Starting phenix.real_space_refine (version: dev) on Mon Apr 4 18:26:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tng_10532/04_2022/6tng_10532.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tng_10532/04_2022/6tng_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tng_10532/04_2022/6tng_10532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tng_10532/04_2022/6tng_10532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tng_10532/04_2022/6tng_10532.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tng_10532/04_2022/6tng_10532.pdb" } resolution = 4.1 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= 0.001 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: 5.88, per 1000 atoms: 0.71 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 - 3.50 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: 3.67 Conformation dependent library (CDL) restraints added in 2.2 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: 0.84 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: 2.88 Time building geometry restraints manager: 3.88 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: 101.29 - 107.82: 115 107.82 - 114.36: 1879 114.36 - 120.89: 4991 120.89 - 127.43: 3252 127.43 - 133.96: 6 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 2.520 nonbonded pdb=" O ALA A 297 " pdb=" N VAL A 300 " model vdw 2.220 2.520 nonbonded pdb=" O LEU B 593 " pdb=" N CYS B 596 " model vdw 2.248 2.520 nonbonded pdb=" O GLN B 659 " pdb=" N SER B 735 " model vdw 2.270 2.520 nonbonded pdb=" O SER B 166 " pdb=" N TRP B 169 " model vdw 2.271 2.520 ... (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 ========== 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 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. 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: 3.300 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 18.070 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.070 Process input model: 28.230 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 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 % 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0704 time to fit residues: 7.2014 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4420 ------------------------------------------------------------------------------- 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: 10.0000 chunk 83 optimal weight: 20.0000 chunk 160 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 8221 Z= 0.127 Angle : 0.516 7.097 10243 Z= 0.310 Chirality : 0.000 0.000 0 Planarity : 0.003 0.028 2041 Dihedral : 5.312 19.989 2041 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.34 % Favored : 89.47 % Rotamer Outliers : 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: -3.04 (0.18), residues: 2022 helix: -0.96 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -3.81 (0.20), residues: 787 *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.061 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0776 time to fit residues: 7.8629 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 154 optimal weight: 0.0970 chunk 126 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 8221 Z= 0.402 Angle : 0.846 8.765 10243 Z= 0.535 Chirality : 0.000 0.000 0 Planarity : 0.006 0.024 2041 Dihedral : 7.012 25.350 2041 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.30 % Allowed : 20.33 % Favored : 79.38 % Rotamer Outliers : 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: -3.90 (0.17), residues: 2022 helix: -1.66 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : -4.13 (0.19), residues: 787 *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.069 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0742 time to fit residues: 7.3926 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 8221 Z= 0.338 Angle : 0.780 8.452 10243 Z= 0.483 Chirality : 0.000 0.000 0 Planarity : 0.005 0.024 2041 Dihedral : 6.835 24.439 2041 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 20.77 % Favored : 79.03 % Rotamer Outliers : 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: -3.78 (0.17), residues: 2022 helix: -1.50 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : -4.20 (0.19), residues: 790 *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.053 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0747 time to fit residues: 7.6258 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 8221 Z= 0.438 Angle : 0.922 9.915 10243 Z= 0.579 Chirality : 0.000 0.000 0 Planarity : 0.006 0.025 2041 Dihedral : 7.692 30.326 2041 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 20.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 25.27 % Favored : 74.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.32 (0.17), residues: 2022 helix: -1.95 (0.14), residues: 1199 sheet: None (None), residues: 0 loop : -4.33 (0.19), residues: 823 *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.071 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0736 time to fit residues: 7.3868 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8221 Z= 0.218 Angle : 0.620 7.700 10243 Z= 0.377 Chirality : 0.000 0.000 0 Planarity : 0.003 0.022 2041 Dihedral : 6.014 22.553 2041 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.20 % Allowed : 16.27 % Favored : 83.53 % Rotamer Outliers : 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: -3.17 (0.18), residues: 2022 helix: -1.00 (0.15), residues: 1255 sheet: None (None), residues: 0 loop : -4.05 (0.20), residues: 767 *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.063 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0723 time to fit residues: 7.3987 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.096 8221 Z= 0.487 Angle : 0.977 10.232 10243 Z= 0.618 Chirality : 0.000 0.000 0 Planarity : 0.007 0.026 2041 Dihedral : 7.900 31.752 2041 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 28.27 Ramachandran Plot: Outliers : 0.35 % Allowed : 26.61 % Favored : 73.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.45 (0.16), residues: 2022 helix: -2.06 (0.13), residues: 1205 sheet: None (None), residues: 0 loop : -4.38 (0.19), residues: 817 *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.107 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0726 time to fit residues: 7.5167 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 0.0000 chunk 155 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 8221 Z= 0.218 Angle : 0.621 7.987 10243 Z= 0.377 Chirality : 0.000 0.000 0 Planarity : 0.003 0.022 2041 Dihedral : 6.011 23.224 2041 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 15.88 % Favored : 83.93 % Rotamer Outliers : 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: -3.18 (0.18), residues: 2022 helix: -0.95 (0.15), residues: 1239 sheet: None (None), residues: 0 loop : -4.11 (0.20), residues: 783 *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.144 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0749 time to fit residues: 7.6834 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8221 Z= 0.263 Angle : 0.667 8.241 10243 Z= 0.411 Chirality : 0.000 0.000 0 Planarity : 0.004 0.024 2041 Dihedral : 6.216 24.513 2041 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 21.76 % Favored : 78.09 % Rotamer Outliers : 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: -3.11 (0.18), residues: 2022 helix: -0.85 (0.15), residues: 1237 sheet: None (None), residues: 0 loop : -4.16 (0.20), residues: 785 *********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.118 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0705 time to fit residues: 7.3495 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.0870 chunk 118 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 129 optimal weight: 0.0970 overall best weight: 2.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8221 Z= 0.204 Angle : 0.581 7.923 10243 Z= 0.354 Chirality : 0.000 0.000 0 Planarity : 0.003 0.022 2041 Dihedral : 5.613 21.710 2041 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 16.77 % Favored : 83.09 % Rotamer Outliers : 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: -2.51 (0.19), residues: 2022 helix: -0.41 (0.15), residues: 1258 sheet: None (None), residues: 0 loop : -3.94 (0.21), residues: 764 ********************** 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 fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.109 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0738 time to fit residues: 7.6823 Evaluate side-chains 42 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.102 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.083530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066411 restraints weight = 47448.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.065725 restraints weight = 39706.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.065811 restraints weight = 35328.540| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.088 8221 Z= 0.438 Angle : 0.900 9.210 10243 Z= 0.568 Chirality : 0.000 0.000 0 Planarity : 0.006 0.023 2041 Dihedral : 7.416 30.674 2041 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 25.37 % Favored : 74.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.92 (0.17), residues: 2022 helix: -1.59 (0.14), residues: 1213 sheet: None (None), residues: 0 loop : -4.25 (0.19), residues: 809 =============================================================================== Job complete usr+sys time: 1374.63 seconds wall clock time: 25 minutes 20.61 seconds (1520.61 seconds total)