Starting phenix.real_space_refine (version: dev) on Tue May 17 09:17:27 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbl_11157/05_2022/6zbl_11157.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbl_11157/05_2022/6zbl_11157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbl_11157/05_2022/6zbl_11157.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbl_11157/05_2022/6zbl_11157.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbl_11157/05_2022/6zbl_11157.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbl_11157/05_2022/6zbl_11157.pdb" } resolution = 3.6 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= 0.002 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 39074 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 11303 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 17, 'TRANS': 647} Chain breaks: 5 Chain: "B" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 8234 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 11, 'TRANS': 486} Chain breaks: 2 Chain: "C" Number of atoms: 11303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 11303 Classifications: {'peptide': 665} Link IDs: {'PTRANS': 17, 'TRANS': 647} Chain breaks: 5 Chain: "D" Number of atoms: 8234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 8234 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 11, 'TRANS': 486} Chain breaks: 2 Time building chain proxies: 18.40, per 1000 atoms: 0.47 Number of scatterers: 39074 At special positions: 0 Unit cell: (179.859, 154.011, 130.317, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 3696 8.00 N 3164 7.00 C 12390 6.00 H 19788 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=1.50 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 845 " distance=2.02 Simple disulfide: pdb=" SG CYS C 211 " - pdb=" SG CYS C 216 " distance=1.50 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 845 " distance=2.02 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: 31.00 Conformation dependent library (CDL) restraints added in 3.0 seconds 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.694A pdb=" N GLU A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.502A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 4.162A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 4.268A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.898A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.611A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 247 removed outlier: 4.186A pdb=" N ASP A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 281 Processing helix chain 'A' and resid 286 through 322 removed outlier: 3.920A pdb=" N SER A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 326 through 338 Processing helix chain 'A' and resid 356 through 374 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 400 removed outlier: 3.816A pdb=" N ASN A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.583A pdb=" N ILE A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 removed outlier: 4.013A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 494 removed outlier: 3.614A pdb=" N ILE A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 522 removed outlier: 3.919A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.725A pdb=" N LYS A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N SER A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 616 removed outlier: 3.648A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 666 removed outlier: 3.617A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 652 " --> pdb=" O ILE A 648 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 664 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 removed outlier: 4.824A pdb=" N LYS A 688 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 710 removed outlier: 3.702A pdb=" N LYS A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 704 " --> pdb=" O LYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 822 removed outlier: 3.918A pdb=" N LYS A 809 " --> pdb=" O GLU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 832 removed outlier: 3.594A pdb=" N TYR A 832 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 844 removed outlier: 4.571A pdb=" N GLU A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.951A pdb=" N ASN A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 891 removed outlier: 3.601A pdb=" N MET A 861 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP A 871 " --> pdb=" O SER A 867 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A 874 " --> pdb=" O ASN A 870 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 877 " --> pdb=" O GLN A 873 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 880 " --> pdb=" O PHE A 876 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 882 " --> pdb=" O GLU A 878 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE A 885 " --> pdb=" O GLN A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'B' and resid 964 through 968 Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.556A pdb=" N VAL B 977 " --> pdb=" O LEU B 973 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1009 Processing helix chain 'B' and resid 1010 through 1014 Processing helix chain 'B' and resid 1015 through 1025 removed outlier: 3.508A pdb=" N LYS B1019 " --> pdb=" O ASN B1015 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS B1023 " --> pdb=" O LYS B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1032 Processing helix chain 'B' and resid 1033 through 1100 removed outlier: 4.287A pdb=" N ASP B1056 " --> pdb=" O GLN B1052 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B1090 " --> pdb=" O THR B1086 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN B1100 " --> pdb=" O LEU B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1146 removed outlier: 3.793A pdb=" N PHE B1113 " --> pdb=" O PHE B1109 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B1122 " --> pdb=" O GLU B1118 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1155 Processing helix chain 'B' and resid 1156 through 1212 removed outlier: 4.461A pdb=" N TYR B1166 " --> pdb=" O THR B1162 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B1167 " --> pdb=" O GLU B1163 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B1179 " --> pdb=" O LEU B1175 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY B1180 " --> pdb=" O SER B1176 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS B1181 " --> pdb=" O LYS B1177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP B1184 " --> pdb=" O GLY B1180 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS B1212 " --> pdb=" O LYS B1208 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1235 removed outlier: 3.502A pdb=" N ASN B1224 " --> pdb=" O SER B1220 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS B1226 " --> pdb=" O SER B1222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B1235 " --> pdb=" O ALA B1231 " (cutoff:3.500A) Processing helix chain 'B' and resid 1236 through 1239 Processing helix chain 'B' and resid 1347 through 1392 removed outlier: 3.617A pdb=" N LEU B1351 " --> pdb=" O TYR B1347 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B1357 " --> pdb=" O GLY B1353 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B1367 " --> pdb=" O GLU B1363 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG B1384 " --> pdb=" O ARG B1380 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B1391 " --> pdb=" O PHE B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1393 through 1399 removed outlier: 3.877A pdb=" N GLN B1397 " --> pdb=" O ASP B1394 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1415 Processing helix chain 'B' and resid 1416 through 1473 removed outlier: 4.040A pdb=" N GLU B1443 " --> pdb=" O LYS B1439 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B1464 " --> pdb=" O GLU B1460 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B1465 " --> pdb=" O SER B1461 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE B1473 " --> pdb=" O GLU B1469 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1554 removed outlier: 3.650A pdb=" N LEU B1500 " --> pdb=" O PHE B1496 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B1519 " --> pdb=" O ASP B1515 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B1530 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B1538 " --> pdb=" O GLU B1534 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.694A pdb=" N GLU C 27 " --> pdb=" O GLU C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 removed outlier: 3.502A pdb=" N LEU C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS C 158 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 174 removed outlier: 4.162A pdb=" N ASP C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 4.268A pdb=" N TYR C 181 " --> pdb=" O HIS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 211 removed outlier: 3.898A pdb=" N GLU C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'C' and resid 225 through 239 removed outlier: 3.611A pdb=" N ASP C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL C 231 " --> pdb=" O ASN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 247 removed outlier: 4.186A pdb=" N ASP C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 281 Processing helix chain 'C' and resid 286 through 322 removed outlier: 3.920A pdb=" N SER C 315 " --> pdb=" O HIS C 311 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 326 through 338 Processing helix chain 'C' and resid 356 through 374 Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 386 through 400 removed outlier: 3.816A pdb=" N ASN C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 442 removed outlier: 3.583A pdb=" N ILE C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 removed outlier: 4.013A pdb=" N ILE C 463 " --> pdb=" O ASN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 494 removed outlier: 3.614A pdb=" N ILE C 472 " --> pdb=" O LYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 522 removed outlier: 3.919A pdb=" N LEU C 512 " --> pdb=" O ASP C 508 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 582 removed outlier: 3.725A pdb=" N LYS C 532 " --> pdb=" O ASP C 528 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 543 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS C 550 " --> pdb=" O ARG C 546 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N SER C 553 " --> pdb=" O ASN C 549 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP C 573 " --> pdb=" O SER C 569 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE C 580 " --> pdb=" O LEU C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 616 removed outlier: 3.648A pdb=" N LYS C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU C 604 " --> pdb=" O LYS C 600 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 607 " --> pdb=" O THR C 603 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 666 removed outlier: 3.617A pdb=" N GLN C 638 " --> pdb=" O ILE C 634 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 652 " --> pdb=" O ILE C 648 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU C 663 " --> pdb=" O LYS C 659 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 664 " --> pdb=" O ASN C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 removed outlier: 4.824A pdb=" N LYS C 688 " --> pdb=" O LEU C 684 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 689 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU C 696 " --> pdb=" O ASP C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 710 removed outlier: 3.702A pdb=" N LYS C 700 " --> pdb=" O GLU C 696 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET C 704 " --> pdb=" O LYS C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 822 removed outlier: 3.918A pdb=" N LYS C 809 " --> pdb=" O GLU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 832 removed outlier: 3.594A pdb=" N TYR C 832 " --> pdb=" O LEU C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 844 removed outlier: 4.571A pdb=" N GLU C 841 " --> pdb=" O GLU C 837 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 842 " --> pdb=" O GLU C 838 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER C 844 " --> pdb=" O ASN C 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.951A pdb=" N ASN C 856 " --> pdb=" O PHE C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 891 removed outlier: 3.601A pdb=" N MET C 861 " --> pdb=" O ASN C 857 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP C 871 " --> pdb=" O SER C 867 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C 874 " --> pdb=" O ASN C 870 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 877 " --> pdb=" O GLN C 873 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 880 " --> pdb=" O PHE C 876 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS C 882 " --> pdb=" O GLU C 878 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE C 885 " --> pdb=" O GLN C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'D' and resid 964 through 968 Processing helix chain 'D' and resid 973 through 981 removed outlier: 3.556A pdb=" N VAL D 977 " --> pdb=" O LEU D 973 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1009 Processing helix chain 'D' and resid 1010 through 1014 Processing helix chain 'D' and resid 1015 through 1025 removed outlier: 3.508A pdb=" N LYS D1019 " --> pdb=" O ASN D1015 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS D1023 " --> pdb=" O LYS D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1025 through 1032 Processing helix chain 'D' and resid 1033 through 1100 removed outlier: 4.287A pdb=" N ASP D1056 " --> pdb=" O GLN D1052 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU D1090 " --> pdb=" O THR D1086 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN D1100 " --> pdb=" O LEU D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1146 removed outlier: 3.793A pdb=" N PHE D1113 " --> pdb=" O PHE D1109 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA D1122 " --> pdb=" O GLU D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1155 Processing helix chain 'D' and resid 1156 through 1212 removed outlier: 4.461A pdb=" N TYR D1166 " --> pdb=" O THR D1162 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA D1167 " --> pdb=" O GLU D1163 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP D1179 " --> pdb=" O LEU D1175 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY D1180 " --> pdb=" O SER D1176 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS D1181 " --> pdb=" O LYS D1177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP D1184 " --> pdb=" O GLY D1180 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS D1212 " --> pdb=" O LYS D1208 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1235 removed outlier: 3.502A pdb=" N ASN D1224 " --> pdb=" O SER D1220 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS D1226 " --> pdb=" O SER D1222 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR D1235 " --> pdb=" O ALA D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1236 through 1239 Processing helix chain 'D' and resid 1347 through 1392 removed outlier: 3.617A pdb=" N LEU D1351 " --> pdb=" O TYR D1347 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D1357 " --> pdb=" O GLY D1353 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE D1367 " --> pdb=" O GLU D1363 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG D1384 " --> pdb=" O ARG D1380 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D1391 " --> pdb=" O PHE D1387 " (cutoff:3.500A) Processing helix chain 'D' and resid 1393 through 1399 removed outlier: 3.877A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1411 through 1415 Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 4.040A pdb=" N GLU D1443 " --> pdb=" O LYS D1439 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS D1464 " --> pdb=" O GLU D1460 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE D1473 " --> pdb=" O GLU D1469 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1554 removed outlier: 3.650A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D1530 " --> pdb=" O ASN D1526 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) 1444 hydrogen bonds defined for protein. 4230 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: 14.27 Time building geometry restraints manager: 32.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19784 1.03 - 1.23: 314 1.23 - 1.42: 7546 1.42 - 1.62: 11672 1.62 - 1.81: 60 Bond restraints: 39376 Sorted by residual: bond pdb=" CA LYS A 809 " pdb=" C LYS A 809 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.29e-02 6.01e+03 2.96e+01 bond pdb=" CA LYS C 809 " pdb=" C LYS C 809 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.29e-02 6.01e+03 2.96e+01 bond pdb=" N ILE A 218 " pdb=" CA ILE A 218 " ideal model delta sigma weight residual 1.454 1.489 -0.034 7.70e-03 1.69e+04 1.95e+01 bond pdb=" N ILE C 218 " pdb=" CA ILE C 218 " ideal model delta sigma weight residual 1.454 1.489 -0.034 7.70e-03 1.69e+04 1.95e+01 bond pdb=" C LEU D1459 " pdb=" O LEU D1459 " ideal model delta sigma weight residual 1.236 1.188 0.049 1.15e-02 7.56e+03 1.80e+01 ... (remaining 39371 not shown) Histogram of bond angle deviations from ideal: 96.51 - 103.60: 160 103.60 - 110.69: 42022 110.69 - 117.78: 12604 117.78 - 124.87: 16080 124.87 - 131.95: 864 Bond angle restraints: 71730 Sorted by residual: angle pdb=" N ILE A 380 " pdb=" CA ILE A 380 " pdb=" C ILE A 380 " ideal model delta sigma weight residual 111.91 106.71 5.20 8.90e-01 1.26e+00 3.42e+01 angle pdb=" N ILE C 380 " pdb=" CA ILE C 380 " pdb=" C ILE C 380 " ideal model delta sigma weight residual 111.91 106.71 5.20 8.90e-01 1.26e+00 3.42e+01 angle pdb=" N TYR A 215 " pdb=" CA TYR A 215 " pdb=" C TYR A 215 " ideal model delta sigma weight residual 111.28 105.61 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" N TYR C 215 " pdb=" CA TYR C 215 " pdb=" C TYR C 215 " ideal model delta sigma weight residual 111.28 105.61 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" N LYS C 261 " pdb=" CA LYS C 261 " pdb=" C LYS C 261 " ideal model delta sigma weight residual 111.36 105.76 5.60 1.09e+00 8.42e-01 2.64e+01 ... (remaining 71725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14451 17.99 - 35.99: 1029 35.99 - 53.98: 182 53.98 - 71.97: 65 71.97 - 89.97: 51 Dihedral angle restraints: 15778 sinusoidal: 7694 harmonic: 8084 Sorted by residual: dihedral pdb=" CB CYS A 813 " pdb=" SG CYS A 813 " pdb=" SG CYS A 845 " pdb=" CB CYS A 845 " ideal model delta sinusoidal sigma weight residual 93.00 147.70 -54.70 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS C 813 " pdb=" SG CYS C 813 " pdb=" SG CYS C 845 " pdb=" CB CYS C 845 " ideal model delta sinusoidal sigma weight residual 93.00 147.70 -54.70 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CA LYS B1399 " pdb=" C LYS B1399 " pdb=" N HIS B1400 " pdb=" CA HIS B1400 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 15775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1956 0.063 - 0.126: 728 0.126 - 0.188: 230 0.188 - 0.251: 32 0.251 - 0.314: 6 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA ILE C 369 " pdb=" N ILE C 369 " pdb=" C ILE C 369 " pdb=" CB ILE C 369 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ILE A 369 " pdb=" N ILE A 369 " pdb=" C ILE A 369 " pdb=" CB ILE A 369 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ILE A 362 " pdb=" N ILE A 362 " pdb=" C ILE A 362 " pdb=" CB ILE A 362 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2949 not shown) Planarity restraints: 5566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 808 " 0.025 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C THR C 808 " -0.086 2.00e-02 2.50e+03 pdb=" O THR C 808 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS C 809 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 808 " 0.025 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C THR A 808 " -0.086 2.00e-02 2.50e+03 pdb=" O THR A 808 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS A 809 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1138 " -0.005 2.00e-02 2.50e+03 2.62e-02 2.06e+01 pdb=" CG TYR B1138 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR B1138 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B1138 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B1138 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B1138 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B1138 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR B1138 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 TYR B1138 " -0.047 2.00e-02 2.50e+03 pdb=" HD2 TYR B1138 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR B1138 " 0.035 2.00e-02 2.50e+03 pdb=" HE2 TYR B1138 " 0.014 2.00e-02 2.50e+03 ... (remaining 5563 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1866 2.20 - 2.80: 83404 2.80 - 3.40: 103323 3.40 - 4.00: 125978 4.00 - 4.60: 204384 Nonbonded interactions: 518955 Sorted by model distance: nonbonded pdb=" HG1 THR A 41 " pdb=" HE1 TYR A 150 " model vdw 1.603 2.100 nonbonded pdb=" HZ3 LYS B1064 " pdb=" O SER B1150 " model vdw 1.621 1.850 nonbonded pdb=" HZ3 LYS D1064 " pdb=" O SER D1150 " model vdw 1.625 1.850 nonbonded pdb=" OD1 ASN B1416 " pdb="HE21 GLN B1419 " model vdw 1.644 1.850 nonbonded pdb=" OD1 ASN D1416 " pdb="HE21 GLN D1419 " model vdw 1.644 1.850 ... (remaining 518950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 12390 2.51 5 N 3164 2.21 5 O 3696 1.98 5 H 19788 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.790 Extract box with map and model: 9.440 Check model and map are aligned: 0.640 Convert atoms to be neutral: 0.300 Process input model: 114.010 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.014 0.121 19588 Z= 0.856 Angle : 1.197 8.884 26284 Z= 0.816 Chirality : 0.071 0.314 2952 Planarity : 0.006 0.050 3314 Dihedral : 14.690 89.843 7698 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.56 (0.16), residues: 2290 helix: -0.15 (0.11), residues: 1816 sheet: None (None), residues: 0 loop : -0.68 (0.27), residues: 474 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.9427 time to fit residues: 242.2862 Evaluate side-chains 84 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 HIS B1070 ASN B1137 HIS C 668 HIS D1070 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 19588 Z= 0.253 Angle : 0.608 6.657 26284 Z= 0.333 Chirality : 0.035 0.145 2952 Planarity : 0.003 0.026 3314 Dihedral : 4.580 24.698 2470 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer Outliers : 0.36 % 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: 1.22 (0.17), residues: 2290 helix: 1.12 (0.12), residues: 1866 sheet: None (None), residues: 0 loop : -0.30 (0.29), residues: 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 90 average time/residue: 0.8507 time to fit residues: 113.9679 Evaluate side-chains 60 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 3.562 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4496 time to fit residues: 7.6940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 167 optimal weight: 0.0970 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1215 ASN D1215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 19588 Z= 0.156 Angle : 0.486 5.825 26284 Z= 0.265 Chirality : 0.032 0.148 2952 Planarity : 0.002 0.025 3314 Dihedral : 4.068 20.060 2470 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer Outliers : 0.27 % 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: 2.26 (0.17), residues: 2290 helix: 1.86 (0.12), residues: 1876 sheet: None (None), residues: 0 loop : -0.05 (0.30), residues: 414 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 72 average time/residue: 0.8227 time to fit residues: 89.3883 Evaluate side-chains 62 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 3.368 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3884 time to fit residues: 5.7711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 209 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 668 HIS C 167 ASN C 668 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 19588 Z= 0.267 Angle : 0.518 5.670 26284 Z= 0.285 Chirality : 0.033 0.136 2952 Planarity : 0.002 0.021 3314 Dihedral : 3.858 20.028 2470 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.36 % 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: 2.61 (0.17), residues: 2290 helix: 2.12 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : -0.03 (0.30), residues: 418 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 61 average time/residue: 0.8976 time to fit residues: 82.7452 Evaluate side-chains 52 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 3.512 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6905 time to fit residues: 6.6022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 961 HIS C 213 ASN D 961 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 19588 Z= 0.323 Angle : 0.547 6.502 26284 Z= 0.305 Chirality : 0.034 0.141 2952 Planarity : 0.003 0.022 3314 Dihedral : 3.801 21.249 2470 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer Outliers : 0.09 % 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: 2.69 (0.17), residues: 2290 helix: 2.20 (0.12), residues: 1874 sheet: None (None), residues: 0 loop : -0.13 (0.29), residues: 416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.7969 time to fit residues: 67.7897 Evaluate side-chains 48 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 3.550 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 73 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 19588 Z= 0.172 Angle : 0.451 5.681 26284 Z= 0.246 Chirality : 0.032 0.135 2952 Planarity : 0.002 0.022 3314 Dihedral : 3.647 19.180 2470 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer Outliers : 0.18 % 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: 3.30 (0.17), residues: 2290 helix: 2.62 (0.12), residues: 1870 sheet: None (None), residues: 0 loop : 0.12 (0.29), residues: 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 0.7881 time to fit residues: 71.5938 Evaluate side-chains 53 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 3.108 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3758 time to fit residues: 5.8009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 221 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 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: 0.7938 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 19588 Z= 0.213 Angle : 0.464 5.472 26284 Z= 0.253 Chirality : 0.032 0.134 2952 Planarity : 0.002 0.022 3314 Dihedral : 3.544 18.600 2470 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.09 % 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: 3.52 (0.17), residues: 2290 helix: 2.78 (0.12), residues: 1870 sheet: None (None), residues: 0 loop : 0.19 (0.30), residues: 420 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 56 average time/residue: 0.8624 time to fit residues: 75.0077 Evaluate side-chains 52 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 3.376 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4047 time to fit residues: 5.8890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 174 optimal weight: 0.5980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7912 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 19588 Z= 0.125 Angle : 0.421 7.037 26284 Z= 0.227 Chirality : 0.031 0.135 2952 Planarity : 0.002 0.023 3314 Dihedral : 3.455 16.987 2470 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer Outliers : 0.36 % 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: 3.85 (0.17), residues: 2290 helix: 2.99 (0.12), residues: 1870 sheet: None (None), residues: 0 loop : 0.38 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 3.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.8017 time to fit residues: 77.6166 Evaluate side-chains 55 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 3.653 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4037 time to fit residues: 9.2765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 2.9990 chunk 212 optimal weight: 0.4980 chunk 193 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 195 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN C 856 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19588 Z= 0.181 Angle : 0.435 4.581 26284 Z= 0.239 Chirality : 0.031 0.133 2952 Planarity : 0.002 0.023 3314 Dihedral : 3.386 16.835 2470 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 0.09 % 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: 3.93 (0.17), residues: 2290 helix: 3.06 (0.12), residues: 1870 sheet: None (None), residues: 0 loop : 0.33 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.8804 time to fit residues: 73.2780 Evaluate side-chains 50 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 3.405 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 229 optimal weight: 0.5980 chunk 210 optimal weight: 2.9990 chunk 182 optimal weight: 0.0270 chunk 18 optimal weight: 7.9990 chunk 140 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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: 0.7900 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 19588 Z= 0.116 Angle : 0.413 9.213 26284 Z= 0.221 Chirality : 0.031 0.135 2952 Planarity : 0.002 0.024 3314 Dihedral : 3.327 15.315 2470 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: 4.20 (0.17), residues: 2290 helix: 3.25 (0.12), residues: 1870 sheet: None (None), residues: 0 loop : 0.44 (0.31), residues: 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4580 Ramachandran restraints generated. 2290 Oldfield, 0 Emsley, 2290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 3.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.8276 time to fit residues: 69.7180 Evaluate side-chains 50 residues out of total 2210 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 168 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.069532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.048652 restraints weight = 261693.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.050829 restraints weight = 104009.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.052160 restraints weight = 63050.311| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 19588 Z= 0.165 Angle : 0.422 7.443 26284 Z= 0.231 Chirality : 0.031 0.133 2952 Planarity : 0.002 0.023 3314 Dihedral : 3.266 15.340 2470 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: 4.19 (0.17), residues: 2290 helix: 3.25 (0.12), residues: 1874 sheet: None (None), residues: 0 loop : 0.29 (0.30), residues: 416 =============================================================================== Job complete usr+sys time: 4803.85 seconds wall clock time: 88 minutes 9.72 seconds (5289.72 seconds total)