS A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.552A pdb=" N ILE A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 775 " --> pdb=" O GLU A 771 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 803 removed outlier: 4.029A pdb=" N THR A 803 " --> pdb=" O ARG A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 816 removed outlier: 3.796A pdb=" N LYS A 815 " --> pdb=" O ALA A 811 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 816 " --> pdb=" O LYS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 843 removed outlier: 3.839A pdb=" N VAL A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 917 removed outlier: 4.079A pdb=" N HIS A 904 " --> pdb=" O GLY A 900 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 915 " --> pdb=" O MET A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 943 removed outlier: 4.044A pdb=" N LEU A 934 " --> pdb=" O VAL A 930 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA A 940 " --> pdb=" O CYS A 936 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 943 " --> pdb=" O LEU A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 988 Processing helix chain 'A' and resid 1005 through 1015 removed outlier: 3.560A pdb=" N ILE A1009 " --> pdb=" O GLU A1005 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A1013 " --> pdb=" O ILE A1009 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL A1014 " --> pdb=" O PHE A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1023 Processing helix chain 'A' and resid 1048 through 1065 removed outlier: 3.615A pdb=" N THR A1052 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1090 removed outlier: 3.501A pdb=" N ALA A1087 " --> pdb=" O ALA A1083 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.640A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A1103 " --> pdb=" O ASP A1099 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1104 " --> pdb=" O ILE A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1116 removed outlier: 3.880A pdb=" N PHE A1115 " --> pdb=" O ALA A1112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A1116 " --> pdb=" O SER A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1125 removed outlier: 3.902A pdb=" N ARG A1123 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A1125 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1134 removed outlier: 3.804A pdb=" N VAL A1130 " --> pdb=" O GLN A1126 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A1131 " --> pdb=" O ALA A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 3.935A pdb=" N TRP A1142 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A1144 " --> pdb=" O SER A1140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1145 " --> pdb=" O PHE A1141 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A1147 " --> pdb=" O LEU A1143 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1167 removed outlier: 4.490A pdb=" N LEU A1161 " --> pdb=" O SER A1157 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1163 " --> pdb=" O LEU A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1173 removed outlier: 3.582A pdb=" N PHE A1172 " --> pdb=" O VAL A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1199 removed outlier: 3.859A pdb=" N LEU A1182 " --> pdb=" O MET A1178 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A1184 " --> pdb=" O ASP A1180 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) Proline residue: A1194 - end of helix Processing helix chain 'A' and resid 1200 through 1203 Processing helix chain 'A' and resid 1205 through 1230 removed outlier: 3.914A pdb=" N TYR A1210 " --> pdb=" O ALA A1206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A1211 " --> pdb=" O ALA A1207 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A1215 " --> pdb=" O THR A1211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1223 " --> pdb=" O LEU A1219 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR A1224 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A1228 " --> pdb=" O THR A1224 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A1230 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1249 removed outlier: 3.573A pdb=" N HIS A1247 " --> pdb=" O LYS A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1274 removed outlier: 3.518A pdb=" N MET A1259 " --> pdb=" O HIS A1255 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A1260 " --> pdb=" O CYS A1256 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A1263 " --> pdb=" O MET A1259 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A1274 " --> pdb=" O THR A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1288 Processing helix chain 'A' and resid 1306 through 1311 Processing helix chain 'A' and resid 1315 through 1326 removed outlier: 3.799A pdb=" N ILE A1319 " --> pdb=" O CYS A1315 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A1320 " --> pdb=" O ALA A1316 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1368 removed outlier: 3.513A pdb=" N ILE A1368 " --> pdb=" O GLU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1421 through 1430 removed outlier: 3.595A pdb=" N THR A1425 " --> pdb=" O GLY A1421 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A1426 " --> pdb=" O LYS A1422 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS A1427 " --> pdb=" O THR A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1483 removed outlier: 3.820A pdb=" N LEU A1477 " --> pdb=" O GLY A1473 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A1480 " --> pdb=" O MET A1476 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1502 removed outlier: 3.696A pdb=" N THR A1498 " --> pdb=" O CYS A1494 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A1500 " --> pdb=" O GLU A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1504 through 1508 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.663A pdb=" N THR A1525 " --> pdb=" O ARG A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1563 removed outlier: 3.861A pdb=" N THR A1556 " --> pdb=" O LEU A1552 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A1561 " --> pdb=" O VAL A1557 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1580 removed outlier: 3.539A pdb=" N ALA A1579 " --> pdb=" O GLU A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1597 through 1606 Processing helix chain 'A' and resid 1619 through 1634 removed outlier: 5.252A pdb=" N GLU A1625 " --> pdb=" O GLN A1621 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A1626 " --> pdb=" O GLU A1622 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1673 removed outlier: 4.685A pdb=" N GLU A1671 " --> pdb=" O GLU A1667 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS A1672 " --> pdb=" O LYS A1668 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A1673 " --> pdb=" O ALA A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1690 Processing helix chain 'A' and resid 1691 through 1696 removed outlier: 4.070A pdb=" N HIS A1694 " --> pdb=" O SER A1691 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A1696 " --> pdb=" O ALA A1693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.587A pdb=" N THR A 241 " --> pdb=" O VAL A1038 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG A1035 " --> pdb=" O VAL A1032 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A1037 " --> pdb=" O ARG A1030 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 109 removed outlier: 3.546A pdb=" N ARG A 108 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLU A 79 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA A 132 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA A 81 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 151 Processing sheet with id=AA4, first strand: chain 'A' and resid 555 through 557 removed outlier: 6.803A pdb=" N LEU A 556 " --> pdb=" O GLY A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 535 through 537 removed outlier: 7.413A pdb=" N LYS A 537 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ARG A 550 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 609 through 611 removed outlier: 6.916A pdb=" N GLY A 609 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU A 686 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN A 560 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 718 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR A 562 " --> pdb=" O LEU A 718 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 561 " --> pdb=" O ARG A 732 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N ALA A 734 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 563 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET A 736 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A 743 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 786 through 788 removed outlier: 3.627A pdb=" N SER A 788 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1387 through 1391 removed outlier: 6.524A pdb=" N LYS A1388 " --> pdb=" O ALA A1398 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A1396 " --> pdb=" O TYR A1390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1410 through 1412 Processing sheet with id=AB1, first strand: chain 'A' and resid 1415 through 1416 removed outlier: 6.871A pdb=" N LEU A1415 " --> pdb=" O MET A1587 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A1591 " --> pdb=" O VAL A1588 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1441 through 1442 removed outlier: 3.903A pdb=" N HIS A1445 " --> pdb=" O VAL A1442 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1614 through 1615 removed outlier: 3.743A pdb=" N ASP A1677 " --> pdb=" O LYS A1614 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3948 1.34 - 1.46: 2625 1.46 - 1.58: 6334 1.58 - 1.70: 4 1.70 - 1.82: 115 Bond restraints: 13026 Sorted by residual: bond pdb=" C29 POV A1806 " pdb="C210 POV A1806 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C29 POV A1805 " pdb="C210 POV A1805 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" C29 POV A1807 " pdb="C210 POV A1807 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" C9 PX4 A1804 " pdb=" O5 PX4 A1804 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 bond pdb=" C9 PX4 A1803 " pdb=" O5 PX4 A1803 " ideal model delta sigma weight residual 1.327 1.453 -0.126 2.00e-02 2.50e+03 3.98e+01 ... (remaining 13021 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 17343 3.40 - 6.81: 247 6.81 - 10.21: 29 10.21 - 13.61: 2 13.61 - 17.02: 7 Bond angle restraints: 17628 Sorted by residual: angle pdb=" C ILE A1233 " pdb=" N PRO A1234 " pdb=" CA PRO A1234 " ideal model delta sigma weight residual 119.84 128.00 -8.16 1.25e+00 6.40e-01 4.26e+01 angle pdb=" N ARG A 155 " pdb=" CA ARG A 155 " pdb=" C ARG A 155 " ideal model delta sigma weight residual 110.80 123.93 -13.13 2.13e+00 2.20e-01 3.80e+01 angle pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N PHE A 156 " ideal model delta sigma weight residual 116.84 127.00 -10.16 1.71e+00 3.42e-01 3.53e+01 angle pdb=" C28 POV A1806 " pdb=" C29 POV A1806 " pdb="C210 POV A1806 " ideal model delta sigma weight residual 127.79 110.77 17.02 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C28 POV A1807 " pdb=" C29 POV A1807 " pdb="C210 POV A1807 " ideal model delta sigma weight residual 127.79 110.91 16.88 3.00e+00 1.11e-01 3.17e+01 ... (remaining 17623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 7560 33.87 - 67.73: 206 67.73 - 101.60: 23 101.60 - 135.47: 7 135.47 - 169.34: 1 Dihedral angle restraints: 7797 sinusoidal: 3161 harmonic: 4636 Sorted by residual: dihedral pdb=" CA ARG A 155 " pdb=" C ARG A 155 " pdb=" N PHE A 156 " pdb=" CA PHE A 156 " ideal model delta harmonic sigma weight residual 180.00 126.71 53.29 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ASN A 140 " pdb=" C ASN A 140 " pdb=" N HIS A 141 " pdb=" CA HIS A 141 " ideal model delta harmonic sigma weight residual -180.00 -136.79 -43.21 0 5.00e+00 4.00e-02 7.47e+01 dihedral pdb=" CA PHE A 156 " pdb=" C PHE A 156 " pdb=" N SER A 157 " pdb=" CA SER A 157 " ideal model delta harmonic sigma weight residual 180.00 147.42 32.58 0 5.00e+00 4.00e-02 4.25e+01 ... (remaining 7794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1934 0.134 - 0.269: 45 0.269 - 0.403: 1 0.403 - 0.537: 0 0.537 - 0.672: 1 Chirality restraints: 1981 Sorted by residual: chirality pdb=" CA PHE A 156 " pdb=" N PHE A 156 " pdb=" C PHE A 156 " pdb=" CB PHE A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA PHE A1172 " pdb=" N PHE A1172 " pdb=" C PHE A1172 " pdb=" CB PHE A1172 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C7 PX4 A1804 " pdb=" C6 PX4 A1804 " pdb=" C8 PX4 A1804 " pdb=" O7 PX4 A1804 " both_signs ideal model delta sigma weight residual False -2.31 -2.55 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1978 not shown) Planarity restraints: 2218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1805 " 0.159 2.00e-02 2.50e+03 3.23e-01 1.04e+03 pdb=" C29 POV A1805 " -0.428 2.00e-02 2.50e+03 pdb="C210 POV A1805 " 0.428 2.00e-02 2.50e+03 pdb="C211 POV A1805 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1806 " -0.321 2.00e-02 2.50e+03 3.22e-01 1.04e+03 pdb=" C29 POV A1806 " 0.317 2.00e-02 2.50e+03 pdb="C210 POV A1806 " 0.328 2.00e-02 2.50e+03 pdb="C211 POV A1806 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1807 " -0.102 2.00e-02 2.50e+03 1.03e-01 1.05e+02 pdb=" C29 POV A1807 " 0.101 2.00e-02 2.50e+03 pdb="C210 POV A1807 " 0.104 2.00e-02 2.50e+03 pdb="C211 POV A1807 " -0.103 2.00e-02 2.50e+03 ... (remaining 2215 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 19 2.35 - 2.99: 6685 2.99 - 3.63: 16998 3.63 - 4.26: 26611 4.26 - 4.90: 45763 Nonbonded interactions: 96076 Sorted by model distance: nonbonded pdb=" O VAL A 968 " pdb=" O GLN A 995 " model vdw 1.717 3.040 nonbonded pdb=" O THR A 966 " pdb=" CB GLU A 993 " model vdw 2.030 3.440 nonbonded pdb=" NE2 GLN A 613 " pdb=" OE1 GLU A 690 " model vdw 2.074 3.120 nonbonded pdb=" OD2 ASP A1149 " pdb=" OH TYR A1197 " model vdw 2.076 3.040 nonbonded pdb=" O LYS A 711 " pdb=" N ASP A 713 " model vdw 2.202 3.120 ... (remaining 96071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 0.190 13029 Z= 0.493 Angle : 1.112 17.015 17636 Z= 0.579 Chirality : 0.060 0.672 1981 Planarity : 0.011 0.323 2216 Dihedral : 16.667 169.336 4802 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.76 % Allowed : 13.30 % Favored : 85.94 % Rotamer: Outliers : 0.60 % Allowed : 0.75 % Favored : 98.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.19), residues: 1586 helix: -2.52 (0.16), residues: 794 sheet: -3.42 (0.41), residues: 134 loop : -3.47 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 340 TYR 0.025 0.002 TYR A 122 PHE 0.087 0.003 PHE A 156 TRP 0.021 0.003 TRP A 920 HIS 0.020 0.002 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.01143 (13026) covalent geometry : angle 1.10636 (17628) SS BOND : bond 0.00131 ( 1) SS BOND : angle 3.61280 ( 2) hydrogen bonds : bond 0.21888 ( 422) hydrogen bonds : angle 7.04624 ( 1224) link_NAG-ASN : bond 0.00678 ( 2) link_NAG-ASN : angle 5.89162 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.406 Fit side-chains REVERT: A 377 PHE cc_start: 0.8685 (t80) cc_final: 0.8337 (t80) REVERT: A 398 TRP cc_start: 0.8003 (m100) cc_final: 0.7245 (m-10) REVERT: A 1019 PHE cc_start: 0.6976 (OUTLIER) cc_final: 0.6034 (t80) REVERT: A 1030 ARG cc_start: 0.6702 (tmm160) cc_final: 0.6480 (tmm-80) REVERT: A 1095 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6211 (tpt170) REVERT: A 1231 MET cc_start: 0.7807 (tpp) cc_final: 0.7469 (ttm) REVERT: A 1310 MET cc_start: 0.8552 (mtm) cc_final: 0.8296 (mtm) outliers start: 8 outliers final: 5 residues processed: 168 average time/residue: 0.1345 time to fit residues: 30.9018 Evaluate side-chains 138 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1240 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1490 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100464 restraints weight = 17649.974| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.12 r_work: 0.2821 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13029 Z= 0.131 Angle : 0.720 12.463 17636 Z= 0.363 Chirality : 0.044 0.218 1981 Planarity : 0.005 0.076 2216 Dihedral : 13.012 171.086 1901 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.77 % Favored : 89.85 % Rotamer: Outliers : 1.27 % Allowed : 7.39 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.19), residues: 1586 helix: -1.92 (0.17), residues: 798 sheet: -3.08 (0.42), residues: 134 loop : -3.15 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 838 TYR 0.026 0.001 TYR A1283 PHE 0.052 0.001 PHE A 156 TRP 0.020 0.001 TRP A 923 HIS 0.006 0.001 HIS A 86 Details of bonding type rmsd covalent geometry : bond 0.00277 (13026) covalent geometry : angle 0.71245 (17628) SS BOND : bond 0.00433 ( 1) SS BOND : angle 3.21785 ( 2) hydrogen bonds : bond 0.04528 ( 422) hydrogen bonds : angle 4.64645 ( 1224) link_NAG-ASN : bond 0.00983 ( 2) link_NAG-ASN : angle 5.53584 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.479 Fit side-chains REVERT: A 370 LYS cc_start: 0.8776 (mttt) cc_final: 0.8184 (mptt) REVERT: A 387 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8960 (mt) REVERT: A 398 TRP cc_start: 0.8016 (m100) cc_final: 0.6936 (m-10) REVERT: A 1019 PHE cc_start: 0.6666 (OUTLIER) cc_final: 0.5820 (t80) REVERT: A 1030 ARG cc_start: 0.6154 (tmm160) cc_final: 0.5860 (tmm-80) REVERT: A 1240 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6157 (tt0) outliers start: 17 outliers final: 9 residues processed: 162 average time/residue: 0.1175 time to fit residues: 27.4096 Evaluate side-chains 146 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1656 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 91 optimal weight: 20.0000 chunk 116 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101769 restraints weight = 17788.580| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.23 r_work: 0.2778 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13029 Z= 0.143 Angle : 0.669 11.970 17636 Z= 0.333 Chirality : 0.044 0.205 1981 Planarity : 0.005 0.077 2216 Dihedral : 11.862 179.214 1893 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.40 % Favored : 89.28 % Rotamer: Outliers : 2.39 % Allowed : 9.86 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.20), residues: 1586 helix: -1.43 (0.18), residues: 803 sheet: -2.92 (0.42), residues: 134 loop : -3.01 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 957 TYR 0.025 0.001 TYR A1283 PHE 0.029 0.001 PHE A 156 TRP 0.026 0.001 TRP A 923 HIS 0.007 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00339 (13026) covalent geometry : angle 0.66143 (17628) SS BOND : bond 0.01594 ( 1) SS BOND : angle 1.84996 ( 2) hydrogen bonds : bond 0.04172 ( 422) hydrogen bonds : angle 4.29318 ( 1224) link_NAG-ASN : bond 0.01058 ( 2) link_NAG-ASN : angle 5.26529 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.458 Fit side-chains REVERT: A 220 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7481 (mtm-85) REVERT: A 370 LYS cc_start: 0.8835 (mttt) cc_final: 0.8483 (mtmm) REVERT: A 387 ILE cc_start: 0.9266 (mm) cc_final: 0.8991 (mt) REVERT: A 398 TRP cc_start: 0.7981 (m100) cc_final: 0.6924 (m-10) REVERT: A 430 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7468 (mtm) REVERT: A 762 LEU cc_start: 0.8632 (mt) cc_final: 0.8351 (mp) REVERT: A 1019 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5860 (t80) REVERT: A 1030 ARG cc_start: 0.6112 (tmm160) cc_final: 0.5848 (tmm-80) REVERT: A 1065 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6579 (pt) REVERT: A 1095 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6086 (tpt170) REVERT: A 1172 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.6808 (p90) REVERT: A 1231 MET cc_start: 0.8326 (tpp) cc_final: 0.7339 (ttm) REVERT: A 1232 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8026 (mtm180) REVERT: A 1240 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6238 (tt0) REVERT: A 1433 GLU cc_start: 0.8585 (tp30) cc_final: 0.8070 (tp30) REVERT: A 1647 MET cc_start: 0.7400 (mtm) cc_final: 0.7200 (mtp) REVERT: A 1686 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8347 (tm-30) outliers start: 32 outliers final: 16 residues processed: 169 average time/residue: 0.1264 time to fit residues: 29.9857 Evaluate side-chains 155 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1656 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 108 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 46 optimal weight: 0.4980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103752 restraints weight = 17680.803| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.19 r_work: 0.2816 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13029 Z= 0.104 Angle : 0.625 12.707 17636 Z= 0.308 Chirality : 0.042 0.200 1981 Planarity : 0.004 0.071 2216 Dihedral : 11.293 177.425 1893 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.95 % Favored : 90.73 % Rotamer: Outliers : 2.61 % Allowed : 11.95 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.21), residues: 1586 helix: -1.01 (0.19), residues: 791 sheet: -2.35 (0.43), residues: 132 loop : -2.97 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 155 TYR 0.027 0.001 TYR A1283 PHE 0.019 0.001 PHE A 156 TRP 0.022 0.001 TRP A 923 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00230 (13026) covalent geometry : angle 0.61791 (17628) SS BOND : bond 0.00515 ( 1) SS BOND : angle 1.32931 ( 2) hydrogen bonds : bond 0.03278 ( 422) hydrogen bonds : angle 4.08442 ( 1224) link_NAG-ASN : bond 0.01064 ( 2) link_NAG-ASN : angle 5.09374 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.319 Fit side-chains REVERT: A 220 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: A 370 LYS cc_start: 0.8798 (mttt) cc_final: 0.8431 (mtpp) REVERT: A 387 ILE cc_start: 0.9286 (mm) cc_final: 0.9022 (mt) REVERT: A 398 TRP cc_start: 0.7924 (m100) cc_final: 0.6785 (m-10) REVERT: A 595 TYR cc_start: 0.8057 (m-10) cc_final: 0.7836 (m-10) REVERT: A 985 HIS cc_start: 0.8191 (m170) cc_final: 0.7773 (m90) REVERT: A 1019 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.5897 (t80) REVERT: A 1030 ARG cc_start: 0.6065 (tmm160) cc_final: 0.5797 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6613 (pt) REVERT: A 1095 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.5913 (tpt170) REVERT: A 1231 MET cc_start: 0.8455 (tpp) cc_final: 0.7411 (ttm) REVERT: A 1232 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8103 (mtm180) REVERT: A 1433 GLU cc_start: 0.8666 (tp30) cc_final: 0.8243 (tp30) REVERT: A 1647 MET cc_start: 0.7387 (mtm) cc_final: 0.7185 (mtp) REVERT: A 1686 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8389 (tm-30) outliers start: 35 outliers final: 21 residues processed: 184 average time/residue: 0.1193 time to fit residues: 31.2349 Evaluate side-chains 167 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 18 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 149 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 GLN A1294 ASN A1687 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.136455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101649 restraints weight = 17862.736| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.33 r_work: 0.2775 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13029 Z= 0.137 Angle : 0.633 12.704 17636 Z= 0.313 Chirality : 0.042 0.184 1981 Planarity : 0.005 0.066 2216 Dihedral : 11.002 175.883 1888 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.46 % Favored : 90.23 % Rotamer: Outliers : 2.84 % Allowed : 13.29 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.21), residues: 1586 helix: -0.83 (0.19), residues: 792 sheet: -2.30 (0.45), residues: 128 loop : -2.89 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 957 TYR 0.016 0.001 TYR A 119 PHE 0.022 0.001 PHE A 156 TRP 0.020 0.001 TRP A 923 HIS 0.007 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00330 (13026) covalent geometry : angle 0.62690 (17628) SS BOND : bond 0.00542 ( 1) SS BOND : angle 1.28959 ( 2) hydrogen bonds : bond 0.03636 ( 422) hydrogen bonds : angle 4.03966 ( 1224) link_NAG-ASN : bond 0.00974 ( 2) link_NAG-ASN : angle 4.91066 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.367 Fit side-chains REVERT: A 370 LYS cc_start: 0.8804 (mttt) cc_final: 0.8401 (mtpp) REVERT: A 387 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9032 (mt) REVERT: A 398 TRP cc_start: 0.7928 (m100) cc_final: 0.6788 (m-10) REVERT: A 430 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7507 (mtm) REVERT: A 595 TYR cc_start: 0.8041 (m-10) cc_final: 0.7808 (m-10) REVERT: A 1019 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.5962 (t80) REVERT: A 1030 ARG cc_start: 0.6028 (tmm160) cc_final: 0.5754 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6717 (pt) REVERT: A 1095 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6004 (tpt170) REVERT: A 1099 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.8984 (t70) REVERT: A 1172 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.6666 (p90) REVERT: A 1433 GLU cc_start: 0.8736 (tp30) cc_final: 0.8322 (tp30) REVERT: A 1621 GLN cc_start: 0.8409 (mm-40) cc_final: 0.7809 (pt0) REVERT: A 1647 MET cc_start: 0.7469 (mtm) cc_final: 0.7254 (mtp) REVERT: A 1686 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8402 (tm-30) outliers start: 38 outliers final: 24 residues processed: 172 average time/residue: 0.1186 time to fit residues: 29.1211 Evaluate side-chains 166 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1238 LEU Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 33 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 109 optimal weight: 0.0030 chunk 81 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104100 restraints weight = 17534.254| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.15 r_work: 0.2840 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13029 Z= 0.102 Angle : 0.604 12.237 17636 Z= 0.298 Chirality : 0.041 0.174 1981 Planarity : 0.004 0.064 2216 Dihedral : 10.733 179.863 1888 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.58 % Favored : 91.11 % Rotamer: Outliers : 2.91 % Allowed : 14.12 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.21), residues: 1586 helix: -0.54 (0.19), residues: 792 sheet: -1.99 (0.44), residues: 142 loop : -2.92 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 155 TYR 0.013 0.001 TYR A1287 PHE 0.017 0.001 PHE A 156 TRP 0.020 0.001 TRP A 923 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00224 (13026) covalent geometry : angle 0.59795 (17628) SS BOND : bond 0.00636 ( 1) SS BOND : angle 1.07362 ( 2) hydrogen bonds : bond 0.02925 ( 422) hydrogen bonds : angle 3.91383 ( 1224) link_NAG-ASN : bond 0.00898 ( 2) link_NAG-ASN : angle 4.58684 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.435 Fit side-chains REVERT: A 220 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7135 (mtm-85) REVERT: A 370 LYS cc_start: 0.8764 (mttt) cc_final: 0.8094 (mptt) REVERT: A 387 ILE cc_start: 0.9283 (mm) cc_final: 0.9042 (mt) REVERT: A 398 TRP cc_start: 0.7805 (m100) cc_final: 0.6700 (m-10) REVERT: A 595 TYR cc_start: 0.8036 (m-10) cc_final: 0.7832 (m-10) REVERT: A 666 SER cc_start: 0.7631 (OUTLIER) cc_final: 0.7312 (m) REVERT: A 1019 PHE cc_start: 0.6591 (OUTLIER) cc_final: 0.5997 (t80) REVERT: A 1030 ARG cc_start: 0.6023 (tmm160) cc_final: 0.5741 (tmm-80) REVERT: A 1065 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6682 (pt) REVERT: A 1095 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.5972 (tpt170) REVERT: A 1099 ASP cc_start: 0.9256 (OUTLIER) cc_final: 0.8942 (t0) REVERT: A 1172 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6587 (p90) REVERT: A 1231 MET cc_start: 0.8448 (tpp) cc_final: 0.7312 (ttm) REVERT: A 1433 GLU cc_start: 0.8759 (tp30) cc_final: 0.8454 (tp30) REVERT: A 1686 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8318 (tm-30) outliers start: 39 outliers final: 23 residues processed: 185 average time/residue: 0.1182 time to fit residues: 30.9797 Evaluate side-chains 169 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 133 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 85 optimal weight: 0.0980 chunk 141 optimal weight: 0.0970 chunk 145 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 742 GLN ** 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 = 0.3624 r_free = 0.3624 target = 0.141180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104556 restraints weight = 17563.073| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.20 r_work: 0.2847 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13029 Z= 0.095 Angle : 0.596 11.802 17636 Z= 0.291 Chirality : 0.040 0.168 1981 Planarity : 0.004 0.061 2216 Dihedral : 10.381 175.059 1886 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.45 % Favored : 91.30 % Rotamer: Outliers : 2.84 % Allowed : 14.79 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.21), residues: 1586 helix: -0.28 (0.19), residues: 792 sheet: -1.85 (0.44), residues: 142 loop : -2.85 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 957 TYR 0.013 0.001 TYR A 396 PHE 0.012 0.001 PHE A 156 TRP 0.022 0.001 TRP A 923 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00209 (13026) covalent geometry : angle 0.59046 (17628) SS BOND : bond 0.00506 ( 1) SS BOND : angle 0.67410 ( 2) hydrogen bonds : bond 0.02760 ( 422) hydrogen bonds : angle 3.79912 ( 1224) link_NAG-ASN : bond 0.00807 ( 2) link_NAG-ASN : angle 4.25105 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.402 Fit side-chains REVERT: A 86 HIS cc_start: 0.7274 (p-80) cc_final: 0.6968 (p90) REVERT: A 136 GLU cc_start: 0.5850 (OUTLIER) cc_final: 0.5569 (mp0) REVERT: A 370 LYS cc_start: 0.8769 (mttt) cc_final: 0.8354 (mtmm) REVERT: A 387 ILE cc_start: 0.9280 (mm) cc_final: 0.9046 (mt) REVERT: A 398 TRP cc_start: 0.7755 (m100) cc_final: 0.7079 (m-10) REVERT: A 643 GLU cc_start: 0.7774 (pm20) cc_final: 0.7373 (pm20) REVERT: A 644 GLU cc_start: 0.7471 (mp0) cc_final: 0.6697 (mp0) REVERT: A 666 SER cc_start: 0.7707 (OUTLIER) cc_final: 0.7408 (m) REVERT: A 1019 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.6038 (t80) REVERT: A 1030 ARG cc_start: 0.6004 (tmm160) cc_final: 0.5707 (tmm-80) REVERT: A 1065 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6611 (pt) REVERT: A 1095 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.5933 (tpt170) REVERT: A 1099 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.9000 (t0) REVERT: A 1172 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.6472 (p90) REVERT: A 1231 MET cc_start: 0.8414 (tpp) cc_final: 0.7305 (ttm) REVERT: A 1392 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6795 (pp30) REVERT: A 1433 GLU cc_start: 0.8771 (tp30) cc_final: 0.8429 (tp30) REVERT: A 1686 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8304 (tm-30) outliers start: 38 outliers final: 22 residues processed: 187 average time/residue: 0.1193 time to fit residues: 32.0353 Evaluate side-chains 178 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1392 GLN Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 HIS A1076 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.138834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.098808 restraints weight = 17507.604| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.14 r_work: 0.2826 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13029 Z= 0.124 Angle : 0.618 11.589 17636 Z= 0.303 Chirality : 0.042 0.149 1981 Planarity : 0.004 0.060 2216 Dihedral : 10.303 168.804 1886 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.08 % Favored : 90.67 % Rotamer: Outliers : 2.69 % Allowed : 15.24 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.21), residues: 1586 helix: -0.22 (0.19), residues: 789 sheet: -1.84 (0.44), residues: 143 loop : -2.77 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 957 TYR 0.010 0.001 TYR A 595 PHE 0.015 0.001 PHE A 349 TRP 0.022 0.001 TRP A 923 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00296 (13026) covalent geometry : angle 0.61333 (17628) SS BOND : bond 0.00505 ( 1) SS BOND : angle 0.90876 ( 2) hydrogen bonds : bond 0.03259 ( 422) hydrogen bonds : angle 3.81840 ( 1224) link_NAG-ASN : bond 0.00702 ( 2) link_NAG-ASN : angle 4.01224 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.498 Fit side-chains REVERT: A 86 HIS cc_start: 0.7231 (p-80) cc_final: 0.6926 (p90) REVERT: A 251 ILE cc_start: 0.8300 (mt) cc_final: 0.8084 (mm) REVERT: A 370 LYS cc_start: 0.8751 (mttt) cc_final: 0.8346 (mtmm) REVERT: A 387 ILE cc_start: 0.9243 (mm) cc_final: 0.9007 (mt) REVERT: A 398 TRP cc_start: 0.7726 (m100) cc_final: 0.7063 (m-10) REVERT: A 643 GLU cc_start: 0.7790 (pm20) cc_final: 0.7417 (pm20) REVERT: A 644 GLU cc_start: 0.7462 (mp0) cc_final: 0.6708 (mp0) REVERT: A 813 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8788 (tt) REVERT: A 1019 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.6039 (t80) REVERT: A 1030 ARG cc_start: 0.6074 (tmm160) cc_final: 0.5772 (tmm-80) REVERT: A 1065 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6614 (pt) REVERT: A 1095 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.5930 (tpt170) REVERT: A 1099 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.8979 (t0) REVERT: A 1172 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.6648 (p90) REVERT: A 1231 MET cc_start: 0.8412 (tpp) cc_final: 0.7264 (ttm) REVERT: A 1392 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6819 (pp30) REVERT: A 1433 GLU cc_start: 0.8735 (tp30) cc_final: 0.8332 (tp30) REVERT: A 1686 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8259 (tm-30) outliers start: 36 outliers final: 22 residues processed: 178 average time/residue: 0.1188 time to fit residues: 30.3034 Evaluate side-chains 175 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1099 ASP Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1181 THR Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1392 GLN Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 52 optimal weight: 1.9990 chunk 131 optimal weight: 0.0170 chunk 78 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 104 optimal weight: 0.0670 chunk 91 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.142639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107406 restraints weight = 17654.537| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.22 r_work: 0.2868 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13029 Z= 0.096 Angle : 0.599 13.451 17636 Z= 0.291 Chirality : 0.040 0.138 1981 Planarity : 0.004 0.060 2216 Dihedral : 9.984 160.447 1886 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.20 % Favored : 91.55 % Rotamer: Outliers : 2.54 % Allowed : 15.24 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.22), residues: 1586 helix: 0.01 (0.19), residues: 789 sheet: -1.64 (0.43), residues: 142 loop : -2.78 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 957 TYR 0.012 0.001 TYR A 122 PHE 0.008 0.001 PHE A 135 TRP 0.025 0.001 TRP A 923 HIS 0.006 0.001 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00211 (13026) covalent geometry : angle 0.59452 (17628) SS BOND : bond 0.00512 ( 1) SS BOND : angle 0.85663 ( 2) hydrogen bonds : bond 0.02625 ( 422) hydrogen bonds : angle 3.73527 ( 1224) link_NAG-ASN : bond 0.00696 ( 2) link_NAG-ASN : angle 3.79744 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.498 Fit side-chains REVERT: A 86 HIS cc_start: 0.7221 (p-80) cc_final: 0.6988 (p90) REVERT: A 251 ILE cc_start: 0.8301 (mt) cc_final: 0.8097 (mm) REVERT: A 370 LYS cc_start: 0.8838 (mttt) cc_final: 0.8486 (mtmm) REVERT: A 387 ILE cc_start: 0.9316 (mm) cc_final: 0.9096 (mt) REVERT: A 398 TRP cc_start: 0.7762 (m100) cc_final: 0.7123 (m-10) REVERT: A 430 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.6960 (mtm) REVERT: A 484 TRP cc_start: 0.8496 (p-90) cc_final: 0.8224 (p-90) REVERT: A 643 GLU cc_start: 0.7848 (pm20) cc_final: 0.7475 (pm20) REVERT: A 644 GLU cc_start: 0.7554 (mp0) cc_final: 0.6811 (mp0) REVERT: A 666 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7451 (m) REVERT: A 970 PHE cc_start: 0.8077 (p90) cc_final: 0.7835 (p90) REVERT: A 1019 PHE cc_start: 0.6692 (OUTLIER) cc_final: 0.6086 (t80) REVERT: A 1065 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6639 (pt) REVERT: A 1095 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.5994 (tpt170) REVERT: A 1172 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.6581 (p90) REVERT: A 1231 MET cc_start: 0.8403 (tpp) cc_final: 0.7388 (ttm) REVERT: A 1392 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6862 (pp30) REVERT: A 1433 GLU cc_start: 0.8730 (tp30) cc_final: 0.8291 (tp30) REVERT: A 1621 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7757 (pm20) REVERT: A 1686 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8254 (tm-30) outliers start: 34 outliers final: 21 residues processed: 183 average time/residue: 0.1232 time to fit residues: 32.0427 Evaluate side-chains 181 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1019 PHE Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1392 GLN Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 9 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 138 optimal weight: 0.3980 chunk 114 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106032 restraints weight = 17548.287| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.24 r_work: 0.2842 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13029 Z= 0.101 Angle : 0.610 11.614 17636 Z= 0.299 Chirality : 0.041 0.157 1981 Planarity : 0.004 0.059 2216 Dihedral : 9.824 157.502 1886 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.39 % Favored : 91.36 % Rotamer: Outliers : 2.17 % Allowed : 16.36 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.22), residues: 1586 helix: 0.12 (0.19), residues: 790 sheet: -1.62 (0.43), residues: 143 loop : -2.73 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1655 TYR 0.011 0.001 TYR A 396 PHE 0.010 0.001 PHE A 349 TRP 0.026 0.001 TRP A 923 HIS 0.015 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00225 (13026) covalent geometry : angle 0.60675 (17628) SS BOND : bond 0.00369 ( 1) SS BOND : angle 0.67429 ( 2) hydrogen bonds : bond 0.02783 ( 422) hydrogen bonds : angle 3.71890 ( 1224) link_NAG-ASN : bond 0.00660 ( 2) link_NAG-ASN : angle 3.68733 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3172 Ramachandran restraints generated. 1586 Oldfield, 0 Emsley, 1586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.515 Fit side-chains REVERT: A 86 HIS cc_start: 0.7161 (p-80) cc_final: 0.6938 (p90) REVERT: A 114 LYS cc_start: 0.7785 (pptt) cc_final: 0.7521 (tppt) REVERT: A 251 ILE cc_start: 0.8274 (mt) cc_final: 0.8064 (mm) REVERT: A 370 LYS cc_start: 0.8784 (mttt) cc_final: 0.8401 (mtmm) REVERT: A 387 ILE cc_start: 0.9284 (mm) cc_final: 0.9062 (mt) REVERT: A 398 TRP cc_start: 0.7736 (m100) cc_final: 0.7086 (m-10) REVERT: A 430 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6946 (mtm) REVERT: A 603 GLN cc_start: 0.7982 (tp40) cc_final: 0.7719 (mm-40) REVERT: A 643 GLU cc_start: 0.7872 (pm20) cc_final: 0.7466 (pm20) REVERT: A 644 GLU cc_start: 0.7526 (mp0) cc_final: 0.6758 (mp0) REVERT: A 666 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7520 (m) REVERT: A 1065 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6594 (pt) REVERT: A 1095 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.5880 (tpt170) REVERT: A 1172 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.6581 (p90) REVERT: A 1231 MET cc_start: 0.8428 (tpp) cc_final: 0.7384 (ttm) REVERT: A 1392 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.6858 (pp30) REVERT: A 1433 GLU cc_start: 0.8758 (tp30) cc_final: 0.8365 (tp30) REVERT: A 1621 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7758 (pm20) REVERT: A 1686 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8301 (tm-30) outliers start: 29 outliers final: 18 residues processed: 177 average time/residue: 0.1202 time to fit residues: 30.2318 Evaluate side-chains 174 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1095 ARG Chi-restraints excluded: chain A residue 1172 PHE Chi-restraints excluded: chain A residue 1232 ARG Chi-restraints excluded: chain A residue 1237 LYS Chi-restraints excluded: chain A residue 1284 CYS Chi-restraints excluded: chain A residue 1293 GLU Chi-restraints excluded: chain A residue 1392 GLN Chi-restraints excluded: chain A residue 1439 ASP Chi-restraints excluded: chain A residue 1512 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 31 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 122 optimal weight: 0.0570 chunk 114 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106264 restraints weight = 17569.360| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.21 r_work: 0.2901 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13029 Z= 0.102 Angle : 0.611 14.325 17636 Z= 0.297 Chirality : 0.040 0.146 1981 Planarity : 0.004 0.059 2216 Dihedral : 9.591 154.372 1884 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.26 % Favored : 91.49 % Rotamer: Outliers : 2.09 % Allowed : 16.65 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.22), residues: 1586 helix: 0.21 (0.19), residues: 791 sheet: -1.56 (0.43), residues: 143 loop : -2.70 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 957 TYR 0.013 0.001 TYR A 122 PHE 0.011 0.001 PHE A 349 TRP 0.025 0.001 TRP A 923 HIS 0.014 0.001 HIS A 779 Details of bonding type rmsd covalent geometry : bond 0.00231 (13026) covalent geometry : angle 0.60799 (17628) SS BOND : bond 0.00379 ( 1) SS BOND : angle 0.71235 ( 2) hydrogen bonds : bond 0.02769 ( 422) hydrogen bonds : angle 3.69239 ( 1224) link_NAG-ASN : bond 0.00643 ( 2) link_NAG-ASN : angle 3.58421 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3264.82 seconds wall clock time: 56 minutes 19.99 seconds (3379.99 seconds total)