Starting phenix.real_space_refine on Sat Mar 7 07:14:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbl_11157/03_2026/6zbl_11157.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbl_11157/03_2026/6zbl_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/cci-nas-00/data/ceres_data/6zbl_11157/03_2026/6zbl_11157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbl_11157/03_2026/6zbl_11157.map" model { file = "/net/cci-nas-00/data/ceres_data/6zbl_11157/03_2026/6zbl_11157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbl_11157/03_2026/6zbl_11157.cif" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 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. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.05, per 1000 atoms: 0.15 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.3 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: 0.83 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: 9.21 Time building geometry restraints manager: 4.89 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: 0.00 - 1.78: 61310 1.78 - 3.55: 9626 3.55 - 5.33: 698 5.33 - 7.11: 84 7.11 - 8.88: 12 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: 16707 17.99 - 35.99: 1103 35.99 - 53.98: 270 53.98 - 71.97: 85 71.97 - 89.97: 51 Dihedral angle restraints: 18216 sinusoidal: 10132 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 18213 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 2.450 nonbonded pdb=" HZ3 LYS D1064 " pdb=" O SER D1150 " model vdw 1.625 2.450 nonbonded pdb=" OD1 ASN B1416 " pdb="HE21 GLN B1419 " model vdw 1.644 2.450 nonbonded pdb=" OD1 ASN D1416 " pdb="HE21 GLN D1419 " model vdw 1.644 2.450 ... (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 Time spend for trying shortcut: 0.05 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 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.200 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 34.750 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:1.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.015 0.534 19592 Z= 0.744 Angle : 1.262 45.484 26292 Z= 0.838 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 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.002 ARG C 537 TYR 0.042 0.004 TYR B1138 PHE 0.028 0.003 PHE B1412 HIS 0.015 0.003 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.01365 (19588) covalent geometry : angle 1.19694 (26284) SS BOND : bond 0.37740 ( 4) SS BOND : angle 22.87694 ( 8) hydrogen bonds : bond 0.16708 ( 1444) hydrogen bonds : angle 5.70392 ( 4230) *********************** 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 to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.042 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 824 MET cc_start: 0.7713 (ttp) cc_final: 0.7416 (ptp) REVERT: B 978 SER cc_start: 0.9395 (m) cc_final: 0.9118 (p) REVERT: B 1534 GLU cc_start: 0.9104 (tt0) cc_final: 0.8873 (pp20) REVERT: C 824 MET cc_start: 0.7709 (ttp) cc_final: 0.7420 (ptp) REVERT: D 978 SER cc_start: 0.9396 (m) cc_final: 0.9119 (p) REVERT: D 1534 GLU cc_start: 0.9108 (tt0) cc_final: 0.8873 (pp20) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.4787 time to fit residues: 119.3680 Evaluate side-chains 92 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 HIS B1070 ASN B1137 HIS B1215 ASN C 668 HIS D1070 ASN D1137 HIS D1215 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.073700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.052966 restraints weight = 252378.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.055430 restraints weight = 94291.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.056869 restraints weight = 54596.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.057668 restraints weight = 40035.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.058174 restraints weight = 33682.672| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19592 Z= 0.137 Angle : 0.588 6.672 26292 Z= 0.317 Chirality : 0.034 0.142 2952 Planarity : 0.003 0.030 3314 Dihedral : 4.584 23.410 2470 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.18 % Allowed : 4.57 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.17), residues: 2290 helix: 1.12 (0.12), residues: 1868 sheet: None (None), residues: 0 loop : -0.18 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1384 TYR 0.018 0.001 TYR A 559 PHE 0.014 0.001 PHE B1021 HIS 0.003 0.001 HIS B1400 Details of bonding type rmsd covalent geometry : bond 0.00279 (19588) covalent geometry : angle 0.58715 (26284) SS BOND : bond 0.00276 ( 4) SS BOND : angle 1.37092 ( 8) hydrogen bonds : bond 0.05573 ( 1444) hydrogen bonds : angle 4.07483 ( 4230) *********************** 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 to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 1.128 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: A 853 ASN cc_start: 0.8506 (t0) cc_final: 0.7756 (t0) REVERT: C 853 ASN cc_start: 0.8507 (t0) cc_final: 0.7755 (t0) outliers start: 4 outliers final: 4 residues processed: 92 average time/residue: 0.4603 time to fit residues: 58.5684 Evaluate side-chains 64 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1460 GLU Chi-restraints excluded: chain D residue 994 ILE Chi-restraints excluded: chain D residue 1460 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 161 optimal weight: 3.9990 chunk 27 optimal weight: 0.0370 chunk 177 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.071353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.050096 restraints weight = 262551.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.052499 restraints weight = 101565.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.053926 restraints weight = 60033.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.054771 restraints weight = 44469.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.055188 restraints weight = 37407.046| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 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 : 0.004 0.032 19592 Z= 0.175 Angle : 0.516 5.954 26292 Z= 0.284 Chirality : 0.033 0.138 2952 Planarity : 0.003 0.028 3314 Dihedral : 4.108 20.698 2470 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.27 % Allowed : 5.38 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.17), residues: 2290 helix: 1.78 (0.12), residues: 1874 sheet: None (None), residues: 0 loop : -0.10 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 470 TYR 0.018 0.001 TYR A 559 PHE 0.008 0.001 PHE A 163 HIS 0.005 0.001 HIS B1400 Details of bonding type rmsd covalent geometry : bond 0.00359 (19588) covalent geometry : angle 0.51549 (26284) SS BOND : bond 0.00243 ( 4) SS BOND : angle 1.03438 ( 8) hydrogen bonds : bond 0.04818 ( 1444) hydrogen bonds : angle 3.84001 ( 4230) *********************** 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 73 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.955 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: B 1145 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8777 (m-10) REVERT: D 1145 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8785 (m-10) outliers start: 6 outliers final: 2 residues processed: 73 average time/residue: 0.4502 time to fit residues: 46.5033 Evaluate side-chains 57 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain B residue 1145 TYR Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain D residue 1145 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 104 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 206 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 668 HIS C 668 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.071200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.049842 restraints weight = 262504.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.052246 restraints weight = 101017.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.053636 restraints weight = 59797.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.054494 restraints weight = 44580.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.054932 restraints weight = 37535.424| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19592 Z= 0.144 Angle : 0.488 5.813 26292 Z= 0.268 Chirality : 0.032 0.135 2952 Planarity : 0.003 0.027 3314 Dihedral : 3.897 19.278 2470 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.54 % Allowed : 5.75 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.17), residues: 2290 helix: 2.10 (0.12), residues: 1878 sheet: None (None), residues: 0 loop : 0.04 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D1384 TYR 0.014 0.001 TYR A 559 PHE 0.008 0.001 PHE C 163 HIS 0.004 0.001 HIS C 814 Details of bonding type rmsd covalent geometry : bond 0.00293 (19588) covalent geometry : angle 0.48748 (26284) SS BOND : bond 0.00226 ( 4) SS BOND : angle 0.86054 ( 8) hydrogen bonds : bond 0.04448 ( 1444) hydrogen bonds : angle 3.67513 ( 4230) *********************** 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 72 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 1.110 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: A 868 MET cc_start: 0.8452 (tpp) cc_final: 0.8248 (tpp) REVERT: C 868 MET cc_start: 0.8452 (tpp) cc_final: 0.8235 (tpp) outliers start: 12 outliers final: 4 residues processed: 70 average time/residue: 0.4419 time to fit residues: 44.3734 Evaluate side-chains 56 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain C residue 181 TYR Chi-restraints excluded: chain C residue 241 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 84 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 51 optimal weight: 0.0970 chunk 116 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN C 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.070006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.048863 restraints weight = 263168.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.051104 restraints weight = 106573.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.052375 restraints weight = 64831.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.053203 restraints weight = 49319.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053645 restraints weight = 41723.691| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19592 Z= 0.183 Angle : 0.500 6.367 26292 Z= 0.277 Chirality : 0.033 0.135 2952 Planarity : 0.003 0.026 3314 Dihedral : 3.738 18.607 2470 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.18 % Allowed : 7.10 % Favored : 92.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.93 (0.17), residues: 2290 helix: 2.36 (0.12), residues: 1868 sheet: None (None), residues: 0 loop : 0.05 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 240 TYR 0.013 0.001 TYR A 559 PHE 0.008 0.001 PHE C 163 HIS 0.004 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00378 (19588) covalent geometry : angle 0.49939 (26284) SS BOND : bond 0.00474 ( 4) SS BOND : angle 1.86528 ( 8) hydrogen bonds : bond 0.04261 ( 1444) hydrogen bonds : angle 3.69106 ( 4230) *********************** 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 56 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.994 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 outliers start: 4 outliers final: 4 residues processed: 54 average time/residue: 0.4138 time to fit residues: 32.9688 Evaluate side-chains 51 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain C residue 181 TYR Chi-restraints excluded: chain D residue 1376 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 638 GLN C 213 ASN C 638 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.068760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.047564 restraints weight = 265684.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.049738 restraints weight = 107781.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.051017 restraints weight = 65833.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.051780 restraints weight = 50055.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.052152 restraints weight = 42633.005| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19592 Z= 0.222 Angle : 0.522 5.982 26292 Z= 0.290 Chirality : 0.033 0.140 2952 Planarity : 0.003 0.028 3314 Dihedral : 3.664 19.482 2470 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.45 % Allowed : 7.65 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.17), residues: 2290 helix: 2.54 (0.12), residues: 1864 sheet: None (None), residues: 0 loop : 0.09 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 577 TYR 0.013 0.001 TYR C 862 PHE 0.010 0.001 PHE B1112 HIS 0.006 0.001 HIS C 814 Details of bonding type rmsd covalent geometry : bond 0.00454 (19588) covalent geometry : angle 0.52176 (26284) SS BOND : bond 0.00239 ( 4) SS BOND : angle 1.54328 ( 8) hydrogen bonds : bond 0.04184 ( 1444) hydrogen bonds : angle 3.75716 ( 4230) *********************** 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 59 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 1.053 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: A 868 MET cc_start: 0.8716 (tpp) cc_final: 0.8510 (tpp) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 0.3688 time to fit residues: 30.2918 Evaluate side-chains 50 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain C residue 181 TYR Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain D residue 1376 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 196 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 175 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 120 optimal weight: 0.4980 chunk 177 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.069492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.048393 restraints weight = 262223.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.050611 restraints weight = 104826.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.051946 restraints weight = 63407.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.052715 restraints weight = 47750.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.053096 restraints weight = 40624.879| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19592 Z= 0.119 Angle : 0.443 4.954 26292 Z= 0.242 Chirality : 0.032 0.134 2952 Planarity : 0.002 0.030 3314 Dihedral : 3.568 17.987 2470 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.36 % Allowed : 7.83 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.17), residues: 2290 helix: 2.78 (0.12), residues: 1866 sheet: None (None), residues: 0 loop : 0.29 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1173 TYR 0.012 0.001 TYR C 862 PHE 0.013 0.001 PHE C 877 HIS 0.003 0.001 HIS C 814 Details of bonding type rmsd covalent geometry : bond 0.00242 (19588) covalent geometry : angle 0.44203 (26284) SS BOND : bond 0.00333 ( 4) SS BOND : angle 1.53254 ( 8) hydrogen bonds : bond 0.04115 ( 1444) hydrogen bonds : angle 3.43771 ( 4230) *********************** 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 59 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 1.070 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: C 868 MET cc_start: 0.8602 (tpp) cc_final: 0.8284 (tpp) outliers start: 8 outliers final: 4 residues processed: 57 average time/residue: 0.3926 time to fit residues: 33.6931 Evaluate side-chains 54 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain C residue 181 TYR Chi-restraints excluded: chain D residue 1376 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 197 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 25 optimal weight: 0.1980 chunk 145 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.070253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.049006 restraints weight = 261789.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.051340 restraints weight = 99211.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.052678 restraints weight = 58591.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.053517 restraints weight = 43940.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.053922 restraints weight = 37049.617| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19592 Z= 0.100 Angle : 0.421 4.816 26292 Z= 0.228 Chirality : 0.031 0.135 2952 Planarity : 0.002 0.030 3314 Dihedral : 3.406 16.055 2470 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.45 % Allowed : 7.74 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.92 (0.17), residues: 2290 helix: 3.03 (0.12), residues: 1864 sheet: None (None), residues: 0 loop : 0.47 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 652 TYR 0.010 0.001 TYR C 303 PHE 0.009 0.001 PHE C 877 HIS 0.003 0.001 HIS C 889 Details of bonding type rmsd covalent geometry : bond 0.00203 (19588) covalent geometry : angle 0.42089 (26284) SS BOND : bond 0.00089 ( 4) SS BOND : angle 1.24135 ( 8) hydrogen bonds : bond 0.03857 ( 1444) hydrogen bonds : angle 3.26257 ( 4230) *********************** 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 67 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 1.070 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: C 868 MET cc_start: 0.8650 (tpp) cc_final: 0.8338 (tpp) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.3823 time to fit residues: 37.6164 Evaluate side-chains 60 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain B residue 972 ASP Chi-restraints excluded: chain B residue 1075 LEU Chi-restraints excluded: chain C residue 181 TYR Chi-restraints excluded: chain D residue 972 ASP Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 96 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 213 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 222 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.069146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.048396 restraints weight = 259742.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.050524 restraints weight = 102997.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.051831 restraints weight = 62293.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.052591 restraints weight = 46716.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.052986 restraints weight = 39606.764| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19592 Z= 0.189 Angle : 0.465 4.592 26292 Z= 0.258 Chirality : 0.032 0.133 2952 Planarity : 0.002 0.030 3314 Dihedral : 3.382 16.131 2470 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.50 % Allowed : 8.01 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.17), residues: 2290 helix: 2.98 (0.12), residues: 1872 sheet: None (None), residues: 0 loop : 0.40 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.013 0.001 TYR C 298 PHE 0.010 0.001 PHE A 877 HIS 0.004 0.001 HIS C 814 Details of bonding type rmsd covalent geometry : bond 0.00386 (19588) covalent geometry : angle 0.46437 (26284) SS BOND : bond 0.00231 ( 4) SS BOND : angle 1.28782 ( 8) hydrogen bonds : bond 0.03863 ( 1444) hydrogen bonds : angle 3.49970 ( 4230) *********************** 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 63 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 1.108 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: A 868 MET cc_start: 0.8698 (tpp) cc_final: 0.8394 (tpp) REVERT: C 868 MET cc_start: 0.8765 (tpp) cc_final: 0.8440 (tpp) outliers start: 11 outliers final: 9 residues processed: 60 average time/residue: 0.4061 time to fit residues: 36.6301 Evaluate side-chains 61 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 1164 ASP Chi-restraints excluded: chain B residue 1376 ILE Chi-restraints excluded: chain C residue 181 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain D residue 1164 ASP Chi-restraints excluded: chain D residue 1376 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 165 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.069880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.048655 restraints weight = 262060.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.050953 restraints weight = 99343.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.052278 restraints weight = 58744.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.053111 restraints weight = 44060.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.053514 restraints weight = 37147.836| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19592 Z= 0.123 Angle : 0.430 4.605 26292 Z= 0.236 Chirality : 0.031 0.134 2952 Planarity : 0.002 0.031 3314 Dihedral : 3.347 16.023 2470 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.36 % Allowed : 8.24 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.03 (0.17), residues: 2290 helix: 3.11 (0.12), residues: 1866 sheet: None (None), residues: 0 loop : 0.53 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 652 TYR 0.009 0.001 TYR C 298 PHE 0.007 0.001 PHE D1021 HIS 0.004 0.001 HIS A 814 Details of bonding type rmsd covalent geometry : bond 0.00250 (19588) covalent geometry : angle 0.42943 (26284) SS BOND : bond 0.00197 ( 4) SS BOND : angle 1.16769 ( 8) hydrogen bonds : bond 0.03842 ( 1444) hydrogen bonds : angle 3.32019 ( 4230) ********************** 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 62 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 1.187 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: C 868 MET cc_start: 0.8779 (tpp) cc_final: 0.8415 (tpp) outliers start: 8 outliers final: 8 residues processed: 58 average time/residue: 0.4253 time to fit residues: 36.6074 Evaluate side-chains 62 residues out of total 2210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain B residue 1164 ASP Chi-restraints excluded: chain C residue 181 TYR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 824 MET Chi-restraints excluded: chain D residue 1164 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 80 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 67 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.069642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.048605 restraints weight = 263484.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.050805 restraints weight = 106442.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.052120 restraints weight = 64691.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.052858 restraints weight = 48803.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.053315 restraints weight = 41674.440| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19592 Z= 0.129 Angle : 0.433 4.443 26292 Z= 0.239 Chirality : 0.032 0.135 2952 Planarity : 0.002 0.031 3314 Dihedral : 3.268 15.814 2470 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.63 % Allowed : 8.05 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.15 (0.17), residues: 2290 helix: 3.18 (0.11), residues: 1870 sheet: None (None), residues: 0 loop : 0.58 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1384 TYR 0.009 0.001 TYR C 862 PHE 0.008 0.001 PHE A 877 HIS 0.004 0.001 HIS C 814 Details of bonding type rmsd covalent geometry : bond 0.00264 (19588) covalent geometry : angle 0.43210 (26284) SS BOND : bond 0.00230 ( 4) SS BOND : angle 1.19789 ( 8) hydrogen bonds : bond 0.03732 ( 1444) hydrogen bonds : angle 3.29372 ( 4230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5425.35 seconds wall clock time: 93 minutes 28.09 seconds (5608.09 seconds total)