Starting phenix.real_space_refine on Wed Mar 12 20:28:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tng_10532/03_2025/6tng_10532.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tng_10532/03_2025/6tng_10532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tng_10532/03_2025/6tng_10532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tng_10532/03_2025/6tng_10532.map" model { file = "/net/cci-nas-00/data/ceres_data/6tng_10532/03_2025/6tng_10532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tng_10532/03_2025/6tng_10532.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 3 Type Number sf(0) Gaussians C 4120 2.51 5 N 2060 2.21 5 O 2060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8240 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 4108 Classifications: {'peptide': 1027} Incomplete info: {'backbone_only': 984} Link IDs: {'PTRANS': 44, 'TRANS': 982} Chain breaks: 7 Unresolved chain link angles: 44 Unresolved non-hydrogen bonds: 4155 Unresolved non-hydrogen angles: 6019 Unresolved non-hydrogen dihedrals: 2606 Unresolved non-hydrogen chiralities: 1316 Planarities with less than four sites: {'GLN:plan1': 60, 'HIS:plan': 23, 'TYR:plan': 21, 'ASN:plan1': 38, 'TRP:plan': 8, 'ASP:plan': 51, 'PHE:plan': 53, 'GLU:plan': 66, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 1787 Chain: "B" Number of atoms: 4132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 4132 Classifications: {'peptide': 1033} Incomplete info: {'backbone_only': 982} Link IDs: {'PTRANS': 29, 'TRANS': 1003} Chain breaks: 10 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 4127 Unresolved non-hydrogen angles: 5959 Unresolved non-hydrogen dihedrals: 2550 Unresolved non-hydrogen chiralities: 1322 Planarities with less than four sites: {'GLN:plan1': 74, 'HIS:plan': 20, 'TYR:plan': 19, 'ASN:plan1': 31, 'TRP:plan': 5, 'ASP:plan': 44, 'PHE:plan': 47, 'GLU:plan': 71, 'ARG:plan': 45} Unresolved non-hydrogen planarities: 1756 Time building chain proxies: 8.73, per 1000 atoms: 1.06 Number of scatterers: 8240 At special positions: 0 Unit cell: (129.87, 166.5, 117.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2060 8.00 N 2060 7.00 C 4120 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 - 3.00 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 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 0 sheets defined 66.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 73 through 85 Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.765A pdb=" N GLY A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 137 through 143 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.692A pdb=" N LEU A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 removed outlier: 4.528A pdb=" N GLU A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.258A pdb=" N VAL A 180 " --> pdb=" O PRO A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.955A pdb=" N GLN A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.713A pdb=" N CYS A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 260 through 271 removed outlier: 4.503A pdb=" N LYS A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 271 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 280 through 291 removed outlier: 4.406A pdb=" N ASN A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.738A pdb=" N ILE A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 removed outlier: 4.867A pdb=" N LEU A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.603A pdb=" N LYS A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 405 " --> pdb=" O GLN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.673A pdb=" N MET A 420 " --> pdb=" O PRO A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 removed outlier: 4.551A pdb=" N ASP A 433 " --> pdb=" O MET A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 removed outlier: 3.658A pdb=" N ILE A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 443 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 467 removed outlier: 3.508A pdb=" N VAL A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 486 removed outlier: 3.528A pdb=" N VAL A 477 " --> pdb=" O GLN A 473 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 504 Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 528 through 544 Processing helix chain 'A' and resid 547 through 567 Processing helix chain 'A' and resid 569 through 588 removed outlier: 4.058A pdb=" N GLN A 574 " --> pdb=" O PRO A 570 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 577 " --> pdb=" O LYS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 624 Processing helix chain 'A' and resid 626 through 643 removed outlier: 4.187A pdb=" N LEU A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 658 removed outlier: 4.514A pdb=" N LYS A 655 " --> pdb=" O GLN A 651 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 662 through 668 removed outlier: 3.508A pdb=" N ASP A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 733 through 745 Processing helix chain 'A' and resid 754 through 758 removed outlier: 3.745A pdb=" N LEU A 757 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 774 Processing helix chain 'A' and resid 779 through 801 Processing helix chain 'A' and resid 807 through 834 Processing helix chain 'A' and resid 962 through 976 removed outlier: 4.830A pdb=" N LYS A 974 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 976 " --> pdb=" O CYS A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1019 Processing helix chain 'A' and resid 1019 through 1041 removed outlier: 4.756A pdb=" N HIS A1025 " --> pdb=" O PRO A1021 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR A1032 " --> pdb=" O ASN A1028 " (cutoff:3.500A) Proline residue: A1038 - end of helix Processing helix chain 'A' and resid 1042 through 1044 No H-bonds generated for 'chain 'A' and resid 1042 through 1044' Processing helix chain 'A' and resid 1045 through 1053 removed outlier: 3.587A pdb=" N TYR A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1072 removed outlier: 3.516A pdb=" N ALA A1072 " --> pdb=" O ARG A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1077 removed outlier: 4.087A pdb=" N SER A1077 " --> pdb=" O SER A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1093 removed outlier: 4.330A pdb=" N VAL A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A1093 " --> pdb=" O LEU A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1121 removed outlier: 4.204A pdb=" N ASN A1119 " --> pdb=" O GLN A1115 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE A1120 " --> pdb=" O TYR A1116 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1141 removed outlier: 3.738A pdb=" N ILE A1132 " --> pdb=" O GLN A1128 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE A1140 " --> pdb=" O VAL A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1163 Processing helix chain 'A' and resid 1179 through 1193 removed outlier: 3.880A pdb=" N THR A1193 " --> pdb=" O TYR A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1211 removed outlier: 4.506A pdb=" N GLU A1202 " --> pdb=" O LYS A1198 " (cutoff:3.500A) Proline residue: A1209 - end of helix Processing helix chain 'A' and resid 1229 through 1244 removed outlier: 3.956A pdb=" N VAL A1233 " --> pdb=" O GLN A1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 removed outlier: 4.262A pdb=" N LEU B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 64 through 79 removed outlier: 3.770A pdb=" N SER B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 97 removed outlier: 4.750A pdb=" N ILE B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 126 through 137 removed outlier: 4.121A pdb=" N PHE B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 174 through 182 removed outlier: 3.688A pdb=" N ALA B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 removed outlier: 3.916A pdb=" N LEU B 199 " --> pdb=" O VAL B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 225 through 247 removed outlier: 4.328A pdb=" N GLY B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE B 233 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 324 through 341 removed outlier: 4.532A pdb=" N ASP B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.511A pdb=" N LYS B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 390 Processing helix chain 'B' and resid 417 through 434 removed outlier: 3.819A pdb=" N SER B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.572A pdb=" N GLU B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 458 through 472 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 488 through 491 removed outlier: 4.378A pdb=" N SER B 491 " --> pdb=" O ASP B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 496 through 506 Processing helix chain 'B' and resid 507 through 511 Processing helix chain 'B' and resid 512 through 529 removed outlier: 3.639A pdb=" N ARG B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE B 528 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 529 " --> pdb=" O LYS B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 544 Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 586 through 597 removed outlier: 4.137A pdb=" N ARG B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 618 removed outlier: 4.117A pdb=" N TYR B 612 " --> pdb=" O TYR B 608 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP B 613 " --> pdb=" O GLU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 635 removed outlier: 3.675A pdb=" N GLN B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 681 removed outlier: 4.511A pdb=" N LYS B 681 " --> pdb=" O LEU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 715 removed outlier: 5.165A pdb=" N ASN B 704 " --> pdb=" O GLY B 700 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 763 removed outlier: 4.125A pdb=" N ILE B 747 " --> pdb=" O ASN B 743 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 749 " --> pdb=" O TYR B 745 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 758 " --> pdb=" O GLU B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 785 removed outlier: 3.829A pdb=" N PHE B 771 " --> pdb=" O SER B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 818 Processing helix chain 'B' and resid 828 through 835 removed outlier: 4.708A pdb=" N LEU B 832 " --> pdb=" O HIS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 856 Processing helix chain 'B' and resid 869 through 886 removed outlier: 4.392A pdb=" N ASN B 876 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 923 Processing helix chain 'B' and resid 928 through 937 removed outlier: 3.569A pdb=" N GLN B 934 " --> pdb=" O PRO B 930 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 935 " --> pdb=" O GLN B 931 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP B 937 " --> pdb=" O LEU B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 972 removed outlier: 3.749A pdb=" N PHE B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 990 removed outlier: 3.621A pdb=" N THR B 981 " --> pdb=" O ASN B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 995 removed outlier: 3.646A pdb=" N LEU B 994 " --> pdb=" O LEU B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1015 removed outlier: 4.218A pdb=" N GLU B1015 " --> pdb=" O LYS B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1029 Processing helix chain 'B' and resid 1044 through 1049 Processing helix chain 'B' and resid 1049 through 1056 Processing helix chain 'B' and resid 1057 through 1062 removed outlier: 5.600A pdb=" N ASP B1060 " --> pdb=" O GLY B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1174 removed outlier: 4.116A pdb=" N SER B1157 " --> pdb=" O SER B1153 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU B1158 " --> pdb=" O CYS B1154 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B1161 " --> pdb=" O SER B1157 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU B1162 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing helix chain 'B' and resid 1174 through 1179 removed outlier: 3.963A pdb=" N ALA B1179 " --> pdb=" O HIS B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1203 removed outlier: 3.636A pdb=" N LYS B1193 " --> pdb=" O GLY B1189 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B1194 " --> pdb=" O ARG B1190 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B1195 " --> pdb=" O LEU B1191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B1202 " --> pdb=" O SER B1198 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B1203 " --> pdb=" O GLY B1199 " (cutoff:3.500A) Processing helix chain 'B' and resid 1251 through 1272 removed outlier: 4.309A pdb=" N ASN B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B1272 " --> pdb=" O ILE B1268 " (cutoff:3.500A) 815 hydrogen bonds defined for protein. 2376 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: 3.36 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 2059 1.27 - 1.34: 1943 1.34 - 1.41: 99 1.41 - 1.48: 1828 1.48 - 1.54: 2292 Bond restraints: 8221 Sorted by residual: bond pdb=" N LEU B 995 " pdb=" CA LEU B 995 " ideal model delta sigma weight residual 1.454 1.498 -0.044 1.32e-02 5.74e+03 1.11e+01 bond pdb=" C GLN B 531 " pdb=" O GLN B 531 " ideal model delta sigma weight residual 1.231 1.280 -0.049 1.47e-02 4.63e+03 1.10e+01 bond pdb=" N GLN B 58 " pdb=" CA GLN B 58 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.22e-02 6.72e+03 1.06e+01 bond pdb=" N ILE A 221 " pdb=" CA ILE A 221 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N GLN B 531 " pdb=" CA GLN B 531 " ideal model delta sigma weight residual 1.461 1.504 -0.044 1.38e-02 5.25e+03 1.00e+01 ... (remaining 8216 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 9454 2.43 - 4.87: 696 4.87 - 7.30: 73 7.30 - 9.73: 15 9.73 - 12.16: 5 Bond angle restraints: 10243 Sorted by residual: angle pdb=" N VAL B 950 " pdb=" CA VAL B 950 " pdb=" C VAL B 950 " ideal model delta sigma weight residual 111.91 103.99 7.92 8.90e-01 1.26e+00 7.91e+01 angle pdb=" N PRO B 646 " pdb=" CA PRO B 646 " pdb=" C PRO B 646 " ideal model delta sigma weight residual 113.53 102.35 11.18 1.39e+00 5.18e-01 6.47e+01 angle pdb=" N GLN B1001 " pdb=" CA GLN B1001 " pdb=" C GLN B1001 " ideal model delta sigma weight residual 111.36 104.29 7.07 1.09e+00 8.42e-01 4.21e+01 angle pdb=" N GLN B 159 " pdb=" CA GLN B 159 " pdb=" C GLN B 159 " ideal model delta sigma weight residual 113.12 105.40 7.72 1.25e+00 6.40e-01 3.82e+01 angle pdb=" N VAL B 115 " pdb=" CA VAL B 115 " pdb=" C VAL B 115 " ideal model delta sigma weight residual 110.82 105.01 5.81 9.70e-01 1.06e+00 3.59e+01 ... (remaining 10238 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 5.99: 1124 5.99 - 11.98: 570 11.98 - 17.96: 243 17.96 - 23.94: 82 23.94 - 29.93: 22 Dihedral angle restraints: 2041 sinusoidal: 0 harmonic: 2041 Sorted by residual: dihedral pdb=" CA THR B 862 " pdb=" C THR B 862 " pdb=" N ASP B 863 " pdb=" CA ASP B 863 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA PHE B 112 " pdb=" C PHE B 112 " pdb=" N VAL B 113 " pdb=" CA VAL B 113 " ideal model delta harmonic sigma weight residual 180.00 151.72 28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA ILE B 292 " pdb=" C ILE B 292 " pdb=" N LYS B 293 " pdb=" CA LYS B 293 " ideal model delta harmonic sigma weight residual 180.00 152.43 27.57 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 2038 not shown) Chirality restraints: 0 Planarity restraints: 2041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 757 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ILE B 757 " 0.061 2.00e-02 2.50e+03 pdb=" O ILE B 757 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU B 758 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 608 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C TYR B 608 " -0.058 2.00e-02 2.50e+03 pdb=" O TYR B 608 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU B 609 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 990 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C THR B 990 " -0.058 2.00e-02 2.50e+03 pdb=" O THR B 990 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B 991 " 0.019 2.00e-02 2.50e+03 ... (remaining 2038 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1288 2.73 - 3.27: 8783 3.27 - 3.81: 10104 3.81 - 4.36: 12030 4.36 - 4.90: 16487 Nonbonded interactions: 48692 Sorted by model distance: nonbonded pdb=" O LEU B 532 " pdb=" N ALA B 534 " model vdw 2.183 3.120 nonbonded pdb=" O ALA A 297 " pdb=" N VAL A 300 " model vdw 2.220 3.120 nonbonded pdb=" O LEU B 593 " pdb=" N CYS B 596 " model vdw 2.248 3.120 nonbonded pdb=" O GLN B 659 " pdb=" N SER B 735 " model vdw 2.270 3.120 nonbonded pdb=" O SER B 166 " pdb=" N TRP B 169 " model vdw 2.271 3.120 ... (remaining 48687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.410 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.640 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.008 0.057 8221 Z= 0.610 Angle : 1.391 12.162 10243 Z= 1.008 Chirality : 0.000 0.000 0 Planarity : 0.009 0.035 2041 Dihedral : 8.740 29.929 2041 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.84 % Allowed : 18.94 % Favored : 80.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -5.16 (0.15), residues: 2022 helix: -3.14 (0.11), residues: 1152 sheet: None (None), residues: 0 loop : -3.77 (0.19), residues: 870 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.898 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0750 time to fit residues: 7.3833 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 83 optimal weight: 20.0000 chunk 160 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.088599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.070211 restraints weight = 45205.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.069723 restraints weight = 36931.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.070282 restraints weight = 32725.410| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8221 Z= 0.143 Angle : 0.536 7.209 10243 Z= 0.322 Chirality : 0.000 0.000 0 Planarity : 0.003 0.025 2041 Dihedral : 5.460 19.319 2041 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.24 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -3.24 (0.17), residues: 2022 helix: -1.13 (0.14), residues: 1238 sheet: None (None), residues: 0 loop : -3.86 (0.20), residues: 784 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0708 time to fit residues: 7.0883 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 65 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.082894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.063061 restraints weight = 44480.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.062993 restraints weight = 35978.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.063464 restraints weight = 30767.555| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 8221 Z= 0.523 Angle : 1.015 10.578 10243 Z= 0.646 Chirality : 0.000 0.000 0 Planarity : 0.007 0.027 2041 Dihedral : 7.799 29.565 2041 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.54 % Allowed : 22.30 % Favored : 77.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -4.56 (0.16), residues: 2022 helix: -2.24 (0.13), residues: 1200 sheet: None (None), residues: 0 loop : -4.24 (0.19), residues: 822 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.942 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0743 time to fit residues: 7.4170 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 6 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 chunk 178 optimal weight: 0.0470 chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 146 optimal weight: 0.0070 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.0258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.088403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068807 restraints weight = 42712.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.067906 restraints weight = 33888.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068527 restraints weight = 30307.624| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8221 Z= 0.126 Angle : 0.507 6.741 10243 Z= 0.302 Chirality : 0.000 0.000 0 Planarity : 0.003 0.019 2041 Dihedral : 5.110 19.872 2041 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.58 % Favored : 89.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -2.54 (0.19), residues: 2022 helix: -0.43 (0.15), residues: 1252 sheet: None (None), residues: 0 loop : -3.90 (0.20), residues: 770 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.247 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0728 time to fit residues: 7.3371 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 196 optimal weight: 0.0030 chunk 99 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.086531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068628 restraints weight = 45906.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.068585 restraints weight = 37883.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.068534 restraints weight = 29682.656| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8221 Z= 0.236 Angle : 0.601 7.361 10243 Z= 0.370 Chirality : 0.000 0.000 0 Planarity : 0.003 0.018 2041 Dihedral : 5.594 21.120 2041 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 16.86 % Favored : 82.99 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -2.38 (0.19), residues: 2022 helix: -0.28 (0.15), residues: 1244 sheet: None (None), residues: 0 loop : -3.87 (0.20), residues: 778 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0762 time to fit residues: 7.7179 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 198 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 chunk 108 optimal weight: 0.1980 chunk 58 optimal weight: 9.9990 chunk 175 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.087755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.068147 restraints weight = 43356.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.067664 restraints weight = 35770.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.068087 restraints weight = 30798.465| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8221 Z= 0.163 Angle : 0.503 6.207 10243 Z= 0.304 Chirality : 0.000 0.000 0 Planarity : 0.003 0.019 2041 Dihedral : 4.921 19.617 2041 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.07 % Favored : 87.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.67 (0.20), residues: 2022 helix: 0.29 (0.16), residues: 1268 sheet: None (None), residues: 0 loop : -3.70 (0.21), residues: 754 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.901 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0735 time to fit residues: 7.3171 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 146 optimal weight: 0.0670 chunk 13 optimal weight: 9.9990 chunk 195 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 overall best weight: 3.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.084911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.067061 restraints weight = 46787.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.066805 restraints weight = 39411.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066634 restraints weight = 34370.609| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8221 Z= 0.359 Angle : 0.765 8.696 10243 Z= 0.480 Chirality : 0.000 0.000 0 Planarity : 0.005 0.020 2041 Dihedral : 6.395 23.998 2041 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 19.68 % Favored : 80.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -2.85 (0.18), residues: 2022 helix: -0.67 (0.15), residues: 1238 sheet: None (None), residues: 0 loop : -4.01 (0.20), residues: 784 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.921 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0692 time to fit residues: 6.9163 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 36 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 78 optimal weight: 0.0570 chunk 175 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.084658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.066668 restraints weight = 47290.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.066151 restraints weight = 41558.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066397 restraints weight = 36197.776| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8221 Z= 0.378 Angle : 0.806 8.827 10243 Z= 0.502 Chirality : 0.000 0.000 0 Planarity : 0.005 0.021 2041 Dihedral : 6.731 24.820 2041 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 20.03 % Favored : 79.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -3.36 (0.18), residues: 2022 helix: -1.12 (0.14), residues: 1231 sheet: None (None), residues: 0 loop : -4.12 (0.20), residues: 791 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.937 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0698 time to fit residues: 6.9962 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 31 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.085329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.067319 restraints weight = 47104.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.066543 restraints weight = 41353.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.066805 restraints weight = 37434.110| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8221 Z= 0.307 Angle : 0.710 8.116 10243 Z= 0.439 Chirality : 0.000 0.000 0 Planarity : 0.004 0.021 2041 Dihedral : 6.275 23.453 2041 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 20.08 % Favored : 79.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -3.13 (0.18), residues: 2022 helix: -0.93 (0.15), residues: 1246 sheet: None (None), residues: 0 loop : -4.07 (0.20), residues: 776 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.017 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0746 time to fit residues: 7.5107 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 131 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 176 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 142 optimal weight: 0.4980 chunk 141 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 146 optimal weight: 0.0050 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.087420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066980 restraints weight = 42918.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.066805 restraints weight = 37923.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067372 restraints weight = 30422.204| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8221 Z= 0.172 Angle : 0.530 6.500 10243 Z= 0.320 Chirality : 0.000 0.000 0 Planarity : 0.003 0.019 2041 Dihedral : 5.193 20.223 2041 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.75 % Favored : 86.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -2.09 (0.19), residues: 2022 helix: -0.01 (0.15), residues: 1249 sheet: None (None), residues: 0 loop : -3.84 (0.21), residues: 773 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.944 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0720 time to fit residues: 7.2435 Evaluate side-chains 42 residues out of total 1850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 94 optimal weight: 7.9990 chunk 158 optimal weight: 0.0980 chunk 115 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 146 optimal weight: 0.0010 overall best weight: 3.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.085585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067687 restraints weight = 46861.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.067117 restraints weight = 38796.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067695 restraints weight = 34771.357| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8221 Z= 0.292 Angle : 0.675 7.993 10243 Z= 0.419 Chirality : 0.000 0.000 0 Planarity : 0.004 0.020 2041 Dihedral : 5.959 22.812 2041 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 19.34 % Favored : 80.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -2.58 (0.19), residues: 2022 helix: -0.45 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -3.95 (0.21), residues: 771 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3502.13 seconds wall clock time: 60 minutes 37.51 seconds (3637.51 seconds total)