Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 19:09:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzk_20536/04_2023/6pzk_20536.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzk_20536/04_2023/6pzk_20536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzk_20536/04_2023/6pzk_20536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzk_20536/04_2023/6pzk_20536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzk_20536/04_2023/6pzk_20536.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pzk_20536/04_2023/6pzk_20536.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.088 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 8407 2.51 5 N 2237 2.21 5 O 2436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 51": "NH1" <-> "NH2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ARG 378": "NH1" <-> "NH2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 711": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 788": "OE1" <-> "OE2" Residue "A GLU 825": "OE1" <-> "OE2" Residue "A GLU 859": "OE1" <-> "OE2" Residue "A ARG 864": "NH1" <-> "NH2" Residue "A ARG 918": "NH1" <-> "NH2" Residue "A GLU 1115": "OE1" <-> "OE2" Residue "A ARG 1123": "NH1" <-> "NH2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A ARG 1209": "NH1" <-> "NH2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A GLU 1379": "OE1" <-> "OE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "E ARG 191": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 13153 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1361, 11106 Classifications: {'peptide': 1361} Link IDs: {'PTRANS': 47, 'TRANS': 1313} Chain breaks: 3 Chain: "B" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 762 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "C" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 437 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain breaks: 1 Time building chain proxies: 6.98, per 1000 atoms: 0.53 Number of scatterers: 13153 At special positions: 0 Unit cell: (97.825, 119.325, 117.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 2436 8.00 N 2237 7.00 C 8407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.43 Conformation dependent library (CDL) restraints added in 1.9 seconds 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3116 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 8 sheets defined 65.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 55 through 63 removed outlier: 4.148A pdb=" N LEU A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 83 through 93 removed outlier: 4.060A pdb=" N PHE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 131 removed outlier: 4.732A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 removed outlier: 3.743A pdb=" N TRP A 207 " --> pdb=" O TRP A 203 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.701A pdb=" N PHE A 269 " --> pdb=" O THR A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 334 through 348 removed outlier: 3.601A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 379 removed outlier: 3.917A pdb=" N ARG A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.626A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.704A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 437 through 449 removed outlier: 4.052A pdb=" N VAL A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASN A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 478 removed outlier: 3.501A pdb=" N ASN A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 490 through 499 removed outlier: 4.363A pdb=" N TYR A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 517 through 519 No H-bonds generated for 'chain 'A' and resid 517 through 519' Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 553 removed outlier: 5.255A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.967A pdb=" N TYR A 565 " --> pdb=" O HIS A 561 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N HIS A 568 " --> pdb=" O ASN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 576 through 580 removed outlier: 4.336A pdb=" N ARG A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 593 through 596 Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 633 through 651 removed outlier: 3.647A pdb=" N VAL A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.644A pdb=" N ALA A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 708 " --> pdb=" O PHE A 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 703 through 708' Processing helix chain 'A' and resid 709 through 712 Processing helix chain 'A' and resid 713 through 724 removed outlier: 3.760A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 781 through 800 removed outlier: 4.183A pdb=" N LEU A 798 " --> pdb=" O ASP A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 850 Processing helix chain 'A' and resid 868 through 872 removed outlier: 4.214A pdb=" N LYS A 871 " --> pdb=" O PHE A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 888 removed outlier: 3.933A pdb=" N LYS A 886 " --> pdb=" O ALA A 882 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 887 " --> pdb=" O SER A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 913 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 removed outlier: 3.719A pdb=" N HIS A 944 " --> pdb=" O LEU A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 979 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 1003 through 1021 removed outlier: 4.226A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1054 through 1060 Processing helix chain 'A' and resid 1072 through 1086 removed outlier: 5.027A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1110 removed outlier: 4.346A pdb=" N SER A1096 " --> pdb=" O ILE A1092 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR A1102 " --> pdb=" O GLN A1098 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A1108 " --> pdb=" O GLU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1142 removed outlier: 3.732A pdb=" N ILE A1137 " --> pdb=" O LYS A1133 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1153 removed outlier: 5.734A pdb=" N LEU A1151 " --> pdb=" O THR A1148 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A1153 " --> pdb=" O ILE A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1180 removed outlier: 5.299A pdb=" N LEU A1176 " --> pdb=" O ASN A1172 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A1177 " --> pdb=" O ILE A1173 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A1178 " --> pdb=" O THR A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1188 Processing helix chain 'A' and resid 1198 through 1210 Processing helix chain 'A' and resid 1223 through 1227 Processing helix chain 'A' and resid 1277 through 1281 removed outlier: 3.529A pdb=" N LEU A1281 " --> pdb=" O ARG A1278 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 4.638A pdb=" N GLN A1288 " --> pdb=" O LYS A1284 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A1290 " --> pdb=" O ARG A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1302 No H-bonds generated for 'chain 'A' and resid 1300 through 1302' Processing helix chain 'A' and resid 1304 through 1316 Processing helix chain 'A' and resid 1320 through 1325 Processing helix chain 'A' and resid 1326 through 1328 No H-bonds generated for 'chain 'A' and resid 1326 through 1328' Processing helix chain 'A' and resid 1354 through 1359 Processing helix chain 'A' and resid 1365 through 1375 removed outlier: 3.822A pdb=" N ARG A1370 " --> pdb=" O SER A1366 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE A1371 " --> pdb=" O PRO A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1404 removed outlier: 3.532A pdb=" N SER A1397 " --> pdb=" O LEU A1393 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A1400 " --> pdb=" O MET A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1419 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1444 through 1447 Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 4.509A pdb=" N GLU A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 150 removed outlier: 4.610A pdb=" N ARG B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 164 removed outlier: 4.000A pdb=" N ASP B 164 " --> pdb=" O SER B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 through 164' Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 203 through 210 Processing helix chain 'B' and resid 217 through 228 removed outlier: 4.535A pdb=" N ASN B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 157 removed outlier: 3.507A pdb=" N ARG C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 144 " --> pdb=" O GLU C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 164 Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'D' and resid 131 through 156 removed outlier: 4.803A pdb=" N ASP D 136 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 154 " --> pdb=" O HIS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 182 removed outlier: 4.011A pdb=" N ILE D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG D 167 " --> pdb=" O ARG D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 155 removed outlier: 3.635A pdb=" N GLY E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 199 removed outlier: 3.762A pdb=" N LEU E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG E 191 " --> pdb=" O MET E 187 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU E 192 " --> pdb=" O THR E 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.415A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL A 263 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA4, first strand: chain 'A' and resid 803 through 809 Processing sheet with id=AA5, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.668A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1228 through 1231 Processing sheet with id=AA7, first strand: chain 'A' and resid 1271 through 1272 Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 159 716 hydrogen bonds defined for protein. 2025 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: 4.82 Time building geometry restraints manager: 5.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2599 1.32 - 1.45: 2997 1.45 - 1.57: 7671 1.57 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 13390 Sorted by residual: bond pdb=" CZ ARG A1357 " pdb=" NH2 ARG A1357 " ideal model delta sigma weight residual 1.330 1.280 0.050 1.30e-02 5.92e+03 1.47e+01 bond pdb=" CZ ARG A 302 " pdb=" NH2 ARG A 302 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" CZ ARG C 167 " pdb=" NH2 ARG C 167 " ideal model delta sigma weight residual 1.330 1.282 0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" CZ ARG A 279 " pdb=" NH2 ARG A 279 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.26e+01 bond pdb=" CZ ARG A1123 " pdb=" NH2 ARG A1123 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.24e+01 ... (remaining 13385 not shown) Histogram of bond angle deviations from ideal: 97.15 - 104.75: 193 104.75 - 112.36: 5617 112.36 - 119.96: 6683 119.96 - 127.56: 5496 127.56 - 135.17: 106 Bond angle restraints: 18095 Sorted by residual: angle pdb=" CA HIS A1444 " pdb=" CB HIS A1444 " pdb=" CG HIS A1444 " ideal model delta sigma weight residual 113.80 122.80 -9.00 1.00e+00 1.00e+00 8.10e+01 angle pdb=" N MET A 869 " pdb=" CA MET A 869 " pdb=" C MET A 869 " ideal model delta sigma weight residual 110.23 121.49 -11.26 1.45e+00 4.76e-01 6.03e+01 angle pdb=" C PHE A 521 " pdb=" N TYR A 522 " pdb=" CA TYR A 522 " ideal model delta sigma weight residual 122.59 133.47 -10.88 1.57e+00 4.06e-01 4.80e+01 angle pdb=" C HIS A1444 " pdb=" CA HIS A1444 " pdb=" CB HIS A1444 " ideal model delta sigma weight residual 110.74 99.49 11.25 1.66e+00 3.63e-01 4.59e+01 angle pdb=" CA ASP A 700 " pdb=" CB ASP A 700 " pdb=" CG ASP A 700 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.49e+01 ... (remaining 18090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7436 17.90 - 35.80: 605 35.80 - 53.71: 98 53.71 - 71.61: 35 71.61 - 89.51: 14 Dihedral angle restraints: 8188 sinusoidal: 3389 harmonic: 4799 Sorted by residual: dihedral pdb=" C MET A 869 " pdb=" N MET A 869 " pdb=" CA MET A 869 " pdb=" CB MET A 869 " ideal model delta harmonic sigma weight residual -122.60 -151.88 29.28 0 2.50e+00 1.60e-01 1.37e+02 dihedral pdb=" N MET A 869 " pdb=" C MET A 869 " pdb=" CA MET A 869 " pdb=" CB MET A 869 " ideal model delta harmonic sigma weight residual 122.80 151.24 -28.44 0 2.50e+00 1.60e-01 1.29e+02 dihedral pdb=" C ARG B 182 " pdb=" N ARG B 182 " pdb=" CA ARG B 182 " pdb=" CB ARG B 182 " ideal model delta harmonic sigma weight residual -122.60 -150.85 28.25 0 2.50e+00 1.60e-01 1.28e+02 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 2038 0.250 - 0.499: 53 0.499 - 0.749: 2 0.749 - 0.998: 2 0.998 - 1.248: 2 Chirality restraints: 2097 Sorted by residual: chirality pdb=" CA MET A 869 " pdb=" N MET A 869 " pdb=" C MET A 869 " pdb=" CB MET A 869 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.89e+01 chirality pdb=" CA ARG B 182 " pdb=" N ARG B 182 " pdb=" C ARG B 182 " pdb=" CB ARG B 182 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" CA GLU A1374 " pdb=" N GLU A1374 " pdb=" C GLU A1374 " pdb=" CB GLU A1374 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.84e+01 ... (remaining 2094 not shown) Planarity restraints: 2271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 586 " -0.173 2.00e-02 2.50e+03 9.34e-02 1.75e+02 pdb=" CG TYR A 586 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 586 " 0.076 2.00e-02 2.50e+03 pdb=" CD2 TYR A 586 " 0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR A 586 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR A 586 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR A 586 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 586 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 770 " -0.164 2.00e-02 2.50e+03 9.14e-02 1.67e+02 pdb=" CG TYR A 770 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 770 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR A 770 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 770 " 0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR A 770 " 0.054 2.00e-02 2.50e+03 pdb=" CZ TYR A 770 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 770 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 834 " -0.141 2.00e-02 2.50e+03 7.96e-02 1.27e+02 pdb=" CG TYR A 834 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 834 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TYR A 834 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 TYR A 834 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 834 " 0.049 2.00e-02 2.50e+03 pdb=" CZ TYR A 834 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 834 " -0.128 2.00e-02 2.50e+03 ... (remaining 2268 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 6445 3.01 - 3.48: 14108 3.48 - 3.95: 21757 3.95 - 4.43: 24915 4.43 - 4.90: 41097 Nonbonded interactions: 108322 Sorted by model distance: nonbonded pdb=" OD1 ASP A1296 " pdb=" OH TYR A1321 " model vdw 2.533 2.440 nonbonded pdb=" OD2 ASP A1003 " pdb=" OG1 THR A1006 " model vdw 2.533 2.440 nonbonded pdb=" OH TYR A1100 " pdb=" OE1 GLU A1135 " model vdw 2.533 2.440 nonbonded pdb=" N TYR A 522 " pdb=" O TYR A 522 " model vdw 2.552 2.496 nonbonded pdb=" OE1 GLU A 27 " pdb=" OG1 THR A 265 " model vdw 2.554 2.440 ... (remaining 108317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and resid 130 through 184) selection = chain 'D' } 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.710 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 35.710 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 0.012 0.061 13390 Z= 0.767 Angle : 1.931 11.263 18095 Z= 1.298 Chirality : 0.117 1.248 2097 Planarity : 0.016 0.142 2271 Dihedral : 14.419 89.507 5072 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 0.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 1.95 % Cbeta Deviations : 1.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.18), residues: 1606 helix: -2.53 (0.12), residues: 925 sheet: 0.53 (0.60), residues: 67 loop : -0.77 (0.24), residues: 614 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 366 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 6 residues processed: 386 average time/residue: 0.3004 time to fit residues: 164.0619 Evaluate side-chains 238 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 232 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1236 time to fit residues: 3.6738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 0.0770 chunk 125 optimal weight: 0.2980 chunk 48 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 0.3980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 52 GLN A 209 ASN A 229 HIS A 248 GLN A 296 ASN A 306 ASN A 362 ASN A 611 ASN A 640 GLN A 727 GLN A 853 HIS A 970 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN A1438 GLN B 224 ASN D 130 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 13390 Z= 0.187 Angle : 0.640 8.980 18095 Z= 0.342 Chirality : 0.043 0.179 2097 Planarity : 0.004 0.035 2271 Dihedral : 5.889 31.254 1771 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1606 helix: -0.35 (0.16), residues: 927 sheet: 0.99 (0.59), residues: 71 loop : -0.04 (0.26), residues: 608 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 247 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 15 residues processed: 271 average time/residue: 0.2980 time to fit residues: 116.4999 Evaluate side-chains 210 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 1.531 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1333 time to fit residues: 5.8609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 129 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** A 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 HIS A 748 HIS ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 13390 Z= 0.327 Angle : 0.628 9.703 18095 Z= 0.327 Chirality : 0.045 0.202 2097 Planarity : 0.004 0.043 2271 Dihedral : 5.286 27.914 1771 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1606 helix: 0.27 (0.17), residues: 930 sheet: 0.94 (0.60), residues: 70 loop : -0.02 (0.26), residues: 606 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 198 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 24 residues processed: 230 average time/residue: 0.2653 time to fit residues: 88.7445 Evaluate side-chains 203 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 179 time to evaluate : 1.522 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1608 time to fit residues: 8.6710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 255 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 HIS ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS A 874 GLN A 970 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 GLN A1444 HIS B 225 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13390 Z= 0.209 Angle : 0.548 8.882 18095 Z= 0.285 Chirality : 0.041 0.184 2097 Planarity : 0.003 0.039 2271 Dihedral : 4.844 26.056 1771 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1606 helix: 0.74 (0.17), residues: 927 sheet: 0.81 (0.61), residues: 70 loop : 0.08 (0.26), residues: 609 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 213 average time/residue: 0.2744 time to fit residues: 85.5137 Evaluate side-chains 195 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 1.619 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1392 time to fit residues: 5.3007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 78 optimal weight: 0.0040 chunk 138 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 296 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13390 Z= 0.181 Angle : 0.526 8.203 18095 Z= 0.271 Chirality : 0.040 0.150 2097 Planarity : 0.003 0.036 2271 Dihedral : 4.556 24.067 1771 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 1.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.21), residues: 1606 helix: 1.05 (0.17), residues: 934 sheet: 0.51 (0.59), residues: 75 loop : 0.23 (0.26), residues: 597 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 209 average time/residue: 0.2536 time to fit residues: 79.5353 Evaluate side-chains 184 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1403 time to fit residues: 4.1264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 306 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 13390 Z= 0.241 Angle : 0.554 9.130 18095 Z= 0.283 Chirality : 0.042 0.190 2097 Planarity : 0.003 0.037 2271 Dihedral : 4.540 22.748 1771 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.21), residues: 1606 helix: 1.05 (0.17), residues: 941 sheet: 0.46 (0.59), residues: 75 loop : 0.36 (0.27), residues: 590 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 183 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 194 average time/residue: 0.2691 time to fit residues: 77.2464 Evaluate side-chains 183 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 175 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1381 time to fit residues: 4.5086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 13390 Z= 0.273 Angle : 0.564 9.012 18095 Z= 0.288 Chirality : 0.042 0.157 2097 Planarity : 0.003 0.037 2271 Dihedral : 4.570 22.076 1771 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1606 helix: 1.09 (0.17), residues: 942 sheet: 0.32 (0.58), residues: 75 loop : 0.28 (0.27), residues: 589 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 193 average time/residue: 0.2860 time to fit residues: 82.7706 Evaluate side-chains 191 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1366 time to fit residues: 5.2232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 GLN A 874 GLN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 13390 Z= 0.176 Angle : 0.524 8.391 18095 Z= 0.267 Chirality : 0.040 0.143 2097 Planarity : 0.003 0.042 2271 Dihedral : 4.371 20.524 1771 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.21), residues: 1606 helix: 1.28 (0.17), residues: 943 sheet: 0.43 (0.58), residues: 74 loop : 0.40 (0.27), residues: 589 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 196 average time/residue: 0.2654 time to fit residues: 77.7973 Evaluate side-chains 181 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 1.609 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1325 time to fit residues: 3.8001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 112 optimal weight: 0.0570 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 13390 Z= 0.208 Angle : 0.537 9.499 18095 Z= 0.274 Chirality : 0.041 0.144 2097 Planarity : 0.003 0.043 2271 Dihedral : 4.347 20.416 1771 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1606 helix: 1.36 (0.17), residues: 949 sheet: 0.37 (0.58), residues: 74 loop : 0.46 (0.27), residues: 583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 1.601 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 177 average time/residue: 0.2740 time to fit residues: 71.5300 Evaluate side-chains 168 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 1.619 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1442 time to fit residues: 2.7536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 0.3980 chunk 105 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 146 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13390 Z= 0.197 Angle : 0.528 11.530 18095 Z= 0.269 Chirality : 0.041 0.147 2097 Planarity : 0.003 0.046 2271 Dihedral : 4.300 20.095 1771 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1606 helix: 1.38 (0.17), residues: 956 sheet: 0.34 (0.58), residues: 74 loop : 0.48 (0.28), residues: 576 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3212 Ramachandran restraints generated. 1606 Oldfield, 0 Emsley, 1606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 1.508 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 177 average time/residue: 0.2733 time to fit residues: 71.1222 Evaluate side-chains 168 residues out of total 1489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.548 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1858 time to fit residues: 2.5257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 0.0050 chunk 53 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 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 = 0.3922 r_free = 0.3922 target = 0.167497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.139434 restraints weight = 14092.119| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.64 r_work: 0.3418 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 13390 Z= 0.197 Angle : 0.532 14.681 18095 Z= 0.270 Chirality : 0.041 0.146 2097 Planarity : 0.003 0.046 2271 Dihedral : 4.290 20.060 1771 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.22), residues: 1606 helix: 1.42 (0.17), residues: 950 sheet: 0.35 (0.58), residues: 74 loop : 0.48 (0.27), residues: 582 =============================================================================== Job complete usr+sys time: 2886.94 seconds wall clock time: 53 minutes 18.59 seconds (3198.59 seconds total)