Starting phenix.real_space_refine on Sun Sep 13 16:19:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25xn_80449/09_2026/25xn_80449.cif Found real_map, /net/cci-nas-00/data/ceres_data/25xn_80449/09_2026/25xn_80449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25xn_80449/09_2026/25xn_80449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25xn_80449/09_2026/25xn_80449.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25xn_80449/09_2026/25xn_80449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25xn_80449/09_2026/25xn_80449.map" } resolution = 3.01 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= 0.019 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 Mn 3 7.51 5 Zn 3 6.06 5 P 40 5.49 5 S 130 5.16 5 C 14670 2.51 5 N 4107 2.21 5 O 4253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23206 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 22344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3094, 22344 Classifications: {'peptide': 3094} Incomplete info: {'truncation_to_alanine': 687} Link IDs: {'PTRANS': 94, 'TRANS': 2999} Chain breaks: 21 Unresolved non-hydrogen bonds: 2401 Unresolved non-hydrogen angles: 2936 Unresolved non-hydrogen dihedrals: 1906 Unresolved non-hydrogen chiralities: 115 Planarities with less than four sites: {'GLN:plan1': 23, 'ASN:plan1': 43, 'ARG:plan': 43, 'ASP:plan': 102, 'GLU:plan': 169, 'TYR:plan': 4, 'PHE:plan': 6, 'HIS:plan': 8} Unresolved non-hydrogen planarities: 1522 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 186 Classifications: {'DNA': 1, 'RNA': 9} Modifications used: {'5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 7} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 3} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 254 Classifications: {'DNA': 1, 'RNA': 12} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 9} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Classifications: {'DNA': 1, 'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 2} Link IDs: {'rna2p': 1, 'rna3p': 2} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' G%5*END:plan': 1, ' G%5*END:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 130 Inner-chain residues flagged as termini: ['pdbres=" C F 16 "'] Classifications: {'DNA': 1, 'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 5} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MN': 3, ' ZN': 3} Classifications: {'undetermined': 6, 'water': 2} Link IDs: {None: 7} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18386 SG CYS A3280 39.455 37.619 65.315 1.00154.02 S ATOM 5101 SG CYS A1028 100.616 65.017 125.356 1.00150.55 S ATOM 5116 SG CYS A1031 102.175 61.645 124.491 1.00157.53 S ATOM 5348 SG CYS A1062 101.035 62.349 128.100 1.00158.51 S ATOM 5365 SG CYS A1065 98.529 61.829 125.476 1.00157.75 S ATOM 6799 SG CYS A1294 53.042 41.086 122.787 1.00124.90 S Time building chain proxies: 4.23, per 1000 atoms: 0.18 Number of scatterers: 23206 At special positions: 0 Unit cell: (118.75, 143.45, 167.2, 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 3 29.99 Mn 3 24.99 S 130 16.00 P 40 15.00 O 4253 8.00 N 4107 7.00 C 14670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1766 " - pdb=" SG CYS A2558 " distance=2.03 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: 1.84 Conformation dependent library (CDL) restraints added in 904.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4001 " pdb="ZN ZN A4001 " - pdb=" SG CYS A3280 " pdb="ZN ZN A4001 " - pdb=" NE2 HIS A3551 " pdb="ZN ZN A4001 " - pdb=" NE2 HIS A3556 " pdb=" ZN A4003 " pdb="ZN ZN A4003 " - pdb=" SG CYS A1065 " pdb="ZN ZN A4003 " - pdb=" SG CYS A1062 " pdb="ZN ZN A4003 " - pdb=" SG CYS A1031 " pdb="ZN ZN A4003 " - pdb=" SG CYS A1028 " pdb=" ZN A4005 " pdb="ZN ZN A4005 " - pdb=" NE2 HIS A1090 " pdb="ZN ZN A4005 " - pdb=" SG CYS A1294 " pdb="ZN ZN A4005 " - pdb=" ND1 HIS A1365 " Number of angles added : 6 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5934 Finding SS restraints... Secondary structure from input PDB file: 153 helices and 21 sheets defined 62.6% alpha, 8.0% beta 11 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 246 through 253 Processing helix chain 'A' and resid 282 through 288 removed outlier: 3.975A pdb=" N GLY A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 316 through 325 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.520A pdb=" N THR A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 357 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 374 Processing helix chain 'A' and resid 375 through 378 Processing helix chain 'A' and resid 380 through 390 removed outlier: 4.304A pdb=" N ASN A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 399 through 424 removed outlier: 5.628A pdb=" N LYS A 414 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 446 through 460 Processing helix chain 'A' and resid 466 through 485 Processing helix chain 'A' and resid 489 through 495 removed outlier: 3.965A pdb=" N GLN A 493 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 522 Processing helix chain 'A' and resid 540 through 554 removed outlier: 3.899A pdb=" N VAL A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 581 Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'A' and resid 594 through 605 Processing helix chain 'A' and resid 606 through 622 removed outlier: 4.091A pdb=" N GLU A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 650 removed outlier: 3.514A pdb=" N ARG A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.844A pdb=" N LYS A 659 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 673 through 681 removed outlier: 3.678A pdb=" N ASP A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 690 removed outlier: 3.681A pdb=" N ARG A 688 " --> pdb=" O PRO A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 761 removed outlier: 3.553A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 818 removed outlier: 3.590A pdb=" N GLN A 815 " --> pdb=" O SER A 811 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 816 " --> pdb=" O GLU A 812 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 817 " --> pdb=" O GLU A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 843 removed outlier: 3.552A pdb=" N TRP A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 854 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 876 through 898 removed outlier: 3.781A pdb=" N SER A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE A 889 " --> pdb=" O ASN A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 912 Processing helix chain 'A' and resid 913 through 914 No H-bonds generated for 'chain 'A' and resid 913 through 914' Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 930 through 947 removed outlier: 5.264A pdb=" N GLU A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 967 Processing helix chain 'A' and resid 973 through 987 removed outlier: 3.611A pdb=" N CYS A 980 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 998 removed outlier: 3.556A pdb=" N THR A 998 " --> pdb=" O GLU A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1024 removed outlier: 3.633A pdb=" N THR A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1042 Processing helix chain 'A' and resid 1044 through 1057 removed outlier: 3.751A pdb=" N GLN A1057 " --> pdb=" O ALA A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 4.127A pdb=" N HIS A1066 " --> pdb=" O SER A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1111 Processing helix chain 'A' and resid 1118 through 1140 Processing helix chain 'A' and resid 1176 through 1187 Processing helix chain 'A' and resid 1196 through 1209 Processing helix chain 'A' and resid 1221 through 1233 Processing helix chain 'A' and resid 1237 through 1254 removed outlier: 3.851A pdb=" N VAL A1241 " --> pdb=" O ARG A1237 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A1242 " --> pdb=" O ASP A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1281 removed outlier: 4.497A pdb=" N PHE A1279 " --> pdb=" O ASP A1275 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A1280 " --> pdb=" O VAL A1276 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1309 removed outlier: 4.112A pdb=" N ARG A1307 " --> pdb=" O GLU A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1328 Processing helix chain 'A' and resid 1330 through 1350 Processing helix chain 'A' and resid 1401 through 1409 removed outlier: 3.909A pdb=" N LEU A1407 " --> pdb=" O ARG A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1426 removed outlier: 3.656A pdb=" N GLN A1421 " --> pdb=" O THR A1417 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN A1424 " --> pdb=" O ILE A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1432 removed outlier: 3.552A pdb=" N VAL A1431 " --> pdb=" O CYS A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1436 through 1464 Processing helix chain 'A' and resid 1465 through 1481 removed outlier: 3.668A pdb=" N SER A1469 " --> pdb=" O ARG A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1505 Processing helix chain 'A' and resid 1507 through 1514 removed outlier: 3.942A pdb=" N ASN A1514 " --> pdb=" O ASN A1510 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1524 Processing helix chain 'A' and resid 1524 through 1531 Processing helix chain 'A' and resid 1532 through 1534 No H-bonds generated for 'chain 'A' and resid 1532 through 1534' Processing helix chain 'A' and resid 1538 through 1547 removed outlier: 4.194A pdb=" N LYS A1544 " --> pdb=" O ASN A1540 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE A1546 " --> pdb=" O LEU A1542 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A1547 " --> pdb=" O GLY A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1572 removed outlier: 4.460A pdb=" N ASP A1572 " --> pdb=" O CYS A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1582 removed outlier: 3.506A pdb=" N LYS A1581 " --> pdb=" O VAL A1577 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A1582 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1612 Processing helix chain 'A' and resid 1613 through 1616 removed outlier: 3.556A pdb=" N ILE A1616 " --> pdb=" O ASN A1613 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1613 through 1616' Processing helix chain 'A' and resid 1623 through 1650 removed outlier: 3.952A pdb=" N GLU A1634 " --> pdb=" O SER A1630 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A1635 " --> pdb=" O VAL A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1666 Processing helix chain 'A' and resid 1758 through 1773 Processing helix chain 'A' and resid 1780 through 1791 Processing helix chain 'A' and resid 1792 through 1795 Processing helix chain 'A' and resid 1796 through 1805 Processing helix chain 'A' and resid 1806 through 1811 removed outlier: 3.551A pdb=" N TRP A1810 " --> pdb=" O PRO A1807 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A1811 " --> pdb=" O LYS A1808 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1816 Processing helix chain 'A' and resid 1831 through 1852 Processing helix chain 'A' and resid 1872 through 1877 Processing helix chain 'A' and resid 1883 through 1895 Processing helix chain 'A' and resid 2017 through 2040 Processing helix chain 'A' and resid 2045 through 2058 Processing helix chain 'A' and resid 2059 through 2061 No H-bonds generated for 'chain 'A' and resid 2059 through 2061' Processing helix chain 'A' and resid 2063 through 2073 Processing helix chain 'A' and resid 2235 through 2247 Processing helix chain 'A' and resid 2250 through 2260 removed outlier: 3.587A pdb=" N LEU A2260 " --> pdb=" O PHE A2256 " (cutoff:3.500A) Processing helix chain 'A' and resid 2286 through 2305 Processing helix chain 'A' and resid 2316 through 2336 Processing helix chain 'A' and resid 2367 through 2379 removed outlier: 3.606A pdb=" N PHE A2371 " --> pdb=" O CYS A2367 " (cutoff:3.500A) Processing helix chain 'A' and resid 2382 through 2398 removed outlier: 3.754A pdb=" N CYS A2398 " --> pdb=" O ILE A2394 " (cutoff:3.500A) Processing helix chain 'A' and resid 2404 through 2420 removed outlier: 3.562A pdb=" N LEU A2415 " --> pdb=" O ILE A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2429 through 2440 Processing helix chain 'A' and resid 2441 through 2445 Processing helix chain 'A' and resid 2447 through 2457 Processing helix chain 'A' and resid 2458 through 2461 Processing helix chain 'A' and resid 2476 through 2503 removed outlier: 3.523A pdb=" N VAL A2482 " --> pdb=" O ALA A2478 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A2483 " --> pdb=" O THR A2479 " (cutoff:3.500A) Processing helix chain 'A' and resid 2531 through 2540 removed outlier: 3.714A pdb=" N THR A2540 " --> pdb=" O GLN A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2540 through 2558 Processing helix chain 'A' and resid 2589 through 2594 removed outlier: 3.541A pdb=" N MET A2594 " --> pdb=" O ILE A2591 " (cutoff:3.500A) Processing helix chain 'A' and resid 2605 through 2623 Processing helix chain 'A' and resid 2626 through 2645 removed outlier: 4.339A pdb=" N PHE A2641 " --> pdb=" O ARG A2637 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A2644 " --> pdb=" O ILE A2640 " (cutoff:3.500A) Processing helix chain 'A' and resid 2645 through 2657 removed outlier: 3.609A pdb=" N ARG A2651 " --> pdb=" O ASP A2647 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE A2654 " --> pdb=" O ARG A2650 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LEU A2655 " --> pdb=" O ARG A2651 " (cutoff:3.500A) Processing helix chain 'A' and resid 2658 through 2659 No H-bonds generated for 'chain 'A' and resid 2658 through 2659' Processing helix chain 'A' and resid 2660 through 2664 Processing helix chain 'A' and resid 2670 through 2675 Processing helix chain 'A' and resid 2678 through 2697 removed outlier: 3.756A pdb=" N ASP A2683 " --> pdb=" O VAL A2679 " (cutoff:3.500A) Processing helix chain 'A' and resid 2753 through 2765 Processing helix chain 'A' and resid 2771 through 2783 Processing helix chain 'A' and resid 2801 through 2805 Processing helix chain 'A' and resid 2806 through 2814 Processing helix chain 'A' and resid 2816 through 2837 removed outlier: 3.678A pdb=" N SER A2826 " --> pdb=" O ASN A2822 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A2827 " --> pdb=" O ARG A2823 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A2837 " --> pdb=" O ALA A2833 " (cutoff:3.500A) Processing helix chain 'A' and resid 2869 through 2890 removed outlier: 4.591A pdb=" N GLU A2875 " --> pdb=" O LYS A2871 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A2877 " --> pdb=" O ARG A2873 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG A2878 " --> pdb=" O ARG A2874 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A2881 " --> pdb=" O GLU A2877 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2910 removed outlier: 3.503A pdb=" N SER A2909 " --> pdb=" O LYS A2905 " (cutoff:3.500A) Processing helix chain 'A' and resid 2916 through 2930 Processing helix chain 'A' and resid 2932 through 2938 removed outlier: 3.946A pdb=" N GLY A2936 " --> pdb=" O ASN A2932 " (cutoff:3.500A) Processing helix chain 'A' and resid 2944 through 2954 Processing helix chain 'A' and resid 2994 through 3003 Processing helix chain 'A' and resid 3043 through 3061 removed outlier: 3.543A pdb=" N LYS A3047 " --> pdb=" O GLN A3043 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A3048 " --> pdb=" O SER A3044 " (cutoff:3.500A) Processing helix chain 'A' and resid 3062 through 3072 Processing helix chain 'A' and resid 3104 through 3114 Processing helix chain 'A' and resid 3115 through 3122 removed outlier: 4.440A pdb=" N SER A3119 " --> pdb=" O GLU A3115 " (cutoff:3.500A) Processing helix chain 'A' and resid 3130 through 3142 removed outlier: 3.531A pdb=" N MET A3139 " --> pdb=" O ARG A3135 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A3142 " --> pdb=" O ILE A3138 " (cutoff:3.500A) Processing helix chain 'A' and resid 3142 through 3163 Processing helix chain 'A' and resid 3167 through 3188 Processing helix chain 'A' and resid 3209 through 3217 removed outlier: 3.518A pdb=" N VAL A3213 " --> pdb=" O VAL A3209 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A3217 " --> pdb=" O VAL A3213 " (cutoff:3.500A) Processing helix chain 'A' and resid 3237 through 3252 Processing helix chain 'A' and resid 3255 through 3268 Processing helix chain 'A' and resid 3272 through 3276 Processing helix chain 'A' and resid 3283 through 3294 removed outlier: 3.787A pdb=" N SER A3288 " --> pdb=" O SER A3284 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A3292 " --> pdb=" O SER A3288 " (cutoff:3.500A) Processing helix chain 'A' and resid 3297 through 3305 Processing helix chain 'A' and resid 3306 through 3309 Processing helix chain 'A' and resid 3311 through 3327 removed outlier: 3.576A pdb=" N LEU A3321 " --> pdb=" O GLY A3317 " (cutoff:3.500A) Processing helix chain 'A' and resid 3328 through 3334 Processing helix chain 'A' and resid 3382 through 3399 removed outlier: 3.501A pdb=" N LEU A3386 " --> pdb=" O SER A3382 " (cutoff:3.500A) Processing helix chain 'A' and resid 3406 through 3417 removed outlier: 3.653A pdb=" N LEU A3417 " --> pdb=" O PHE A3413 " (cutoff:3.500A) Processing helix chain 'A' and resid 3419 through 3423 removed outlier: 3.564A pdb=" N CYS A3423 " --> pdb=" O SER A3420 " (cutoff:3.500A) Processing helix chain 'A' and resid 3504 through 3514 Processing helix chain 'A' and resid 3543 through 3556 removed outlier: 4.379A pdb=" N LEU A3549 " --> pdb=" O ASN A3545 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A3550 " --> pdb=" O SER A3546 " (cutoff:3.500A) Processing helix chain 'A' and resid 3556 through 3569 removed outlier: 3.601A pdb=" N ASP A3560 " --> pdb=" O HIS A3556 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A3563 " --> pdb=" O SER A3559 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A3567 " --> pdb=" O MET A3563 " (cutoff:3.500A) Processing helix chain 'A' and resid 3569 through 3579 removed outlier: 3.527A pdb=" N HIS A3573 " --> pdb=" O SER A3569 " (cutoff:3.500A) Processing helix chain 'A' and resid 3585 through 3596 removed outlier: 4.158A pdb=" N LEU A3589 " --> pdb=" O ASN A3585 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS A3596 " --> pdb=" O GLU A3592 " (cutoff:3.500A) Processing helix chain 'A' and resid 3606 through 3624 Processing helix chain 'A' and resid 3627 through 3629 No H-bonds generated for 'chain 'A' and resid 3627 through 3629' Processing helix chain 'A' and resid 3630 through 3641 Processing helix chain 'A' and resid 3678 through 3686 Processing helix chain 'A' and resid 3691 through 3699 removed outlier: 4.938A pdb=" N ALA A3696 " --> pdb=" O PHE A3693 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A3699 " --> pdb=" O ALA A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3700 through 3722 removed outlier: 3.964A pdb=" N ASN A3706 " --> pdb=" O GLU A3702 " (cutoff:3.500A) Processing helix chain 'A' and resid 3724 through 3739 removed outlier: 3.772A pdb=" N PHE A3737 " --> pdb=" O THR A3733 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3758 Processing helix chain 'A' and resid 3802 through 3817 removed outlier: 3.563A pdb=" N ARG A3809 " --> pdb=" O VAL A3805 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A3817 " --> pdb=" O HIS A3813 " (cutoff:3.500A) Processing helix chain 'A' and resid 3824 through 3832 Processing helix chain 'A' and resid 3859 through 3868 Processing helix chain 'A' and resid 3869 through 3888 removed outlier: 3.684A pdb=" N ARG A3874 " --> pdb=" O MET A3870 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU A3875 " --> pdb=" O GLU A3871 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ALA A3876 " --> pdb=" O LYS A3872 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A3888 " --> pdb=" O ILE A3884 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 260 removed outlier: 6.146A pdb=" N THR A 265 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 744 through 746 removed outlier: 3.947A pdb=" N SER A 744 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 970 through 972 removed outlier: 5.867A pdb=" N VAL A 725 " --> pdb=" O ARG A1671 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1003 through 1004 Processing sheet with id=AA5, first strand: chain 'A' and resid 1151 through 1152 removed outlier: 3.927A pdb=" N CYS A1143 " --> pdb=" O VAL A1220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1357 through 1362 removed outlier: 4.394A pdb=" N LEU A1383 " --> pdb=" O LYS A1373 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU A1386 " --> pdb=" O GLY A1396 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY A1396 " --> pdb=" O LEU A1386 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1821 through 1825 removed outlier: 6.847A pdb=" N VAL A2231 " --> pdb=" O ALA A1824 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2278 through 2285 removed outlier: 3.886A pdb=" N GLN A2275 " --> pdb=" O GLY A2278 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A2270 " --> pdb=" O GLU A2402 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A2399 " --> pdb=" O SER A2467 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2507 through 2515 removed outlier: 3.814A pdb=" N ASP A2518 " --> pdb=" O SER A2515 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2574 through 2576 Processing sheet with id=AB2, first strand: chain 'A' and resid 2956 through 2960 removed outlier: 4.380A pdb=" N ILE A2990 " --> pdb=" O ASP A2960 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3005 through 3009 removed outlier: 6.149A pdb=" N SER A3005 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A3041 " --> pdb=" O SER A3005 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER A3007 " --> pdb=" O VAL A3041 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 3078 through 3080 removed outlier: 3.804A pdb=" N SER A3078 " --> pdb=" O ARG A3224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 3086 through 3094 Processing sheet with id=AB6, first strand: chain 'A' and resid 3343 through 3346 removed outlier: 7.161A pdb=" N VAL A3456 " --> pdb=" O LEU A3374 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE A3376 " --> pdb=" O VAL A3456 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A3455 " --> pdb=" O VAL A3435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 3466 through 3469 Processing sheet with id=AB8, first strand: chain 'A' and resid 3479 through 3480 removed outlier: 6.409A pdb=" N LEU A3487 " --> pdb=" O ARG A3535 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG A3535 " --> pdb=" O LEU A3487 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE A3489 " --> pdb=" O LEU A3533 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 3598 through 3599 Processing sheet with id=AC1, first strand: chain 'A' and resid 3646 through 3651 Processing sheet with id=AC2, first strand: chain 'A' and resid 3772 through 3773 Processing sheet with id=AC3, first strand: chain 'A' and resid 3777 through 3778 1402 hydrogen bonds defined for protein. 4017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 8.09 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7354 1.34 - 1.46: 3594 1.46 - 1.58: 12470 1.58 - 1.70: 77 1.70 - 1.82: 186 Bond restraints: 23681 Sorted by residual: bond pdb=" O3' U B4004 " pdb=" P G B4005 " ideal model delta sigma weight residual 1.607 1.573 0.034 1.20e-02 6.94e+03 8.21e+00 bond pdb=" C TYR A2519 " pdb=" N ALA A2520 " ideal model delta sigma weight residual 1.331 1.293 0.038 1.44e-02 4.82e+03 6.95e+00 bond pdb=" N GLU A3072 " pdb=" CA GLU A3072 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.16e-02 7.43e+03 5.99e+00 bond pdb=" O3' U B4002 " pdb=" P U B4003 " ideal model delta sigma weight residual 1.607 1.578 0.029 1.20e-02 6.94e+03 5.74e+00 bond pdb=" N ARG A3025 " pdb=" CA ARG A3025 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.22e-02 6.72e+03 5.31e+00 ... (remaining 23676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 32157 2.25 - 4.51: 244 4.51 - 6.76: 12 6.76 - 9.02: 6 9.02 - 11.27: 2 Bond angle restraints: 32421 Sorted by residual: angle pdb=" O5' A D 7 " pdb=" C5' A D 7 " pdb=" C4' A D 7 " ideal model delta sigma weight residual 109.40 112.60 -3.20 8.00e-01 1.56e+00 1.60e+01 angle pdb=" CB MET A 808 " pdb=" CG MET A 808 " pdb=" SD MET A 808 " ideal model delta sigma weight residual 112.70 123.97 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" O5' U B4008 " pdb=" C5' U B4008 " pdb=" C4' U B4008 " ideal model delta sigma weight residual 109.40 112.40 -3.00 8.00e-01 1.56e+00 1.41e+01 angle pdb=" C SER A2515 " pdb=" N SER A2516 " pdb=" CA SER A2516 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" O5' G E 2 " pdb=" C5' G E 2 " pdb=" C4' G E 2 " ideal model delta sigma weight residual 109.40 111.97 -2.57 8.00e-01 1.56e+00 1.03e+01 ... (remaining 32416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 13161 23.81 - 47.63: 871 47.63 - 71.44: 148 71.44 - 95.26: 29 95.26 - 119.07: 1 Dihedral angle restraints: 14210 sinusoidal: 5128 harmonic: 9082 Sorted by residual: dihedral pdb=" CB CYS A1766 " pdb=" SG CYS A1766 " pdb=" SG CYS A2558 " pdb=" CB CYS A2558 " ideal model delta sinusoidal sigma weight residual 93.00 128.20 -35.20 1 1.00e+01 1.00e-02 1.76e+01 dihedral pdb=" CA SER A2515 " pdb=" C SER A2515 " pdb=" N SER A2516 " pdb=" CA SER A2516 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" O4' U B4002 " pdb=" C2' U B4002 " pdb=" C1' U B4002 " pdb=" C3' U B4002 " ideal model delta sinusoidal sigma weight residual 25.59 37.94 -12.35 3 3.80e+00 6.93e-02 1.49e+01 ... (remaining 14207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3135 0.039 - 0.078: 662 0.078 - 0.118: 173 0.118 - 0.157: 40 0.157 - 0.196: 4 Chirality restraints: 4014 Sorted by residual: chirality pdb=" C3' G B4005 " pdb=" C4' G B4005 " pdb=" O3' G B4005 " pdb=" C2' G B4005 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" C2' C F 16 " pdb=" C3' C F 16 " pdb=" O2' C F 16 " pdb=" C1' C F 16 " both_signs ideal model delta sigma weight residual False -2.62 -2.79 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CB ILE A3087 " pdb=" CA ILE A3087 " pdb=" CG1 ILE A3087 " pdb=" CG2 ILE A3087 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 4011 not shown) Planarity restraints: 3925 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1146 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A1147 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A1147 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1147 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2363 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A2364 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A2364 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A2364 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2605 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO A2606 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A2606 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A2606 " 0.019 5.00e-02 4.00e+02 ... (remaining 3922 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 68 2.53 - 3.12: 17822 3.12 - 3.71: 37651 3.71 - 4.31: 50240 4.31 - 4.90: 84441 Nonbonded interactions: 190222 Sorted by model distance: nonbonded pdb=" OE2 GLU A3286 " pdb="ZN ZN A4001 " model vdw 1.936 2.230 nonbonded pdb=" OE2 GLU A2788 " pdb="ZN ZN A4005 " model vdw 2.015 2.230 nonbonded pdb=" OP2 G E 1 " pdb="MN MN A4002 " model vdw 2.049 2.320 nonbonded pdb=" O VAL A 826 " pdb="MN MN A4002 " model vdw 2.085 2.320 nonbonded pdb=" OD2 ASP A 693 " pdb="MN MN A4002 " model vdw 2.111 2.320 ... (remaining 190217 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: 0.010 Normalize map: mean=0, sd=1: 3.040 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: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 28.610 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 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 : 0.002 0.039 23692 Z= 0.124 Angle : 0.449 11.272 32429 Z= 0.252 Chirality : 0.037 0.196 4014 Planarity : 0.003 0.047 3925 Dihedral : 16.083 119.070 8273 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 21.94 % Favored : 78.06 % 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: 1.18 (0.16), residues: 3050 helix: 1.77 (0.13), residues: 1715 sheet: -0.56 (0.33), residues: 264 loop : -0.41 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2232 TYR 0.009 0.001 TYR A2468 PHE 0.010 0.001 PHE A3001 TRP 0.010 0.001 TRP A 494 HIS 0.008 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (23681) covalent geometry : angle 0.44751 / 0.25 (32421) SS BOND : bond 0.00005 / 0.00 ( 1) SS BOND : angle 0.12185 / 0.07 ( 2) hydrogen bonds : bond 0.21547 / 15.09 ( 1428) hydrogen bonds : angle 6.39609 / 4.64 ( 4069) metal coordination : bond 0.00454 / 0.27 ( 10) metal coordination : angle 2.53737 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.906 Fit side-chains REVERT: A 2442 ASP cc_start: 0.9049 (m-30) cc_final: 0.8613 (t0) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1355 time to fit residues: 29.4924 Evaluate side-chains 117 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 HIS A 473 ASN A 567 GLN A2911 ASN A3285 HIS ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3421 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.072589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.055336 restraints weight = 58759.471| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.67 r_work: 0.2636 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23692 Z= 0.173 Angle : 0.503 12.789 32429 Z= 0.271 Chirality : 0.039 0.200 4014 Planarity : 0.004 0.046 3925 Dihedral : 8.943 116.029 3833 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.63 % Allowed : 21.52 % Favored : 76.85 % 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: 1.40 (0.16), residues: 3050 helix: 1.98 (0.12), residues: 1752 sheet: -0.63 (0.32), residues: 266 loop : -0.44 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2232 TYR 0.012 0.001 TYR A 641 PHE 0.014 0.001 PHE A1781 TRP 0.011 0.001 TRP A2542 HIS 0.005 0.001 HIS A 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (23681) covalent geometry : angle 0.50226 / 0.27 (32421) SS BOND : bond 0.00004 / 0.00 ( 1) SS BOND : angle 0.56214 / 0.30 ( 2) hydrogen bonds : bond 0.05077 / 3.62 ( 1428) hydrogen bonds : angle 4.53647 / 3.30 ( 4069) metal coordination : bond 0.00572 / 0.37 ( 10) metal coordination : angle 1.89904 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 0.861 Fit side-chains REVERT: A 808 MET cc_start: 0.8279 (tmm) cc_final: 0.7140 (tmm) REVERT: A 1382 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8551 (mtp) REVERT: A 2442 ASP cc_start: 0.9076 (m-30) cc_final: 0.8607 (t0) REVERT: A 2951 ILE cc_start: 0.9239 (tp) cc_final: 0.8974 (tp) outliers start: 35 outliers final: 17 residues processed: 159 average time/residue: 0.1259 time to fit residues: 35.5916 Evaluate side-chains 139 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1630 SER Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3193 THR Chi-restraints excluded: chain A residue 3514 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 7 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 chunk 273 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 294 optimal weight: 9.9990 chunk 287 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 ASN A1521 GLN A2476 HIS ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3421 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.073774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.056509 restraints weight = 58418.515| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.68 r_work: 0.2663 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23692 Z= 0.112 Angle : 0.433 8.550 32429 Z= 0.234 Chirality : 0.037 0.171 4014 Planarity : 0.003 0.051 3925 Dihedral : 8.884 115.344 3833 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.53 % Allowed : 21.99 % Favored : 76.48 % 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: 1.60 (0.16), residues: 3050 helix: 2.17 (0.13), residues: 1747 sheet: -0.54 (0.32), residues: 265 loop : -0.40 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2232 TYR 0.018 0.001 TYR A3738 PHE 0.016 0.001 PHE A1609 TRP 0.011 0.001 TRP A2542 HIS 0.006 0.001 HIS A3421 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (23681) covalent geometry : angle 0.43147 / 0.23 (32421) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 0.52202 / 0.27 ( 2) hydrogen bonds : bond 0.04146 / 2.96 ( 1428) hydrogen bonds : angle 4.12845 / 3.01 ( 4069) metal coordination : bond 0.01463 / 0.74 ( 10) metal coordination : angle 2.96176 / 1.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.887 Fit side-chains REVERT: A 808 MET cc_start: 0.8327 (tmm) cc_final: 0.7500 (tmm) REVERT: A 1382 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8551 (mtp) REVERT: A 2442 ASP cc_start: 0.9080 (m-30) cc_final: 0.8623 (t0) REVERT: A 2951 ILE cc_start: 0.9181 (tp) cc_final: 0.8883 (tp) outliers start: 33 outliers final: 13 residues processed: 162 average time/residue: 0.1221 time to fit residues: 35.1506 Evaluate side-chains 138 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3868 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 309 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 276 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1002 HIS ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3421 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.070571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.053335 restraints weight = 59109.992| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.65 r_work: 0.2590 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 23692 Z= 0.286 Angle : 0.548 8.741 32429 Z= 0.287 Chirality : 0.041 0.177 4014 Planarity : 0.003 0.051 3925 Dihedral : 8.968 115.516 3833 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.51 % Allowed : 21.85 % Favored : 75.64 % 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: 1.50 (0.16), residues: 3050 helix: 2.10 (0.13), residues: 1759 sheet: -0.68 (0.32), residues: 268 loop : -0.46 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1108 TYR 0.014 0.001 TYR A2468 PHE 0.015 0.001 PHE A1781 TRP 0.011 0.001 TRP A2362 HIS 0.006 0.001 HIS A3551 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.29 (23681) covalent geometry : angle 0.54714 / 0.29 (32421) SS BOND : bond 0.00200 / 0.11 ( 1) SS BOND : angle 0.67768 / 0.36 ( 2) hydrogen bonds : bond 0.04395 / 3.14 ( 1428) hydrogen bonds : angle 4.19957 / 3.07 ( 4069) metal coordination : bond 0.01340 / 0.87 ( 10) metal coordination : angle 2.61101 / 1.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 116 time to evaluate : 0.694 Fit side-chains REVERT: A 808 MET cc_start: 0.8413 (tmm) cc_final: 0.7499 (tmm) REVERT: A 1382 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8589 (mtp) REVERT: A 2890 MET cc_start: 0.9058 (mmm) cc_final: 0.8673 (tpt) outliers start: 54 outliers final: 36 residues processed: 164 average time/residue: 0.1166 time to fit residues: 33.6899 Evaluate side-chains 149 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1595 THR Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2042 SER Chi-restraints excluded: chain A residue 2287 THR Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3182 SER Chi-restraints excluded: chain A residue 3193 THR Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3532 VAL Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3868 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 235 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 307 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 285 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN A1563 GLN ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.055563 restraints weight = 58084.657| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.66 r_work: 0.2642 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23692 Z= 0.114 Angle : 0.442 12.097 32429 Z= 0.236 Chirality : 0.037 0.168 4014 Planarity : 0.003 0.053 3925 Dihedral : 8.960 115.702 3833 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.19 % Allowed : 22.08 % Favored : 75.73 % 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: 1.68 (0.16), residues: 3050 helix: 2.25 (0.13), residues: 1753 sheet: -0.59 (0.32), residues: 265 loop : -0.39 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2232 TYR 0.011 0.001 TYR A 641 PHE 0.014 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.005 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (23681) covalent geometry : angle 0.44029 / 0.24 (32421) SS BOND : bond 0.00009 / 0.00 ( 1) SS BOND : angle 0.44672 / 0.24 ( 2) hydrogen bonds : bond 0.03689 / 2.64 ( 1428) hydrogen bonds : angle 3.95386 / 2.89 ( 4069) metal coordination : bond 0.00678 / 0.39 ( 10) metal coordination : angle 3.12286 / 1.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 0.807 Fit side-chains REVERT: A 455 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7747 (t) REVERT: A 808 MET cc_start: 0.8398 (tmm) cc_final: 0.7447 (tmm) REVERT: A 1382 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8548 (mtp) REVERT: A 1831 MET cc_start: 0.8553 (mmp) cc_final: 0.8275 (mmp) REVERT: A 2890 MET cc_start: 0.8927 (mmm) cc_final: 0.8528 (tpt) REVERT: A 2951 ILE cc_start: 0.9208 (tp) cc_final: 0.8940 (tp) outliers start: 47 outliers final: 32 residues processed: 168 average time/residue: 0.1178 time to fit residues: 34.3439 Evaluate side-chains 155 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2496 ILE Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3182 SER Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3532 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3868 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 161 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 289 optimal weight: 0.0050 chunk 52 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 139 optimal weight: 0.4980 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 ASN A1579 HIS ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3411 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.072829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.055506 restraints weight = 58507.433| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 2.68 r_work: 0.2643 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23692 Z= 0.128 Angle : 0.443 9.937 32429 Z= 0.234 Chirality : 0.037 0.171 4014 Planarity : 0.003 0.054 3925 Dihedral : 8.905 113.597 3833 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.23 % Allowed : 22.18 % Favored : 75.59 % 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: 1.77 (0.16), residues: 3050 helix: 2.34 (0.13), residues: 1751 sheet: -0.58 (0.32), residues: 265 loop : -0.36 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 800 TYR 0.011 0.001 TYR A 641 PHE 0.014 0.001 PHE A2633 TRP 0.011 0.001 TRP A2542 HIS 0.004 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (23681) covalent geometry : angle 0.44216 / 0.23 (32421) SS BOND : bond 0.00042 / 0.02 ( 1) SS BOND : angle 0.54748 / 0.29 ( 2) hydrogen bonds : bond 0.03506 / 2.50 ( 1428) hydrogen bonds : angle 3.84602 / 2.81 ( 4069) metal coordination : bond 0.00637 / 0.41 ( 10) metal coordination : angle 2.46698 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.932 Fit side-chains REVERT: A 455 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7728 (t) REVERT: A 808 MET cc_start: 0.8434 (tmm) cc_final: 0.7482 (tmm) REVERT: A 1382 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8597 (mtp) REVERT: A 1831 MET cc_start: 0.8563 (mmp) cc_final: 0.8284 (mmp) REVERT: A 2951 ILE cc_start: 0.9180 (tp) cc_final: 0.8891 (tp) outliers start: 48 outliers final: 35 residues processed: 165 average time/residue: 0.1068 time to fit residues: 31.8789 Evaluate side-chains 155 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3182 SER Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3532 VAL Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3887 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 87 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 597 ASN ** A3409 GLN ** 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 = 0.3136 r_free = 0.3136 target = 0.071917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.054644 restraints weight = 58990.869| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 2.67 r_work: 0.2621 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23692 Z= 0.188 Angle : 0.473 9.835 32429 Z= 0.248 Chirality : 0.038 0.173 4014 Planarity : 0.003 0.054 3925 Dihedral : 8.921 113.487 3833 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.46 % Allowed : 21.94 % Favored : 75.59 % 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: 1.77 (0.16), residues: 3050 helix: 2.35 (0.13), residues: 1746 sheet: -0.58 (0.32), residues: 265 loop : -0.36 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 401 TYR 0.012 0.001 TYR A2468 PHE 0.014 0.001 PHE A2633 TRP 0.010 0.001 TRP A2542 HIS 0.004 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (23681) covalent geometry : angle 0.47207 / 0.25 (32421) SS BOND : bond 0.00097 / 0.05 ( 1) SS BOND : angle 0.56950 / 0.30 ( 2) hydrogen bonds : bond 0.03652 / 2.61 ( 1428) hydrogen bonds : angle 3.88413 / 2.83 ( 4069) metal coordination : bond 0.00790 / 0.53 ( 10) metal coordination : angle 2.27607 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 118 time to evaluate : 0.805 Fit side-chains REVERT: A 455 SER cc_start: 0.8012 (OUTLIER) cc_final: 0.7742 (t) REVERT: A 808 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7487 (tmm) REVERT: A 1382 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8581 (mtp) REVERT: A 1831 MET cc_start: 0.8606 (mmp) cc_final: 0.8311 (mmp) REVERT: A 2951 ILE cc_start: 0.9202 (tp) cc_final: 0.8909 (tp) outliers start: 53 outliers final: 42 residues processed: 163 average time/residue: 0.1133 time to fit residues: 33.0241 Evaluate side-chains 159 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 962 MET Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1382 MET Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 2882 SER Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3138 ILE Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3182 SER Chi-restraints excluded: chain A residue 3193 THR Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3532 VAL Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3887 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 301 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 215 optimal weight: 0.0770 chunk 155 optimal weight: 0.7980 chunk 291 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.055436 restraints weight = 58262.917| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.68 r_work: 0.2641 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23692 Z= 0.128 Angle : 0.442 9.912 32429 Z= 0.233 Chirality : 0.037 0.171 4014 Planarity : 0.003 0.055 3925 Dihedral : 8.919 113.202 3833 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.14 % Allowed : 22.41 % Favored : 75.45 % 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: 1.83 (0.16), residues: 3050 helix: 2.40 (0.13), residues: 1746 sheet: -0.54 (0.32), residues: 265 loop : -0.35 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 401 TYR 0.010 0.001 TYR A 641 PHE 0.015 0.001 PHE A2633 TRP 0.011 0.001 TRP A2542 HIS 0.004 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (23681) covalent geometry : angle 0.44122 / 0.23 (32421) SS BOND : bond 0.00042 / 0.02 ( 1) SS BOND : angle 0.49687 / 0.26 ( 2) hydrogen bonds : bond 0.03436 / 2.46 ( 1428) hydrogen bonds : angle 3.81596 / 2.78 ( 4069) metal coordination : bond 0.00545 / 0.36 ( 10) metal coordination : angle 1.95358 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 118 time to evaluate : 0.951 Fit side-chains REVERT: A 455 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7724 (t) REVERT: A 808 MET cc_start: 0.8470 (tmm) cc_final: 0.7488 (tmm) REVERT: A 1831 MET cc_start: 0.8612 (mmp) cc_final: 0.8333 (mmp) REVERT: A 2951 ILE cc_start: 0.9186 (tp) cc_final: 0.8886 (tp) REVERT: A 3343 LYS cc_start: 0.8980 (ttmm) cc_final: 0.8710 (tttt) outliers start: 46 outliers final: 41 residues processed: 156 average time/residue: 0.1203 time to fit residues: 33.5574 Evaluate side-chains 157 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 115 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 962 MET Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2830 ILE Chi-restraints excluded: chain A residue 2882 SER Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3138 ILE Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3182 SER Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3532 VAL Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3887 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 147 optimal weight: 30.0000 chunk 89 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.070997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.053558 restraints weight = 58569.342| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.67 r_work: 0.2593 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 23692 Z= 0.245 Angle : 0.515 10.913 32429 Z= 0.268 Chirality : 0.040 0.172 4014 Planarity : 0.003 0.057 3925 Dihedral : 8.973 113.777 3833 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.56 % Allowed : 22.04 % Favored : 75.41 % 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: 1.71 (0.16), residues: 3050 helix: 2.30 (0.13), residues: 1750 sheet: -0.65 (0.31), residues: 267 loop : -0.40 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 401 TYR 0.014 0.001 TYR A2468 PHE 0.014 0.001 PHE A1781 TRP 0.011 0.001 TRP A2362 HIS 0.006 0.001 HIS A3551 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 (23681) covalent geometry : angle 0.51429 / 0.27 (32421) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.58483 / 0.31 ( 2) hydrogen bonds : bond 0.03912 / 2.80 ( 1428) hydrogen bonds : angle 3.96203 / 2.89 ( 4069) metal coordination : bond 0.01035 / 0.71 ( 10) metal coordination : angle 2.30428 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 111 time to evaluate : 0.888 Fit side-chains REVERT: A 455 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7716 (t) REVERT: A 808 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7539 (tmm) REVERT: A 1831 MET cc_start: 0.8642 (mmp) cc_final: 0.8345 (mmp) REVERT: A 2951 ILE cc_start: 0.9182 (tp) cc_final: 0.8893 (tp) REVERT: A 3343 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8706 (tttt) outliers start: 55 outliers final: 45 residues processed: 158 average time/residue: 0.1184 time to fit residues: 33.8139 Evaluate side-chains 158 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 962 MET Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1262 LEU Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1635 THR Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2679 VAL Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2818 LEU Chi-restraints excluded: chain A residue 2882 SER Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 2995 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3138 ILE Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3182 SER Chi-restraints excluded: chain A residue 3193 THR Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3532 VAL Chi-restraints excluded: chain A residue 3581 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3714 VAL Chi-restraints excluded: chain A residue 3887 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 141 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 279 optimal weight: 0.7980 chunk 238 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 249 optimal weight: 0.0020 chunk 138 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.073010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.055716 restraints weight = 57927.845| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.67 r_work: 0.2647 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23692 Z= 0.104 Angle : 0.442 11.542 32429 Z= 0.232 Chirality : 0.036 0.171 4014 Planarity : 0.003 0.055 3925 Dihedral : 8.950 113.353 3833 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.86 % Allowed : 22.59 % Favored : 75.55 % 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: 1.87 (0.16), residues: 3050 helix: 2.42 (0.13), residues: 1746 sheet: -0.54 (0.32), residues: 264 loop : -0.32 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 401 TYR 0.010 0.001 TYR A3239 PHE 0.014 0.001 PHE A2633 TRP 0.013 0.001 TRP A2542 HIS 0.004 0.001 HIS A2366 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (23681) covalent geometry : angle 0.44190 / 0.23 (32421) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.39651 / 0.21 ( 2) hydrogen bonds : bond 0.03351 / 2.40 ( 1428) hydrogen bonds : angle 3.78135 / 2.76 ( 4069) metal coordination : bond 0.00397 / 0.26 ( 10) metal coordination : angle 1.75463 / 0.94 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6100 Ramachandran restraints generated. 3050 Oldfield, 0 Emsley, 3050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.807 Fit side-chains REVERT: A 455 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7666 (t) REVERT: A 808 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7511 (tmm) REVERT: A 1831 MET cc_start: 0.8641 (mmp) cc_final: 0.8366 (mmp) REVERT: A 2951 ILE cc_start: 0.9172 (tp) cc_final: 0.8861 (tp) REVERT: A 3343 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8691 (tttm) outliers start: 40 outliers final: 36 residues processed: 150 average time/residue: 0.1252 time to fit residues: 33.4290 Evaluate side-chains 150 residues out of total 2838 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 808 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 953 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1876 LEU Chi-restraints excluded: chain A residue 2458 ILE Chi-restraints excluded: chain A residue 2507 THR Chi-restraints excluded: chain A residue 2603 VAL Chi-restraints excluded: chain A residue 2605 SER Chi-restraints excluded: chain A residue 2610 MET Chi-restraints excluded: chain A residue 2661 SER Chi-restraints excluded: chain A residue 2769 THR Chi-restraints excluded: chain A residue 2882 SER Chi-restraints excluded: chain A residue 2914 THR Chi-restraints excluded: chain A residue 2962 VAL Chi-restraints excluded: chain A residue 2995 THR Chi-restraints excluded: chain A residue 3014 VAL Chi-restraints excluded: chain A residue 3027 VAL Chi-restraints excluded: chain A residue 3068 LEU Chi-restraints excluded: chain A residue 3087 ILE Chi-restraints excluded: chain A residue 3126 VAL Chi-restraints excluded: chain A residue 3130 ASN Chi-restraints excluded: chain A residue 3151 MET Chi-restraints excluded: chain A residue 3182 SER Chi-restraints excluded: chain A residue 3359 SER Chi-restraints excluded: chain A residue 3362 SER Chi-restraints excluded: chain A residue 3397 MET Chi-restraints excluded: chain A residue 3499 THR Chi-restraints excluded: chain A residue 3514 SER Chi-restraints excluded: chain A residue 3532 VAL Chi-restraints excluded: chain A residue 3598 VAL Chi-restraints excluded: chain A residue 3887 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 202 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 304 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.054159 restraints weight = 58086.870| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.65 r_work: 0.2609 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 23692 Z= 0.210 Angle : 0.491 10.153 32429 Z= 0.256 Chirality : 0.039 0.170 4014 Planarity : 0.003 0.056 3925 Dihedral : 8.961 112.959 3833 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.19 % Allowed : 22.32 % Favored : 75.50 % 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: 1.78 (0.16), residues: 3050 helix: 2.36 (0.13), residues: 1752 sheet: -0.61 (0.32), residues: 266 loop : -0.37 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 401 TYR 0.012 0.001 TYR A2468 PHE 0.013 0.001 PHE A1781 TRP 0.010 0.001 TRP A2362 HIS 0.005 0.001 HIS A3551 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (23681) covalent geometry : angle 0.49058 / 0.26 (32421) SS BOND : bond 0.00114 / 0.06 ( 1) SS BOND : angle 0.56584 / 0.30 ( 2) hydrogen bonds : bond 0.03719 / 2.66 ( 1428) hydrogen bonds : angle 3.88459 / 2.83 ( 4069) metal coordination : bond 0.00889 / 0.61 ( 10) metal coordination : angle 2.12788 / 1.15 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4612.04 seconds wall clock time: 80 minutes 11.49 seconds (4811.49 seconds total)