Starting phenix.real_space_refine on Sat Aug 8 17:01:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uq0_64408/08_2026/9uq0_64408.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uq0_64408/08_2026/9uq0_64408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uq0_64408/08_2026/9uq0_64408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uq0_64408/08_2026/9uq0_64408.map" model { file = "/net/cci-nas-00/data/ceres_data/9uq0_64408/08_2026/9uq0_64408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uq0_64408/08_2026/9uq0_64408.cif" } resolution = 3.47 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= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 13 5.49 5 Mg 3 5.21 5 S 147 5.16 5 C 17909 2.51 5 N 4982 2.21 5 O 5522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28580 Number of models: 1 Model: "" Number of chains: 11 Chain: "2" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5342 Classifications: {'peptide': 697} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 29, 'TRANS': 667} Chain breaks: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 3, 'ARG:plan': 8, 'GLU:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 113 Chain: "3" Number of atoms: 4463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4463 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 20, 'TRANS': 584} Chain breaks: 4 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 16, 'ASP:plan': 7, 'ASN:plan1': 1, 'GLN:plan1': 6, 'GLU:plan': 9, 'PHE:plan': 1, 'HIS:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 194 Chain: "4" Number of atoms: 4919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 4919 Classifications: {'peptide': 663} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 25, 'TRANS': 637} Chain breaks: 3 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 318 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 7, 'ARG:plan': 18, 'GLN:plan1': 5, 'GLU:plan': 11, 'ASP:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 227 Chain: "5" Number of atoms: 4218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4218 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 21, 'TRANS': 538} Chain breaks: 6 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 16, 'GLU:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 124 Chain: "6" Number of atoms: 5250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5250 Classifications: {'peptide': 667} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 21, 'TRANS': 645} Chain breaks: 3 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 7, 'PHE:plan': 1, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "7" Number of atoms: 4234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4234 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 25, 'TRANS': 538} Chain breaks: 3 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 4, 'PHE:plan': 1, 'ARG:plan': 15, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 135 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1129 SG CYS 2 329 42.228 76.044 77.554 1.00217.89 S ATOM 1152 SG CYS 2 332 40.414 74.753 80.566 1.00222.64 S ATOM 1303 SG CYS 2 352 44.243 74.947 80.652 1.00223.30 S ATOM 1325 SG CYS 2 355 42.648 72.359 78.581 1.00229.04 S ATOM 10829 SG CYS 4 306 24.763 80.827 96.221 1.00213.96 S ATOM 10851 SG CYS 4 309 21.924 80.284 98.580 1.00217.95 S ATOM 10997 SG CYS 4 328 22.442 77.911 95.723 1.00233.57 S ATOM 11012 SG CYS 4 331 21.255 81.719 95.155 1.00233.38 S ATOM 20082 SG CYS 6 158 33.017 93.823 85.829 1.00198.18 S ATOM 20104 SG CYS 6 161 31.191 95.414 86.008 1.00202.32 S ATOM 20304 SG CYS 6 185 29.285 92.859 83.372 1.00210.87 S ATOM 25257 SG CYS 7 184 17.368 52.959 84.063 1.00285.98 S ATOM 25280 SG CYS 7 187 14.113 51.261 82.488 1.00299.01 S ATOM 25423 SG CYS 7 206 16.787 52.894 80.376 1.00298.99 S ATOM 25460 SG CYS 7 211 14.531 55.017 82.478 1.00323.40 S Time building chain proxies: 5.92, per 1000 atoms: 0.21 Number of scatterers: 28580 At special positions: 0 Unit cell: (149.46, 143.1, 163.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 147 16.00 P 13 15.00 Mg 3 11.99 O 5522 8.00 N 4982 7.00 C 17909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21002 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 352 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21002 " - pdb=" SG CYS 2 329 " pdb=" ZN 4 901 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb=" ZN 6 901 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 185 " pdb=" ZN 7 802 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 206 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 211 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 7 802 " - pdb=" SG CYS 7 184 " Number of angles added : 18 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7150 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 38 sheets defined 43.6% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain '2' and resid 191 through 206 Processing helix chain '2' and resid 213 through 224 removed outlier: 3.883A pdb=" N ASP 2 221 " --> pdb=" O GLU 2 217 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS 2 224 " --> pdb=" O SER 2 220 " (cutoff:3.500A) Processing helix chain '2' and resid 234 through 239 Processing helix chain '2' and resid 241 through 251 Proline residue: 2 249 - end of helix Processing helix chain '2' and resid 251 through 271 removed outlier: 3.743A pdb=" N LEU 2 255 " --> pdb=" O ALA 2 251 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN 2 257 " --> pdb=" O ALA 2 253 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP 2 260 " --> pdb=" O LEU 2 256 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU 2 261 " --> pdb=" O GLN 2 257 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU 2 265 " --> pdb=" O GLU 2 261 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) Processing helix chain '2' and resid 272 through 276 removed outlier: 3.574A pdb=" N ARG 2 276 " --> pdb=" O LYS 2 273 " (cutoff:3.500A) Processing helix chain '2' and resid 293 through 297 removed outlier: 3.535A pdb=" N LEU 2 297 " --> pdb=" O LEU 2 294 " (cutoff:3.500A) Processing helix chain '2' and resid 298 through 302 Processing helix chain '2' and resid 399 through 403 removed outlier: 3.933A pdb=" N VAL 2 403 " --> pdb=" O ALA 2 400 " (cutoff:3.500A) Processing helix chain '2' and resid 446 through 451 removed outlier: 3.550A pdb=" N LYS 2 450 " --> pdb=" O LYS 2 447 " (cutoff:3.500A) Processing helix chain '2' and resid 459 through 470 Processing helix chain '2' and resid 472 through 477 removed outlier: 3.752A pdb=" N LYS 2 476 " --> pdb=" O GLN 2 472 " (cutoff:3.500A) Processing helix chain '2' and resid 488 through 501 Processing helix chain '2' and resid 528 through 540 removed outlier: 3.765A pdb=" N PHE 2 532 " --> pdb=" O ALA 2 528 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU 2 533 " --> pdb=" O LYS 2 529 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS 2 538 " --> pdb=" O LYS 2 534 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 579 Processing helix chain '2' and resid 593 through 606 removed outlier: 3.524A pdb=" N SER 2 599 " --> pdb=" O GLN 2 595 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS 2 601 " --> pdb=" O ARG 2 597 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU 2 602 " --> pdb=" O THR 2 598 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN 2 606 " --> pdb=" O GLU 2 602 " (cutoff:3.500A) Processing helix chain '2' and resid 612 through 616 Processing helix chain '2' and resid 632 through 636 removed outlier: 4.039A pdb=" N ARG 2 636 " --> pdb=" O ILE 2 633 " (cutoff:3.500A) Processing helix chain '2' and resid 642 through 647 removed outlier: 3.508A pdb=" N VAL 2 647 " --> pdb=" O PHE 2 643 " (cutoff:3.500A) Processing helix chain '2' and resid 650 through 656 removed outlier: 3.574A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) Processing helix chain '2' and resid 668 through 686 Processing helix chain '2' and resid 719 through 728 removed outlier: 3.747A pdb=" N ILE 2 724 " --> pdb=" O LEU 2 720 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE 2 725 " --> pdb=" O LYS 2 721 " (cutoff:3.500A) Processing helix chain '2' and resid 739 through 758 removed outlier: 3.756A pdb=" N VAL 2 743 " --> pdb=" O ASP 2 739 " (cutoff:3.500A) Processing helix chain '2' and resid 763 through 781 removed outlier: 3.701A pdb=" N ARG 2 772 " --> pdb=" O GLU 2 768 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 803 Processing helix chain '2' and resid 807 through 818 removed outlier: 4.301A pdb=" N SER 2 813 " --> pdb=" O SER 2 809 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS 2 816 " --> pdb=" O ARG 2 812 " (cutoff:3.500A) Processing helix chain '2' and resid 827 through 851 removed outlier: 3.561A pdb=" N LEU 2 832 " --> pdb=" O ASN 2 828 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE 2 835 " --> pdb=" O LEU 2 831 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR 2 845 " --> pdb=" O ALA 2 841 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR 2 846 " --> pdb=" O GLU 2 842 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN 2 849 " --> pdb=" O THR 2 845 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG 2 850 " --> pdb=" O TYR 2 846 " (cutoff:3.500A) Processing helix chain '2' and resid 862 through 873 removed outlier: 4.106A pdb=" N VAL 2 866 " --> pdb=" O GLU 2 862 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP 2 867 " --> pdb=" O LYS 2 863 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS 2 868 " --> pdb=" O ASP 2 864 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN 2 871 " --> pdb=" O ASP 2 867 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE 2 872 " --> pdb=" O LYS 2 868 " (cutoff:3.500A) Processing helix chain '2' and resid 877 through 882 Processing helix chain '2' and resid 883 through 889 removed outlier: 3.542A pdb=" N ARG 2 887 " --> pdb=" O SER 2 883 " (cutoff:3.500A) Processing helix chain '3' and resid 30 through 35 Processing helix chain '3' and resid 38 through 43 Processing helix chain '3' and resid 51 through 58 Processing helix chain '3' and resid 59 through 68 Processing helix chain '3' and resid 69 through 86 removed outlier: 3.839A pdb=" N VAL 3 74 " --> pdb=" O PHE 3 70 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA 3 75 " --> pdb=" O GLU 3 71 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA 3 79 " --> pdb=" O ALA 3 75 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP 3 82 " --> pdb=" O ARG 3 78 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA 3 85 " --> pdb=" O LYS 3 81 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 94 removed outlier: 4.139A pdb=" N ALA 3 92 " --> pdb=" O ASP 3 88 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN 3 94 " --> pdb=" O THR 3 90 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 121 Processing helix chain '3' and resid 279 through 291 removed outlier: 4.372A pdb=" N LYS 3 285 " --> pdb=" O ILE 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 295 through 302 Processing helix chain '3' and resid 310 through 323 Processing helix chain '3' and resid 350 through 361 removed outlier: 3.599A pdb=" N LEU 3 354 " --> pdb=" O ALA 3 350 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU 3 355 " --> pdb=" O LYS 3 351 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYS 3 360 " --> pdb=" O ARG 3 356 " (cutoff:3.500A) Processing helix chain '3' and resid 411 through 414 removed outlier: 3.582A pdb=" N MET 3 414 " --> pdb=" O PHE 3 411 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 411 through 414' Processing helix chain '3' and resid 415 through 427 removed outlier: 3.587A pdb=" N ALA 3 421 " --> pdb=" O MET 3 417 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N HIS 3 423 " --> pdb=" O ARG 3 419 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 464 through 469 removed outlier: 3.514A pdb=" N ILE 3 469 " --> pdb=" O PRO 3 465 " (cutoff:3.500A) Processing helix chain '3' and resid 472 through 478 removed outlier: 3.712A pdb=" N LEU 3 476 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG 3 478 " --> pdb=" O SER 3 474 " (cutoff:3.500A) Processing helix chain '3' and resid 490 through 507 removed outlier: 3.641A pdb=" N ARG 3 495 " --> pdb=" O PRO 3 491 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU 3 496 " --> pdb=" O GLU 3 492 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS 3 500 " --> pdb=" O GLU 3 496 " (cutoff:3.500A) Processing helix chain '3' and resid 564 through 574 Processing helix chain '3' and resid 583 through 598 Processing helix chain '3' and resid 615 through 631 removed outlier: 3.921A pdb=" N GLU 3 619 " --> pdb=" O ALA 3 615 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG 3 623 " --> pdb=" O GLU 3 619 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA 3 631 " --> pdb=" O ALA 3 627 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 654 removed outlier: 3.878A pdb=" N ALA 3 642 " --> pdb=" O ASP 3 638 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU 3 643 " --> pdb=" O LEU 3 639 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU 3 644 " --> pdb=" O GLN 3 640 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA 3 645 " --> pdb=" O ASP 3 641 " (cutoff:3.500A) Processing helix chain '3' and resid 741 through 759 Processing helix chain '3' and resid 765 through 776 removed outlier: 3.758A pdb=" N ASP 3 775 " --> pdb=" O SER 3 771 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER 3 776 " --> pdb=" O ILE 3 772 " (cutoff:3.500A) Processing helix chain '3' and resid 781 through 795 Processing helix chain '4' and resid 194 through 199 removed outlier: 3.971A pdb=" N LEU 4 197 " --> pdb=" O MET 4 194 " (cutoff:3.500A) Processing helix chain '4' and resid 211 through 219 removed outlier: 3.981A pdb=" N SER 4 217 " --> pdb=" O GLU 4 213 " (cutoff:3.500A) Processing helix chain '4' and resid 219 through 229 Processing helix chain '4' and resid 229 through 248 removed outlier: 3.599A pdb=" N ILE 4 234 " --> pdb=" O PRO 4 230 " (cutoff:3.500A) Proline residue: 4 235 - end of helix removed outlier: 3.601A pdb=" N MET 4 239 " --> pdb=" O PRO 4 235 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE 4 246 " --> pdb=" O ASN 4 242 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 279 Processing helix chain '4' and resid 444 through 455 removed outlier: 3.751A pdb=" N LEU 4 448 " --> pdb=" O LYS 4 444 " (cutoff:3.500A) Processing helix chain '4' and resid 457 through 465 Processing helix chain '4' and resid 473 through 486 Processing helix chain '4' and resid 517 through 527 Processing helix chain '4' and resid 561 through 566 Processing helix chain '4' and resid 580 through 593 removed outlier: 3.511A pdb=" N SER 4 585 " --> pdb=" O GLU 4 581 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET 4 591 " --> pdb=" O LEU 4 587 " (cutoff:3.500A) Processing helix chain '4' and resid 629 through 635 Processing helix chain '4' and resid 637 through 643 removed outlier: 3.891A pdb=" N ARG 4 643 " --> pdb=" O THR 4 639 " (cutoff:3.500A) Processing helix chain '4' and resid 655 through 671 removed outlier: 3.568A pdb=" N TYR 4 671 " --> pdb=" O VAL 4 667 " (cutoff:3.500A) Processing helix chain '4' and resid 675 through 698 removed outlier: 4.220A pdb=" N GLU 4 679 " --> pdb=" O GLU 4 675 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA 4 692 " --> pdb=" O LYS 4 688 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER 4 696 " --> pdb=" O ALA 4 692 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE 4 698 " --> pdb=" O ALA 4 694 " (cutoff:3.500A) Processing helix chain '4' and resid 703 through 723 removed outlier: 3.542A pdb=" N ILE 4 720 " --> pdb=" O ASP 4 716 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY 4 721 " --> pdb=" O MET 4 717 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER 4 723 " --> pdb=" O LYS 4 719 " (cutoff:3.500A) Processing helix chain '4' and resid 731 through 748 removed outlier: 3.911A pdb=" N GLU 4 735 " --> pdb=" O PRO 4 731 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE 4 738 " --> pdb=" O LEU 4 734 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG 4 739 " --> pdb=" O GLU 4 735 " (cutoff:3.500A) Processing helix chain '4' and resid 754 through 772 removed outlier: 3.778A pdb=" N VAL 4 758 " --> pdb=" O GLU 4 754 " (cutoff:3.500A) Processing helix chain '4' and resid 800 through 811 removed outlier: 4.124A pdb=" N LYS 4 807 " --> pdb=" O GLU 4 803 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU 4 808 " --> pdb=" O ALA 4 804 " (cutoff:3.500A) Processing helix chain '4' and resid 820 through 831 Processing helix chain '4' and resid 836 through 847 Processing helix chain '5' and resid 30 through 40 Processing helix chain '5' and resid 53 through 63 Processing helix chain '5' and resid 73 through 78 Processing helix chain '5' and resid 82 through 89 removed outlier: 3.738A pdb=" N ASP 5 86 " --> pdb=" O GLU 5 82 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU 5 88 " --> pdb=" O LEU 5 84 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR 5 89 " --> pdb=" O ALA 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 91 through 96 removed outlier: 3.593A pdb=" N HIS 5 95 " --> pdb=" O GLN 5 91 " (cutoff:3.500A) Processing helix chain '5' and resid 97 through 99 No H-bonds generated for 'chain '5' and resid 97 through 99' Processing helix chain '5' and resid 100 through 107 removed outlier: 3.737A pdb=" N LYS 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU 5 105 " --> pdb=" O GLU 5 101 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA 5 107 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 140 Processing helix chain '5' and resid 250 through 254 removed outlier: 4.258A pdb=" N CYS 5 254 " --> pdb=" O ARG 5 251 " (cutoff:3.500A) Processing helix chain '5' and resid 316 through 328 removed outlier: 3.889A pdb=" N GLU 5 320 " --> pdb=" O PRO 5 316 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLU 5 321 " --> pdb=" O GLN 5 317 " (cutoff:3.500A) Processing helix chain '5' and resid 331 through 339 Processing helix chain '5' and resid 346 through 359 Processing helix chain '5' and resid 383 through 388 removed outlier: 3.878A pdb=" N LYS 5 387 " --> pdb=" O PRO 5 383 " (cutoff:3.500A) Processing helix chain '5' and resid 391 through 398 removed outlier: 4.041A pdb=" N GLU 5 395 " --> pdb=" O LEU 5 391 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS 5 396 " --> pdb=" O LYS 5 392 " (cutoff:3.500A) Processing helix chain '5' and resid 432 through 437 removed outlier: 3.591A pdb=" N ALA 5 437 " --> pdb=" O ALA 5 433 " (cutoff:3.500A) Processing helix chain '5' and resid 446 through 450 Processing helix chain '5' and resid 457 through 462 removed outlier: 3.973A pdb=" N MET 5 462 " --> pdb=" O ILE 5 458 " (cutoff:3.500A) Processing helix chain '5' and resid 555 through 568 removed outlier: 3.951A pdb=" N VAL 5 568 " --> pdb=" O ALA 5 564 " (cutoff:3.500A) Processing helix chain '5' and resid 575 through 591 removed outlier: 3.742A pdb=" N ILE 5 588 " --> pdb=" O ASN 5 584 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET 5 589 " --> pdb=" O ARG 5 585 " (cutoff:3.500A) Processing helix chain '5' and resid 597 through 602 removed outlier: 4.262A pdb=" N ARG 5 602 " --> pdb=" O ARG 5 598 " (cutoff:3.500A) Processing helix chain '5' and resid 609 through 627 removed outlier: 3.549A pdb=" N GLU 5 614 " --> pdb=" O VAL 5 610 " (cutoff:3.500A) Processing helix chain '5' and resid 633 through 643 Processing helix chain '5' and resid 647 through 652 Processing helix chain '5' and resid 664 through 667 removed outlier: 3.931A pdb=" N GLU 5 667 " --> pdb=" O THR 5 664 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 664 through 667' Processing helix chain '5' and resid 668 through 683 removed outlier: 3.830A pdb=" N ARG 5 681 " --> pdb=" O LYS 5 677 " (cutoff:3.500A) Processing helix chain '5' and resid 691 through 700 removed outlier: 3.783A pdb=" N LYS 5 700 " --> pdb=" O LYS 5 696 " (cutoff:3.500A) Processing helix chain '5' and resid 704 through 719 Processing helix chain '6' and resid 21 through 36 Processing helix chain '6' and resid 44 through 54 removed outlier: 4.395A pdb=" N GLN 6 48 " --> pdb=" O ILE 6 44 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU 6 49 " --> pdb=" O LYS 6 45 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) Processing helix chain '6' and resid 65 through 70 Processing helix chain '6' and resid 72 through 82 Processing helix chain '6' and resid 82 through 100 Proline residue: 6 88 - end of helix removed outlier: 3.737A pdb=" N ARG 6 92 " --> pdb=" O PRO 6 88 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA 6 93 " --> pdb=" O TYR 6 89 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 6 98 " --> pdb=" O LEU 6 94 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP 6 100 " --> pdb=" O THR 6 96 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 126 Processing helix chain '6' and resid 186 through 189 removed outlier: 4.122A pdb=" N ARG 6 189 " --> pdb=" O ALA 6 186 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 186 through 189' Processing helix chain '6' and resid 231 through 233 No H-bonds generated for 'chain '6' and resid 231 through 233' Processing helix chain '6' and resid 321 through 329 Processing helix chain '6' and resid 330 through 343 Processing helix chain '6' and resid 345 through 355 removed outlier: 3.527A pdb=" N CYS 6 351 " --> pdb=" O TYR 6 347 " (cutoff:3.500A) Processing helix chain '6' and resid 361 through 374 removed outlier: 3.880A pdb=" N PHE 6 373 " --> pdb=" O LEU 6 369 " (cutoff:3.500A) Processing helix chain '6' and resid 401 through 412 removed outlier: 4.020A pdb=" N LEU 6 406 " --> pdb=" O LYS 6 402 " (cutoff:3.500A) Processing helix chain '6' and resid 437 through 440 Processing helix chain '6' and resid 462 through 465 removed outlier: 3.837A pdb=" N MET 6 465 " --> pdb=" O PHE 6 462 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 462 through 465' Processing helix chain '6' and resid 466 through 476 removed outlier: 3.551A pdb=" N VAL 6 471 " --> pdb=" O VAL 6 467 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA 6 472 " --> pdb=" O ARG 6 468 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU 6 475 " --> pdb=" O VAL 6 471 " (cutoff:3.500A) Processing helix chain '6' and resid 515 through 520 Processing helix chain '6' and resid 523 through 530 Processing helix chain '6' and resid 542 through 558 removed outlier: 3.532A pdb=" N ALA 6 547 " --> pdb=" O VAL 6 543 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG 6 551 " --> pdb=" O ALA 6 547 " (cutoff:3.500A) Processing helix chain '6' and resid 571 through 580 Processing helix chain '6' and resid 587 through 605 removed outlier: 3.650A pdb=" N ASP 6 592 " --> pdb=" O LYS 6 588 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP 6 605 " --> pdb=" O LEU 6 601 " (cutoff:3.500A) Processing helix chain '6' and resid 617 through 635 removed outlier: 3.960A pdb=" N LEU 6 621 " --> pdb=" O THR 6 617 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 656 removed outlier: 3.867A pdb=" N VAL 6 645 " --> pdb=" O GLN 6 641 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG 6 650 " --> pdb=" O LYS 6 646 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 739 removed outlier: 3.915A pdb=" N ASP 6 739 " --> pdb=" O GLU 6 735 " (cutoff:3.500A) Processing helix chain '6' and resid 749 through 759 removed outlier: 3.577A pdb=" N LEU 6 753 " --> pdb=" O VAL 6 749 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS 6 754 " --> pdb=" O ASN 6 750 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE 6 756 " --> pdb=" O TYR 6 752 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU 6 759 " --> pdb=" O GLU 6 755 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 777 removed outlier: 4.116A pdb=" N ARG 6 771 " --> pdb=" O ILE 6 767 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU 6 774 " --> pdb=" O LYS 6 770 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS 6 775 " --> pdb=" O ARG 6 771 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 10 Processing helix chain '7' and resid 31 through 42 removed outlier: 3.762A pdb=" N VAL 7 38 " --> pdb=" O GLY 7 34 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG 7 39 " --> pdb=" O ASN 7 35 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 56 Processing helix chain '7' and resid 59 through 69 removed outlier: 3.573A pdb=" N ASP 7 64 " --> pdb=" O PRO 7 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS 7 67 " --> pdb=" O VAL 7 63 " (cutoff:3.500A) Processing helix chain '7' and resid 69 through 85 removed outlier: 3.874A pdb=" N TYR 7 73 " --> pdb=" O ASN 7 69 " (cutoff:3.500A) Processing helix chain '7' and resid 128 through 132 removed outlier: 3.586A pdb=" N MET 7 131 " --> pdb=" O ALA 7 128 " (cutoff:3.500A) Processing helix chain '7' and resid 148 through 153 removed outlier: 4.544A pdb=" N ARG 7 153 " --> pdb=" O ILE 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 213 removed outlier: 3.794A pdb=" N THR 7 213 " --> pdb=" O GLU 7 210 " (cutoff:3.500A) Processing helix chain '7' and resid 241 through 244 removed outlier: 3.781A pdb=" N VAL 7 244 " --> pdb=" O SER 7 241 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 241 through 244' Processing helix chain '7' and resid 326 through 330 removed outlier: 3.514A pdb=" N GLU 7 330 " --> pdb=" O ILE 7 327 " (cutoff:3.500A) Processing helix chain '7' and resid 332 through 340 removed outlier: 4.119A pdb=" N ALA 7 338 " --> pdb=" O GLU 7 334 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE 7 340 " --> pdb=" O LEU 7 336 " (cutoff:3.500A) Processing helix chain '7' and resid 347 through 360 removed outlier: 3.751A pdb=" N VAL 7 359 " --> pdb=" O LEU 7 355 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 removed outlier: 3.908A pdb=" N ARG 7 396 " --> pdb=" O SER 7 392 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU 7 397 " --> pdb=" O TYR 7 393 " (cutoff:3.500A) Processing helix chain '7' and resid 424 through 428 removed outlier: 3.686A pdb=" N LEU 7 427 " --> pdb=" O SER 7 424 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR 7 428 " --> pdb=" O GLY 7 425 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 424 through 428' Processing helix chain '7' and resid 446 through 450 removed outlier: 3.711A pdb=" N MET 7 450 " --> pdb=" O PHE 7 447 " (cutoff:3.500A) Processing helix chain '7' and resid 451 through 464 removed outlier: 3.674A pdb=" N THR 7 456 " --> pdb=" O GLU 7 452 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA 7 457 " --> pdb=" O ALA 7 453 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU 7 463 " --> pdb=" O HIS 7 459 " (cutoff:3.500A) Processing helix chain '7' and resid 500 through 505 Processing helix chain '7' and resid 508 through 515 removed outlier: 3.838A pdb=" N PHE 7 515 " --> pdb=" O LEU 7 511 " (cutoff:3.500A) Processing helix chain '7' and resid 526 through 544 removed outlier: 3.769A pdb=" N ARG 7 532 " --> pdb=" O ASP 7 528 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS 7 543 " --> pdb=" O TYR 7 539 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 568 removed outlier: 3.650A pdb=" N ARG 7 560 " --> pdb=" O MET 7 556 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG 7 561 " --> pdb=" O LYS 7 557 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU 7 568 " --> pdb=" O ALA 7 564 " (cutoff:3.500A) Processing helix chain '7' and resid 574 through 576 No H-bonds generated for 'chain '7' and resid 574 through 576' Processing helix chain '7' and resid 577 through 596 removed outlier: 3.770A pdb=" N ALA 7 583 " --> pdb=" O ASP 7 579 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS 7 596 " --> pdb=" O ALA 7 592 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 620 removed outlier: 4.135A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU 7 607 " --> pdb=" O ALA 7 603 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 7 615 " --> pdb=" O ARG 7 611 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU 7 619 " --> pdb=" O ALA 7 615 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG 7 620 " --> pdb=" O LEU 7 616 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 641 Processing sheet with id=AA1, first strand: chain '2' and resid 229 through 233 removed outlier: 6.529A pdb=" N LEU 2 230 " --> pdb=" O ARG 2 284 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N SER 2 286 " --> pdb=" O LEU 2 230 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL 2 232 " --> pdb=" O SER 2 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '2' and resid 304 through 305 removed outlier: 3.641A pdb=" N GLN 2 304 " --> pdb=" O TYR 2 418 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN 2 421 " --> pdb=" O ALA 2 436 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N SER 2 393 " --> pdb=" O THR 2 437 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ILE 2 439 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP 2 395 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG 2 375 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 304 through 305 removed outlier: 3.641A pdb=" N GLN 2 304 " --> pdb=" O TYR 2 418 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN 2 421 " --> pdb=" O ALA 2 436 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N SER 2 393 " --> pdb=" O THR 2 437 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N ILE 2 439 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASP 2 395 " --> pdb=" O ILE 2 439 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG 2 375 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU 2 571 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR 2 570 " --> pdb=" O GLN 2 561 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 322 through 329 removed outlier: 7.791A pdb=" N LEU 2 322 " --> pdb=" O THR 2 368 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR 2 368 " --> pdb=" O LEU 2 322 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET 2 324 " --> pdb=" O GLU 2 366 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU 2 366 " --> pdb=" O MET 2 324 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS 2 326 " --> pdb=" O ASN 2 364 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN 2 364 " --> pdb=" O LYS 2 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 519 through 522 removed outlier: 6.246A pdb=" N ILE 2 544 " --> pdb=" O LEU 2 585 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ASP 2 587 " --> pdb=" O ILE 2 544 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR 2 546 " --> pdb=" O ASP 2 587 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 608 through 611 Processing sheet with id=AA7, first strand: chain '3' and resid 47 through 50 removed outlier: 5.327A pdb=" N LEU 3 47 " --> pdb=" O GLY 3 101 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU 3 103 " --> pdb=" O LEU 3 47 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL 3 49 " --> pdb=" O GLU 3 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '3' and resid 124 through 126 removed outlier: 3.617A pdb=" N VAL 3 125 " --> pdb=" O GLY 3 239 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY 3 129 " --> pdb=" O VAL 3 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 259 through 261 removed outlier: 3.652A pdb=" N VAL 3 217 " --> pdb=" O ILE 3 201 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR 3 198 " --> pdb=" O CYS 3 134 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS 3 134 " --> pdb=" O THR 3 198 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR 3 200 " --> pdb=" O THR 3 132 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY 3 129 " --> pdb=" O VAL 3 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 368 through 369 removed outlier: 7.702A pdb=" N THR 3 368 " --> pdb=" O ASP 3 409 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE 3 341 " --> pdb=" O ALA 3 450 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 430 through 432 Processing sheet with id=AB3, first strand: chain '3' and resid 581 through 582 removed outlier: 7.560A pdb=" N VAL 3 581 " --> pdb=" O VAL 3 637 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain '3' and resid 762 through 764 Processing sheet with id=AB5, first strand: chain '4' and resid 281 through 286 removed outlier: 3.523A pdb=" N GLN 4 281 " --> pdb=" O TYR 4 394 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE 4 285 " --> pdb=" O VAL 4 390 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL 4 390 " --> pdb=" O ILE 4 285 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR 4 391 " --> pdb=" O ILE 4 419 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE 4 371 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS 4 375 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N HIS 4 420 " --> pdb=" O HIS 4 375 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '4' and resid 313 through 315 removed outlier: 3.674A pdb=" N ALA 4 302 " --> pdb=" O VAL 4 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 408 through 409 removed outlier: 3.626A pdb=" N VAL 4 408 " --> pdb=" O PHE 7 200 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE 7 200 " --> pdb=" O VAL 4 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '4' and resid 533 through 534 removed outlier: 3.568A pdb=" N CYS 4 571 " --> pdb=" O SER 4 612 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY 4 510 " --> pdb=" O ALA 4 617 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU 4 507 " --> pdb=" O PHE 4 648 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU 4 650 " --> pdb=" O LEU 4 507 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N CYS 4 509 " --> pdb=" O LEU 4 650 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '4' and resid 546 through 550 removed outlier: 3.556A pdb=" N GLN 4 555 " --> pdb=" O ASP 4 550 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 595 through 596 Processing sheet with id=AC2, first strand: chain '4' and resid 599 through 600 removed outlier: 3.648A pdb=" N LYS 4 600 " --> pdb=" O ILE 4 603 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '5' and resid 154 through 155 removed outlier: 3.793A pdb=" N ILE 5 154 " --> pdb=" O GLN 5 230 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU 5 227 " --> pdb=" O LEU 5 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '5' and resid 377 through 379 removed outlier: 6.668A pdb=" N LEU 5 378 " --> pdb=" O PHE 5 518 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain '5' and resid 401 through 403 removed outlier: 3.721A pdb=" N VAL 5 402 " --> pdb=" O VAL 5 441 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS 5 443 " --> pdb=" O VAL 5 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '5' and resid 573 through 574 removed outlier: 7.282A pdb=" N ARG 5 573 " --> pdb=" O ALA 5 632 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain '5' and resid 689 through 690 removed outlier: 3.696A pdb=" N ARG 5 724 " --> pdb=" O VAL 5 729 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '6' and resid 60 through 64 removed outlier: 6.027A pdb=" N LEU 6 61 " --> pdb=" O ALA 6 113 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLN 6 115 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL 6 63 " --> pdb=" O GLN 6 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain '6' and resid 135 through 138 removed outlier: 3.613A pdb=" N THR 6 245 " --> pdb=" O CYS 6 302 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS 6 302 " --> pdb=" O THR 6 245 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '6' and resid 140 through 144 removed outlier: 6.436A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR 6 144 " --> pdb=" O LYS 6 205 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS 6 205 " --> pdb=" O THR 6 144 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ARG 6 199 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL 6 152 " --> pdb=" O ARG 6 199 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL 6 201 " --> pdb=" O GLU 6 150 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE 6 203 " --> pdb=" O HIS 6 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS 6 148 " --> pdb=" O PHE 6 203 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '6' and resid 164 through 169 removed outlier: 3.990A pdb=" N ASP 6 167 " --> pdb=" O GLY 6 154 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY 6 154 " --> pdb=" O ASP 6 167 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLU 6 169 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL 6 152 " --> pdb=" O GLU 6 169 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N HIS 6 148 " --> pdb=" O PHE 6 203 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE 6 203 " --> pdb=" O HIS 6 148 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL 6 201 " --> pdb=" O GLU 6 150 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL 6 152 " --> pdb=" O ARG 6 199 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ARG 6 199 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE 6 208 " --> pdb=" O LEU 6 224 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N SER 6 223 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N PHE 6 298 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU 6 225 " --> pdb=" O PHE 6 298 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA 6 300 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE 6 227 " --> pdb=" O ALA 6 300 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 417 through 420 removed outlier: 3.589A pdb=" N VAL 6 417 " --> pdb=" O VAL 6 456 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS 6 457 " --> pdb=" O SER 6 498 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL 6 392 " --> pdb=" O ALA 6 501 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '6' and resid 433 through 435 Processing sheet with id=AD5, first strand: chain '6' and resid 481 through 482 Processing sheet with id=AD6, first strand: chain '6' and resid 585 through 586 removed outlier: 7.451A pdb=" N LYS 6 585 " --> pdb=" O VAL 6 640 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain '7' and resid 47 through 49 removed outlier: 6.260A pdb=" N LEU 7 48 " --> pdb=" O TYR 7 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain '7' and resid 238 through 239 removed outlier: 4.107A pdb=" N ASP 7 269 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '7' and resid 174 through 177 removed outlier: 3.688A pdb=" N LYS 7 174 " --> pdb=" O PHE 7 232 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '7' and resid 190 through 194 removed outlier: 3.563A pdb=" N THR 7 191 " --> pdb=" O TYR 7 182 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR 7 221 " --> pdb=" O THR 7 183 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 401 through 402 removed outlier: 6.526A pdb=" N CYS 7 442 " --> pdb=" O LEU 7 485 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA 7 487 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ALA 7 488 " --> pdb=" O ILE 7 377 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU 7 379 " --> pdb=" O ALA 7 488 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 2985 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: 6.48 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9722 1.34 - 1.46: 5547 1.46 - 1.58: 13515 1.58 - 1.70: 14 1.70 - 1.81: 226 Bond restraints: 29024 Sorted by residual: bond pdb=" N VAL 3 798 " pdb=" CA VAL 3 798 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.07e+01 bond pdb=" N ILE 2 611 " pdb=" CA ILE 2 611 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.14e-02 7.69e+03 1.02e+01 bond pdb=" N ILE 3 763 " pdb=" CA ILE 3 763 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.18e-02 7.18e+03 1.02e+01 bond pdb=" N VAL 6 233 " pdb=" CA VAL 6 233 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.69e+00 bond pdb=" N VAL 2 513 " pdb=" CA VAL 2 513 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.41e+00 ... (remaining 29019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 37905 1.43 - 2.85: 1186 2.85 - 4.28: 238 4.28 - 5.70: 55 5.70 - 7.13: 6 Bond angle restraints: 39390 Sorted by residual: angle pdb=" C ALA 6 230 " pdb=" CA ALA 6 230 " pdb=" CB ALA 6 230 " ideal model delta sigma weight residual 116.63 110.97 5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" N ARG 6 633 " pdb=" CA ARG 6 633 " pdb=" C ARG 6 633 " ideal model delta sigma weight residual 112.90 107.76 5.14 1.31e+00 5.83e-01 1.54e+01 angle pdb=" N GLY 2 758 " pdb=" CA GLY 2 758 " pdb=" C GLY 2 758 " ideal model delta sigma weight residual 115.21 110.12 5.09 1.30e+00 5.92e-01 1.53e+01 angle pdb=" N MET 6 631 " pdb=" CA MET 6 631 " pdb=" C MET 6 631 " ideal model delta sigma weight residual 111.28 107.03 4.25 1.09e+00 8.42e-01 1.52e+01 angle pdb=" CA GLY 3 764 " pdb=" C GLY 3 764 " pdb=" O GLY 3 764 " ideal model delta sigma weight residual 121.41 118.00 3.41 8.80e-01 1.29e+00 1.50e+01 ... (remaining 39385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 16941 22.99 - 45.97: 730 45.97 - 68.96: 111 68.96 - 91.94: 25 91.94 - 114.93: 1 Dihedral angle restraints: 17808 sinusoidal: 6826 harmonic: 10982 Sorted by residual: dihedral pdb=" O2A ADP 7 801 " pdb=" O3A ADP 7 801 " pdb=" PA ADP 7 801 " pdb=" PB ADP 7 801 " ideal model delta sinusoidal sigma weight residual -60.00 54.93 -114.93 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA GLN 5 645 " pdb=" C GLN 5 645 " pdb=" N VAL 5 646 " pdb=" CA VAL 5 646 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA SER 5 665 " pdb=" C SER 5 665 " pdb=" N GLN 5 666 " pdb=" CA GLN 5 666 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 17805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3654 0.050 - 0.101: 738 0.101 - 0.151: 195 0.151 - 0.201: 28 0.201 - 0.251: 8 Chirality restraints: 4623 Sorted by residual: chirality pdb=" CA VAL 2 617 " pdb=" N VAL 2 617 " pdb=" C VAL 2 617 " pdb=" CB VAL 2 617 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA ILE 2 762 " pdb=" N ILE 2 762 " pdb=" C ILE 2 762 " pdb=" CB ILE 2 762 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA ILE 3 805 " pdb=" N ILE 3 805 " pdb=" C ILE 3 805 " pdb=" CB ILE 3 805 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 4620 not shown) Planarity restraints: 5120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 751 " -0.356 9.50e-02 1.11e+02 1.60e-01 1.57e+01 pdb=" NE ARG 2 751 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG 2 751 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 751 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 751 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 615 " 0.284 9.50e-02 1.11e+02 1.27e-01 9.92e+00 pdb=" NE ARG 6 615 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG 6 615 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 615 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 615 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 514 " 0.261 9.50e-02 1.11e+02 1.17e-01 8.47e+00 pdb=" NE ARG 2 514 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG 2 514 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 514 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 514 " 0.008 2.00e-02 2.50e+03 ... (remaining 5117 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 14 2.49 - 3.09: 21301 3.09 - 3.70: 43101 3.70 - 4.30: 60651 4.30 - 4.90: 97594 Nonbonded interactions: 222661 Sorted by model distance: nonbonded pdb=" O1G ATP 21001 " pdb="MG MG 21003 " model vdw 1.891 2.170 nonbonded pdb=" OG SER 4 517 " pdb="MG MG 4 903 " model vdw 1.927 2.170 nonbonded pdb=" OG SER 2 530 " pdb="MG MG 21003 " model vdw 1.946 2.170 nonbonded pdb=" OG SER 6 403 " pdb="MG MG 6 903 " model vdw 2.045 2.170 nonbonded pdb=" OD2 ASP 6 460 " pdb="MG MG 6 903 " model vdw 2.379 2.170 ... (remaining 222656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 31.510 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 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 : 0.004 0.042 29039 Z= 0.253 Angle : 0.604 9.481 39408 Z= 0.372 Chirality : 0.046 0.251 4623 Planarity : 0.006 0.160 5120 Dihedral : 12.900 114.926 10658 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.56 % Favored : 95.38 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.26 % 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: -1.08 (0.14), residues: 3704 helix: -0.42 (0.14), residues: 1401 sheet: -1.16 (0.28), residues: 364 loop : -0.75 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 445 TYR 0.010 0.001 TYR 4 670 PHE 0.011 0.001 PHE 6 462 TRP 0.008 0.001 TRP 5 69 HIS 0.005 0.001 HIS 6 644 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.25 (29024) covalent geometry : angle 0.59865 / 0.37 (39390) hydrogen bonds : bond 0.25497 / 17.38 ( 1034) hydrogen bonds : angle 8.42557 / 5.98 ( 2985) metal coordination : bond 0.00639 / 0.41 ( 15) metal coordination : angle 3.62416 / 2.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 265 time to evaluate : 1.140 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: 2 306 ILE cc_start: 0.9022 (pt) cc_final: 0.8243 (pt) REVERT: 2 477 ILE cc_start: 0.9464 (tp) cc_final: 0.9150 (tt) REVERT: 3 743 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8086 (ttt90) outliers start: 2 outliers final: 0 residues processed: 267 average time/residue: 0.1867 time to fit residues: 81.2003 Evaluate side-chains 170 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 743 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 40.0000 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.0060 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.9980 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 299 GLN 2 379 GLN ** 2 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 828 ASN 3 761 GLN 3 766 ASN 3 793 GLN 4 256 HIS 4 341 HIS 4 375 HIS 4 407 ASN ** 4 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 459 HIS 6 635 HIS 7 376 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.056850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.040066 restraints weight = 197530.284| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 6.07 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29039 Z= 0.119 Angle : 0.604 11.452 39408 Z= 0.298 Chirality : 0.042 0.184 4623 Planarity : 0.004 0.052 5120 Dihedral : 6.407 112.870 4157 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 0.81 % Allowed : 5.42 % Favored : 93.77 % 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: -0.75 (0.14), residues: 3704 helix: 0.17 (0.14), residues: 1432 sheet: -1.09 (0.25), residues: 442 loop : -0.79 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 765 TYR 0.022 0.001 TYR 5 731 PHE 0.013 0.001 PHE 3 780 TRP 0.011 0.001 TRP 5 69 HIS 0.008 0.001 HIS 2 732 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (29024) covalent geometry : angle 0.59989 / 0.30 (39390) hydrogen bonds : bond 0.04948 / 3.37 ( 1034) hydrogen bonds : angle 5.60943 / 3.95 ( 2985) metal coordination : bond 0.00576 / 0.39 ( 15) metal coordination : angle 3.40901 / 2.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.168 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: 2 306 ILE cc_start: 0.9762 (pt) cc_final: 0.9506 (mp) REVERT: 2 592 MET cc_start: 0.9195 (mmm) cc_final: 0.8973 (mmm) REVERT: 2 604 MET cc_start: 0.8990 (mtp) cc_final: 0.8623 (mtm) REVERT: 2 740 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.9088 (mp10) REVERT: 2 793 MET cc_start: 0.9307 (tpt) cc_final: 0.9039 (tpp) REVERT: 3 479 PHE cc_start: 0.9308 (t80) cc_final: 0.9031 (t80) REVERT: 4 351 MET cc_start: 0.8902 (tpp) cc_final: 0.8637 (tpp) REVERT: 4 548 MET cc_start: 0.8752 (tpp) cc_final: 0.8532 (tpp) REVERT: 4 589 GLU cc_start: 0.9203 (tt0) cc_final: 0.8955 (tp30) REVERT: 5 127 MET cc_start: 0.8278 (mmm) cc_final: 0.7960 (mmm) REVERT: 5 679 LEU cc_start: 0.9792 (OUTLIER) cc_final: 0.9513 (pp) REVERT: 6 371 MET cc_start: 0.9473 (tmm) cc_final: 0.9173 (tmm) REVERT: 6 624 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9081 (tpt) REVERT: 7 169 ARG cc_start: 0.9188 (ttm170) cc_final: 0.8948 (tpp80) outliers start: 24 outliers final: 10 residues processed: 208 average time/residue: 0.1706 time to fit residues: 59.9077 Evaluate side-chains 182 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 740 GLN Chi-restraints excluded: chain 2 residue 773 MET Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 768 LEU Chi-restraints excluded: chain 3 residue 801 SER Chi-restraints excluded: chain 3 residue 802 GLU Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 5 residue 126 VAL Chi-restraints excluded: chain 5 residue 456 VAL Chi-restraints excluded: chain 5 residue 679 LEU Chi-restraints excluded: chain 6 residue 499 ILE Chi-restraints excluded: chain 6 residue 624 MET Chi-restraints excluded: chain 7 residue 458 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 261 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 287 optimal weight: 8.9990 chunk 109 optimal weight: 0.0370 chunk 87 optimal weight: 0.2980 chunk 161 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 overall best weight: 3.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 838 GLN 3 196 HIS ** 4 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 483 GLN ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 713 GLN 7 374 ASN 7 376 ASN 7 465 GLN 7 535 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.054953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.037706 restraints weight = 206461.020| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 6.13 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29039 Z= 0.154 Angle : 0.588 12.457 39408 Z= 0.291 Chirality : 0.042 0.359 4623 Planarity : 0.003 0.043 5120 Dihedral : 6.334 113.716 4153 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.10 % Favored : 95.87 % Rotamer: Outliers : 0.77 % Allowed : 7.72 % Favored : 91.51 % 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: -0.58 (0.14), residues: 3704 helix: 0.45 (0.14), residues: 1448 sheet: -1.29 (0.24), residues: 452 loop : -0.75 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 730 TYR 0.014 0.001 TYR 4 714 PHE 0.016 0.001 PHE 3 411 TRP 0.014 0.001 TRP 5 69 HIS 0.006 0.001 HIS 3 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (29024) covalent geometry : angle 0.58283 / 0.29 (39390) hydrogen bonds : bond 0.03857 / 2.66 ( 1034) hydrogen bonds : angle 5.17660 / 3.63 ( 2985) metal coordination : bond 0.00799 / 0.46 ( 15) metal coordination : angle 3.56658 / 2.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 1.024 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: 2 270 MET cc_start: 0.9021 (mtt) cc_final: 0.8592 (mmm) REVERT: 2 324 MET cc_start: 0.8310 (ppp) cc_final: 0.7919 (ppp) REVERT: 2 604 MET cc_start: 0.9064 (mtp) cc_final: 0.8711 (mtm) REVERT: 2 793 MET cc_start: 0.9353 (tpt) cc_final: 0.9011 (tpp) REVERT: 2 814 MET cc_start: 0.9813 (mmm) cc_final: 0.9434 (mmm) REVERT: 3 479 PHE cc_start: 0.9449 (t80) cc_final: 0.9180 (t80) REVERT: 3 792 MET cc_start: 0.9329 (mpp) cc_final: 0.9114 (mpp) REVERT: 4 351 MET cc_start: 0.8957 (tpp) cc_final: 0.8566 (tpp) REVERT: 4 548 MET cc_start: 0.8907 (tpp) cc_final: 0.8659 (tpp) REVERT: 6 329 MET cc_start: 0.9172 (ptp) cc_final: 0.8807 (ttp) REVERT: 6 371 MET cc_start: 0.9477 (tmm) cc_final: 0.9132 (tmm) REVERT: 6 465 MET cc_start: 0.7898 (ptm) cc_final: 0.7555 (tmm) REVERT: 6 624 MET cc_start: 0.9302 (OUTLIER) cc_final: 0.8998 (tpt) REVERT: 6 736 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8840 (pt0) REVERT: 7 169 ARG cc_start: 0.9238 (ttm170) cc_final: 0.8980 (tpp80) REVERT: 7 639 MET cc_start: 0.9150 (mpp) cc_final: 0.8729 (mpp) outliers start: 23 outliers final: 9 residues processed: 181 average time/residue: 0.1699 time to fit residues: 52.5203 Evaluate side-chains 170 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 773 MET Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 801 SER Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 5 residue 126 VAL Chi-restraints excluded: chain 5 residue 456 VAL Chi-restraints excluded: chain 5 residue 679 LEU Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 624 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 170 optimal weight: 2.9990 chunk 229 optimal weight: 8.9990 chunk 201 optimal weight: 9.9990 chunk 220 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 176 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 511 HIS 3 52 ASN ** 4 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 355 GLN 5 459 HIS ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 148 HIS 6 603 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.053722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.036459 restraints weight = 209506.048| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 6.10 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29039 Z= 0.184 Angle : 0.597 14.054 39408 Z= 0.297 Chirality : 0.042 0.316 4623 Planarity : 0.003 0.040 5120 Dihedral : 6.423 111.921 4153 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.01 % Allowed : 9.60 % Favored : 89.39 % 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: -0.49 (0.14), residues: 3704 helix: 0.57 (0.14), residues: 1462 sheet: -1.35 (0.24), residues: 484 loop : -0.69 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 6 722 TYR 0.023 0.001 TYR 5 731 PHE 0.014 0.001 PHE 3 411 TRP 0.014 0.001 TRP 5 69 HIS 0.006 0.001 HIS 5 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (29024) covalent geometry : angle 0.59033 / 0.30 (39390) hydrogen bonds : bond 0.03454 / 2.38 ( 1034) hydrogen bonds : angle 4.97731 / 3.48 ( 2985) metal coordination : bond 0.01015 / 0.58 ( 15) metal coordination : angle 4.16680 / 2.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 270 MET cc_start: 0.9039 (mtt) cc_final: 0.8709 (mmm) REVERT: 2 324 MET cc_start: 0.8531 (ppp) cc_final: 0.8159 (ppp) REVERT: 2 592 MET cc_start: 0.9199 (mmm) cc_final: 0.8833 (mmm) REVERT: 2 604 MET cc_start: 0.9136 (mtp) cc_final: 0.8805 (mtm) REVERT: 2 793 MET cc_start: 0.9406 (tpt) cc_final: 0.9063 (tpp) REVERT: 2 798 MET cc_start: 0.9303 (tpp) cc_final: 0.9056 (tpp) REVERT: 2 814 MET cc_start: 0.9831 (mmm) cc_final: 0.9437 (mmm) REVERT: 3 479 PHE cc_start: 0.9416 (t80) cc_final: 0.9107 (t80) REVERT: 3 597 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9429 (mm) REVERT: 3 792 MET cc_start: 0.9363 (mpp) cc_final: 0.9136 (mpp) REVERT: 4 337 MET cc_start: 0.8772 (mmm) cc_final: 0.8542 (mmm) REVERT: 4 351 MET cc_start: 0.8988 (tpp) cc_final: 0.8539 (tpp) REVERT: 4 548 MET cc_start: 0.8974 (tpp) cc_final: 0.8770 (tpp) REVERT: 5 127 MET cc_start: 0.8363 (mmm) cc_final: 0.7968 (mmm) REVERT: 5 679 LEU cc_start: 0.9810 (OUTLIER) cc_final: 0.9536 (pp) REVERT: 6 329 MET cc_start: 0.9256 (ptp) cc_final: 0.8980 (ttp) REVERT: 6 369 LEU cc_start: 0.9807 (tp) cc_final: 0.9501 (tt) REVERT: 6 371 MET cc_start: 0.9489 (tmm) cc_final: 0.9146 (tmm) REVERT: 6 372 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9458 (mm) REVERT: 7 380 MET cc_start: 0.8856 (tpp) cc_final: 0.8267 (tpp) REVERT: 7 639 MET cc_start: 0.9124 (mpp) cc_final: 0.8768 (mpp) outliers start: 30 outliers final: 15 residues processed: 178 average time/residue: 0.1658 time to fit residues: 50.9347 Evaluate side-chains 166 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 773 MET Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 597 LEU Chi-restraints excluded: chain 3 residue 801 SER Chi-restraints excluded: chain 4 residue 355 GLN Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 5 residue 126 VAL Chi-restraints excluded: chain 5 residue 331 VAL Chi-restraints excluded: chain 5 residue 456 VAL Chi-restraints excluded: chain 5 residue 679 LEU Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 405 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 359 optimal weight: 0.0980 chunk 245 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 195 optimal weight: 50.0000 chunk 203 optimal weight: 40.0000 chunk 71 optimal weight: 30.0000 chunk 264 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 321 GLN 2 379 GLN ** 2 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 355 GLN ** 5 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 701 GLN 6 182 ASN 6 600 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.053173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.036083 restraints weight = 212502.513| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 6.05 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29039 Z= 0.220 Angle : 0.618 12.208 39408 Z= 0.309 Chirality : 0.041 0.241 4623 Planarity : 0.003 0.040 5120 Dihedral : 6.520 109.830 4153 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.21 % Allowed : 11.05 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.44 (0.14), residues: 3704 helix: 0.64 (0.14), residues: 1448 sheet: -1.37 (0.23), residues: 497 loop : -0.66 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 6 722 TYR 0.014 0.001 TYR 6 174 PHE 0.020 0.001 PHE 3 411 TRP 0.012 0.002 TRP 5 69 HIS 0.007 0.001 HIS 6 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (29024) covalent geometry : angle 0.61003 / 0.31 (39390) hydrogen bonds : bond 0.03451 / 2.37 ( 1034) hydrogen bonds : angle 4.97996 / 3.47 ( 2985) metal coordination : bond 0.01195 / 0.66 ( 15) metal coordination : angle 4.70471 / 3.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.115 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: 2 270 MET cc_start: 0.9093 (mtt) cc_final: 0.8720 (mmm) REVERT: 2 324 MET cc_start: 0.8701 (ppp) cc_final: 0.8349 (ppp) REVERT: 2 592 MET cc_start: 0.9159 (mmm) cc_final: 0.8749 (mmm) REVERT: 2 604 MET cc_start: 0.9200 (mtp) cc_final: 0.8893 (mtm) REVERT: 2 770 MET cc_start: 0.9553 (mmm) cc_final: 0.9265 (mmm) REVERT: 2 793 MET cc_start: 0.9436 (tpt) cc_final: 0.9098 (tpp) REVERT: 2 798 MET cc_start: 0.9229 (tpp) cc_final: 0.8977 (tmm) REVERT: 2 814 MET cc_start: 0.9844 (mmm) cc_final: 0.9466 (mmm) REVERT: 3 479 PHE cc_start: 0.9434 (t80) cc_final: 0.9105 (t80) REVERT: 4 351 MET cc_start: 0.8836 (tpp) cc_final: 0.8446 (tpp) REVERT: 5 127 MET cc_start: 0.8568 (mmm) cc_final: 0.8189 (mmm) REVERT: 5 264 THR cc_start: 0.5668 (OUTLIER) cc_final: 0.5448 (p) REVERT: 5 450 MET cc_start: 0.8878 (ppp) cc_final: 0.8605 (ppp) REVERT: 5 679 LEU cc_start: 0.9827 (OUTLIER) cc_final: 0.9579 (pp) REVERT: 6 329 MET cc_start: 0.9273 (ptp) cc_final: 0.9044 (ttp) REVERT: 6 369 LEU cc_start: 0.9824 (tp) cc_final: 0.9585 (tt) REVERT: 6 371 MET cc_start: 0.9486 (tmm) cc_final: 0.9127 (tmm) REVERT: 6 372 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9484 (mm) REVERT: 6 465 MET cc_start: 0.8155 (ptm) cc_final: 0.7699 (tmm) REVERT: 7 306 MET cc_start: 0.9161 (ppp) cc_final: 0.8950 (mmt) REVERT: 7 380 MET cc_start: 0.8853 (tpp) cc_final: 0.8401 (tpp) REVERT: 7 639 MET cc_start: 0.9209 (mpp) cc_final: 0.8838 (mtm) outliers start: 36 outliers final: 20 residues processed: 177 average time/residue: 0.1441 time to fit residues: 44.3681 Evaluate side-chains 168 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 773 MET Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 801 SER Chi-restraints excluded: chain 3 residue 805 ILE Chi-restraints excluded: chain 4 residue 289 VAL Chi-restraints excluded: chain 4 residue 355 GLN Chi-restraints excluded: chain 4 residue 480 ILE Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 5 residue 72 VAL Chi-restraints excluded: chain 5 residue 126 VAL Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 456 VAL Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 679 LEU Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 405 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 352 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 325 optimal weight: 0.0060 chunk 125 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 321 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 349 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 211 optimal weight: 40.0000 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 849 ASN 5 30 GLN 6 635 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.054003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.036832 restraints weight = 208873.312| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 6.09 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29039 Z= 0.111 Angle : 0.569 13.390 39408 Z= 0.277 Chirality : 0.041 0.322 4623 Planarity : 0.003 0.036 5120 Dihedral : 6.399 104.384 4153 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.98 % Allowed : 12.13 % Favored : 86.89 % 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: -0.31 (0.14), residues: 3704 helix: 0.76 (0.14), residues: 1447 sheet: -1.23 (0.24), residues: 486 loop : -0.63 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 590 TYR 0.011 0.001 TYR 6 546 PHE 0.010 0.001 PHE 3 411 TRP 0.011 0.001 TRP 5 69 HIS 0.005 0.001 HIS 3 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (29024) covalent geometry : angle 0.56259 / 0.28 (39390) hydrogen bonds : bond 0.03067 / 2.10 ( 1034) hydrogen bonds : angle 4.75748 / 3.33 ( 2985) metal coordination : bond 0.00721 / 0.41 ( 15) metal coordination : angle 3.98172 / 2.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 270 MET cc_start: 0.9102 (mtt) cc_final: 0.8684 (mmm) REVERT: 2 324 MET cc_start: 0.8744 (ppp) cc_final: 0.8361 (ppp) REVERT: 2 592 MET cc_start: 0.9223 (mmm) cc_final: 0.8617 (mmm) REVERT: 2 793 MET cc_start: 0.9379 (tpt) cc_final: 0.9045 (tpp) REVERT: 2 814 MET cc_start: 0.9848 (mmm) cc_final: 0.9455 (mmm) REVERT: 3 479 PHE cc_start: 0.9446 (t80) cc_final: 0.8975 (t80) REVERT: 3 805 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.9249 (mp) REVERT: 4 317 MET cc_start: 0.9443 (ttp) cc_final: 0.9185 (mtm) REVERT: 4 351 MET cc_start: 0.8798 (tpp) cc_final: 0.8441 (tpp) REVERT: 5 127 MET cc_start: 0.8546 (mmm) cc_final: 0.8202 (mmm) REVERT: 5 264 THR cc_start: 0.5664 (OUTLIER) cc_final: 0.5448 (p) REVERT: 5 450 MET cc_start: 0.8903 (ppp) cc_final: 0.8622 (ppp) REVERT: 5 679 LEU cc_start: 0.9826 (OUTLIER) cc_final: 0.9571 (pp) REVERT: 6 329 MET cc_start: 0.9310 (ptp) cc_final: 0.9106 (ttp) REVERT: 6 369 LEU cc_start: 0.9805 (tp) cc_final: 0.9591 (tt) REVERT: 6 371 MET cc_start: 0.9454 (tmm) cc_final: 0.9059 (tmm) REVERT: 6 465 MET cc_start: 0.8099 (ptm) cc_final: 0.7737 (tmm) REVERT: 7 306 MET cc_start: 0.9129 (ppp) cc_final: 0.8926 (mmt) REVERT: 7 380 MET cc_start: 0.8796 (tpp) cc_final: 0.8310 (tpp) REVERT: 7 639 MET cc_start: 0.9174 (mpp) cc_final: 0.8773 (mtm) outliers start: 29 outliers final: 18 residues processed: 181 average time/residue: 0.1439 time to fit residues: 45.8208 Evaluate side-chains 169 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 440 LEU Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 480 SER Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 773 MET Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 801 SER Chi-restraints excluded: chain 3 residue 805 ILE Chi-restraints excluded: chain 4 residue 480 ILE Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 72 VAL Chi-restraints excluded: chain 5 residue 126 VAL Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 456 VAL Chi-restraints excluded: chain 5 residue 511 LEU Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 679 LEU Chi-restraints excluded: chain 7 residue 167 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 137 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 357 optimal weight: 5.9990 chunk 194 optimal weight: 50.0000 chunk 189 optimal weight: 40.0000 chunk 98 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 344 optimal weight: 3.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.053715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.036575 restraints weight = 209798.277| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 6.09 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29039 Z= 0.125 Angle : 0.587 12.567 39408 Z= 0.285 Chirality : 0.041 0.322 4623 Planarity : 0.003 0.036 5120 Dihedral : 6.327 102.376 4153 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.98 % Allowed : 12.87 % Favored : 86.15 % 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: -0.28 (0.14), residues: 3704 helix: 0.77 (0.14), residues: 1442 sheet: -1.19 (0.24), residues: 488 loop : -0.60 (0.16), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 590 TYR 0.026 0.001 TYR 5 731 PHE 0.012 0.001 PHE 3 411 TRP 0.011 0.001 TRP 5 69 HIS 0.008 0.001 HIS 4 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (29024) covalent geometry : angle 0.58103 / 0.28 (39390) hydrogen bonds : bond 0.03015 / 2.06 ( 1034) hydrogen bonds : angle 4.74754 / 3.32 ( 2985) metal coordination : bond 0.00739 / 0.43 ( 15) metal coordination : angle 3.80522 / 2.83 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 270 MET cc_start: 0.9126 (mtt) cc_final: 0.8690 (mmm) REVERT: 2 324 MET cc_start: 0.8785 (ppp) cc_final: 0.8358 (ppp) REVERT: 2 592 MET cc_start: 0.9199 (mmm) cc_final: 0.8622 (mmm) REVERT: 2 793 MET cc_start: 0.9387 (tpt) cc_final: 0.9062 (mpp) REVERT: 2 814 MET cc_start: 0.9856 (mmm) cc_final: 0.9471 (mmm) REVERT: 3 479 PHE cc_start: 0.9493 (t80) cc_final: 0.9092 (t80) REVERT: 3 805 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9284 (mp) REVERT: 4 317 MET cc_start: 0.9513 (ttp) cc_final: 0.9181 (tpp) REVERT: 4 351 MET cc_start: 0.8840 (tpp) cc_final: 0.8491 (tpp) REVERT: 5 264 THR cc_start: 0.5694 (OUTLIER) cc_final: 0.5472 (p) REVERT: 5 349 MET cc_start: 0.9485 (tmm) cc_final: 0.9256 (ppp) REVERT: 5 450 MET cc_start: 0.8891 (ppp) cc_final: 0.8638 (ppp) REVERT: 5 679 LEU cc_start: 0.9828 (OUTLIER) cc_final: 0.9565 (pp) REVERT: 6 329 MET cc_start: 0.9314 (ptp) cc_final: 0.9107 (ttp) REVERT: 6 369 LEU cc_start: 0.9800 (tp) cc_final: 0.9538 (tt) REVERT: 6 371 MET cc_start: 0.9444 (tmm) cc_final: 0.9059 (tmm) REVERT: 6 372 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9438 (mm) REVERT: 6 465 MET cc_start: 0.8061 (ptm) cc_final: 0.7628 (tmm) REVERT: 6 624 MET cc_start: 0.9427 (tpp) cc_final: 0.9016 (tpt) REVERT: 7 639 MET cc_start: 0.9172 (mpp) cc_final: 0.8761 (mtm) outliers start: 29 outliers final: 21 residues processed: 174 average time/residue: 0.1485 time to fit residues: 45.3604 Evaluate side-chains 173 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 773 MET Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 801 SER Chi-restraints excluded: chain 3 residue 805 ILE Chi-restraints excluded: chain 4 residue 480 ILE Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 72 VAL Chi-restraints excluded: chain 5 residue 126 VAL Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 456 VAL Chi-restraints excluded: chain 5 residue 511 LEU Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 679 LEU Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 182 ASN Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 187 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 270 optimal weight: 0.2980 chunk 163 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 360 optimal weight: 0.9980 chunk 64 optimal weight: 20.0000 chunk 255 optimal weight: 9.9990 chunk 276 optimal weight: 0.0770 chunk 253 optimal weight: 10.0000 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.053751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.037122 restraints weight = 206282.272| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 5.87 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 29039 Z= 0.105 Angle : 0.604 17.744 39408 Z= 0.287 Chirality : 0.041 0.311 4623 Planarity : 0.003 0.044 5120 Dihedral : 6.241 98.233 4153 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.04 % Allowed : 13.07 % Favored : 85.88 % 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: -0.23 (0.14), residues: 3704 helix: 0.82 (0.14), residues: 1442 sheet: -1.11 (0.24), residues: 469 loop : -0.60 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 5 724 TYR 0.027 0.001 TYR 5 731 PHE 0.008 0.001 PHE 4 373 TRP 0.012 0.001 TRP 5 69 HIS 0.005 0.001 HIS 3 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (29024) covalent geometry : angle 0.59950 / 0.29 (39390) hydrogen bonds : bond 0.02864 / 1.97 ( 1034) hydrogen bonds : angle 4.63069 / 3.24 ( 2985) metal coordination : bond 0.00631 / 0.38 ( 15) metal coordination : angle 3.53597 / 2.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 270 MET cc_start: 0.9104 (mtt) cc_final: 0.8696 (mmm) REVERT: 2 324 MET cc_start: 0.8804 (ppp) cc_final: 0.8403 (ppp) REVERT: 2 592 MET cc_start: 0.9217 (mmm) cc_final: 0.8732 (mmm) REVERT: 2 793 MET cc_start: 0.9394 (tpt) cc_final: 0.9042 (mpp) REVERT: 2 814 MET cc_start: 0.9850 (mmm) cc_final: 0.9509 (mmm) REVERT: 3 479 PHE cc_start: 0.9494 (t80) cc_final: 0.9060 (t80) REVERT: 3 805 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9273 (mp) REVERT: 4 317 MET cc_start: 0.9536 (ttp) cc_final: 0.9243 (mtm) REVERT: 4 351 MET cc_start: 0.8856 (tpp) cc_final: 0.8497 (tpp) REVERT: 4 611 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9343 (p) REVERT: 5 127 MET cc_start: 0.8242 (mmm) cc_final: 0.7576 (mmm) REVERT: 5 264 THR cc_start: 0.5762 (OUTLIER) cc_final: 0.5518 (p) REVERT: 5 349 MET cc_start: 0.9490 (tmm) cc_final: 0.9266 (ppp) REVERT: 5 450 MET cc_start: 0.8832 (ppp) cc_final: 0.8611 (ppp) REVERT: 5 679 LEU cc_start: 0.9831 (OUTLIER) cc_final: 0.9562 (pp) REVERT: 6 369 LEU cc_start: 0.9775 (tp) cc_final: 0.9502 (tt) REVERT: 6 371 MET cc_start: 0.9473 (tmm) cc_final: 0.9074 (tmm) REVERT: 6 372 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9425 (mm) REVERT: 6 465 MET cc_start: 0.7901 (ptm) cc_final: 0.7522 (tmm) REVERT: 6 624 MET cc_start: 0.9364 (tpp) cc_final: 0.9053 (tpt) REVERT: 7 639 MET cc_start: 0.9179 (mpp) cc_final: 0.8757 (mtm) outliers start: 31 outliers final: 21 residues processed: 175 average time/residue: 0.1356 time to fit residues: 42.2833 Evaluate side-chains 173 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 480 SER Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 801 SER Chi-restraints excluded: chain 3 residue 805 ILE Chi-restraints excluded: chain 4 residue 480 ILE Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 611 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 72 VAL Chi-restraints excluded: chain 5 residue 126 VAL Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 456 VAL Chi-restraints excluded: chain 5 residue 511 LEU Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 679 LEU Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 182 ASN Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 450 MET Chi-restraints excluded: chain 7 residue 38 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 348 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 145 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 356 optimal weight: 20.0000 chunk 372 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 264 ASN ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 355 GLN 5 30 GLN 5 479 ASN 6 635 HIS 7 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.051930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.034903 restraints weight = 219797.621| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 6.01 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29039 Z= 0.243 Angle : 0.687 12.095 39408 Z= 0.340 Chirality : 0.042 0.297 4623 Planarity : 0.004 0.046 5120 Dihedral : 6.456 100.144 4153 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.72 % Favored : 94.25 % Rotamer: Outliers : 1.28 % Allowed : 13.01 % Favored : 85.71 % 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: -0.38 (0.14), residues: 3704 helix: 0.68 (0.14), residues: 1456 sheet: -1.22 (0.23), residues: 492 loop : -0.67 (0.16), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 5 724 TYR 0.016 0.001 TYR 5 731 PHE 0.019 0.002 PHE 3 567 TRP 0.022 0.002 TRP 6 334 HIS 0.006 0.001 HIS 6 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.24 (29024) covalent geometry : angle 0.67977 / 0.34 (39390) hydrogen bonds : bond 0.03410 / 2.32 ( 1034) hydrogen bonds : angle 4.93183 / 3.43 ( 2985) metal coordination : bond 0.01297 / 0.71 ( 15) metal coordination : angle 4.78695 / 3.47 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 270 MET cc_start: 0.9135 (mtt) cc_final: 0.8718 (mmm) REVERT: 2 324 MET cc_start: 0.8809 (ppp) cc_final: 0.8384 (ppp) REVERT: 2 463 MET cc_start: 0.9238 (ppp) cc_final: 0.8923 (pmm) REVERT: 2 592 MET cc_start: 0.9208 (mmm) cc_final: 0.8560 (mmm) REVERT: 2 770 MET cc_start: 0.9493 (mmt) cc_final: 0.9218 (mmm) REVERT: 2 793 MET cc_start: 0.9399 (tpt) cc_final: 0.9073 (mpp) REVERT: 2 814 MET cc_start: 0.9855 (mmm) cc_final: 0.9499 (mmm) REVERT: 3 479 PHE cc_start: 0.9496 (t80) cc_final: 0.9073 (t80) REVERT: 4 317 MET cc_start: 0.9613 (ttp) cc_final: 0.9215 (tpp) REVERT: 4 351 MET cc_start: 0.8830 (tpp) cc_final: 0.8493 (tpp) REVERT: 4 611 THR cc_start: 0.9494 (OUTLIER) cc_final: 0.9227 (p) REVERT: 5 264 THR cc_start: 0.5745 (OUTLIER) cc_final: 0.5509 (p) REVERT: 5 679 LEU cc_start: 0.9854 (OUTLIER) cc_final: 0.9606 (pp) REVERT: 6 369 LEU cc_start: 0.9808 (tp) cc_final: 0.9586 (tt) REVERT: 6 371 MET cc_start: 0.9502 (tmm) cc_final: 0.9114 (tmm) REVERT: 6 372 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9469 (mm) REVERT: 6 465 MET cc_start: 0.8214 (ptm) cc_final: 0.7663 (tmm) REVERT: 7 380 MET cc_start: 0.8828 (tpp) cc_final: 0.8321 (tpp) outliers start: 38 outliers final: 25 residues processed: 170 average time/residue: 0.1576 time to fit residues: 47.2467 Evaluate side-chains 168 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 480 SER Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 773 MET Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 801 SER Chi-restraints excluded: chain 3 residue 805 ILE Chi-restraints excluded: chain 4 residue 193 TYR Chi-restraints excluded: chain 4 residue 480 ILE Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 611 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 72 VAL Chi-restraints excluded: chain 5 residue 126 VAL Chi-restraints excluded: chain 5 residue 264 THR Chi-restraints excluded: chain 5 residue 456 VAL Chi-restraints excluded: chain 5 residue 511 LEU Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 679 LEU Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 182 ASN Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 7 residue 38 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 357 LEU Chi-restraints excluded: chain 7 residue 405 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 93 optimal weight: 9.9990 chunk 204 optimal weight: 40.0000 chunk 337 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 368 optimal weight: 3.9990 chunk 16 optimal weight: 40.0000 chunk 342 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 331 ASN ** 7 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.056475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.041781 restraints weight = 252050.217| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 5.90 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 29039 Z= 0.227 Angle : 0.683 14.531 39408 Z= 0.336 Chirality : 0.042 0.305 4623 Planarity : 0.003 0.035 5120 Dihedral : 6.543 96.424 4153 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.15 % Allowed : 13.27 % Favored : 85.58 % 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: -0.45 (0.14), residues: 3704 helix: 0.64 (0.14), residues: 1448 sheet: -1.32 (0.23), residues: 495 loop : -0.71 (0.16), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 4 643 TYR 0.012 0.001 TYR 4 249 PHE 0.019 0.001 PHE 3 567 TRP 0.013 0.002 TRP 2 569 HIS 0.008 0.001 HIS 6 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 (29024) covalent geometry : angle 0.67503 / 0.34 (39390) hydrogen bonds : bond 0.03428 / 2.31 ( 1034) hydrogen bonds : angle 4.96941 / 3.45 ( 2985) metal coordination : bond 0.01262 / 0.70 ( 15) metal coordination : angle 4.97210 / 3.66 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 270 MET cc_start: 0.9198 (mtt) cc_final: 0.8740 (mmm) REVERT: 2 324 MET cc_start: 0.8795 (ppp) cc_final: 0.8359 (ppp) REVERT: 2 463 MET cc_start: 0.9134 (ppp) cc_final: 0.8700 (pmm) REVERT: 2 592 MET cc_start: 0.9257 (mmm) cc_final: 0.8812 (mmm) REVERT: 2 770 MET cc_start: 0.9314 (mmt) cc_final: 0.9056 (mmm) REVERT: 2 793 MET cc_start: 0.9371 (tpt) cc_final: 0.9057 (mpp) REVERT: 2 814 MET cc_start: 0.9850 (mmm) cc_final: 0.9488 (mmm) REVERT: 3 479 PHE cc_start: 0.9455 (t80) cc_final: 0.9041 (t80) REVERT: 3 568 MET cc_start: 0.9465 (pmm) cc_final: 0.9141 (pmm) REVERT: 3 805 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9367 (mp) REVERT: 4 317 MET cc_start: 0.9611 (ttp) cc_final: 0.9385 (mtm) REVERT: 4 351 MET cc_start: 0.8834 (tpp) cc_final: 0.8492 (tpp) REVERT: 4 611 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9291 (p) REVERT: 5 127 MET cc_start: 0.8219 (mmm) cc_final: 0.7843 (mmm) REVERT: 5 349 MET cc_start: 0.9483 (tmm) cc_final: 0.9185 (ppp) REVERT: 5 679 LEU cc_start: 0.9860 (OUTLIER) cc_final: 0.9644 (pp) REVERT: 5 725 MET cc_start: 0.9315 (ppp) cc_final: 0.8876 (pmm) REVERT: 6 369 LEU cc_start: 0.9807 (tp) cc_final: 0.9594 (tt) REVERT: 6 371 MET cc_start: 0.9405 (tmm) cc_final: 0.9041 (tmm) REVERT: 6 372 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9463 (mm) REVERT: 7 380 MET cc_start: 0.8715 (tpp) cc_final: 0.8243 (tpp) outliers start: 34 outliers final: 22 residues processed: 171 average time/residue: 0.1484 time to fit residues: 44.4198 Evaluate side-chains 166 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 312 VAL Chi-restraints excluded: chain 2 residue 444 VAL Chi-restraints excluded: chain 2 residue 480 SER Chi-restraints excluded: chain 2 residue 583 VAL Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 768 GLU Chi-restraints excluded: chain 2 residue 773 MET Chi-restraints excluded: chain 3 residue 379 THR Chi-restraints excluded: chain 3 residue 400 LEU Chi-restraints excluded: chain 3 residue 801 SER Chi-restraints excluded: chain 3 residue 805 ILE Chi-restraints excluded: chain 4 residue 480 ILE Chi-restraints excluded: chain 4 residue 560 THR Chi-restraints excluded: chain 4 residue 611 THR Chi-restraints excluded: chain 4 residue 614 LEU Chi-restraints excluded: chain 5 residue 72 VAL Chi-restraints excluded: chain 5 residue 456 VAL Chi-restraints excluded: chain 5 residue 511 LEU Chi-restraints excluded: chain 5 residue 608 ILE Chi-restraints excluded: chain 5 residue 679 LEU Chi-restraints excluded: chain 6 residue 152 VAL Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 7 residue 38 VAL Chi-restraints excluded: chain 7 residue 167 VAL Chi-restraints excluded: chain 7 residue 357 LEU Chi-restraints excluded: chain 7 residue 405 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 13 optimal weight: 10.0000 chunk 224 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 313 optimal weight: 0.0770 chunk 277 optimal weight: 10.0000 chunk 191 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 203 optimal weight: 10.0000 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 621 GLN ** 2 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 30 GLN 6 182 ASN ** 7 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.052769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.036194 restraints weight = 212051.023| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 5.86 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29039 Z= 0.123 Angle : 0.639 14.399 39408 Z= 0.309 Chirality : 0.042 0.303 4623 Planarity : 0.003 0.035 5120 Dihedral : 6.374 89.129 4153 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.91 % Allowed : 13.75 % Favored : 85.34 % 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: -0.28 (0.14), residues: 3704 helix: 0.84 (0.14), residues: 1438 sheet: -1.23 (0.23), residues: 475 loop : -0.66 (0.16), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 724 TYR 0.023 0.001 TYR 5 731 PHE 0.011 0.001 PHE 6 462 TRP 0.010 0.001 TRP 5 69 HIS 0.005 0.001 HIS 3 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (29024) covalent geometry : angle 0.63314 / 0.31 (39390) hydrogen bonds : bond 0.03032 / 2.06 ( 1034) hydrogen bonds : angle 4.78078 / 3.33 ( 2985) metal coordination : bond 0.00835 / 0.48 ( 15) metal coordination : angle 4.21494 / 3.21 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5925.93 seconds wall clock time: 102 minutes 56.20 seconds (6176.20 seconds total)