Starting phenix.real_space_refine on Thu Feb 5 04:27:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kz7_62653/02_2026/9kz7_62653.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kz7_62653/02_2026/9kz7_62653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kz7_62653/02_2026/9kz7_62653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kz7_62653/02_2026/9kz7_62653.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kz7_62653/02_2026/9kz7_62653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kz7_62653/02_2026/9kz7_62653.map" } resolution = 2.77 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= 0.004 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 9354 2.51 5 N 2395 2.21 5 O 2852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14659 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 14221 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1771, 14204 Classifications: {'peptide': 1771} Link IDs: {'CIS': 3, 'PCIS': 7, 'PTRANS': 101, 'TRANS': 1659} Conformer: "B" Number of residues, atoms: 1771, 14204 Classifications: {'peptide': 1771} Link IDs: {'CIS': 3, 'PCIS': 7, 'PTRANS': 101, 'TRANS': 1659} bond proxies already assigned to first conformer: 14607 Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'AC1': 1, 'BGC': 1, 'GLC': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'AC1': 1, 'BGC': 1, 'GLC': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALYS A1427 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A1427 " occ=0.50 residue: pdb=" N AMET A1701 " occ=0.52 ... (14 atoms not shown) pdb=" CE BMET A1701 " occ=0.48 Time building chain proxies: 5.50, per 1000 atoms: 0.38 Number of scatterers: 14659 At special positions: 0 Unit cell: (140.27, 117.86, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 2852 8.00 N 2395 7.00 C 9354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 84 " distance=2.04 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 97 " distance=2.04 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A 637 " distance=2.07 Simple disulfide: pdb=" SG CYS A 933 " - pdb=" SG CYS A 950 " distance=2.00 Simple disulfide: pdb=" SG CYS A 945 " - pdb=" SG CYS A 963 " distance=2.60 Simple disulfide: pdb=" SG CYS A1524 " - pdb=" SG CYS A1535 " distance=2.42 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 Links applied ?1-4 " GLC B 3 " - " AC1 B 4 " " GLC C 3 " - " AC1 C 4 " ALPHA1-4 " BGC B 1 " - " GLC B 2 " " GLC B 2 " - " GLC B 3 " " BGC C 1 " - " GLC C 2 " " GLC C 2 " - " GLC C 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " BETA1-6 " NAG G 1 " - " FUC G 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 3 " NAG-ASN " NAG A1901 " - " ASN A1331 " " NAG A1902 " - " ASN A1570 " " NAG D 1 " - " ASN A 424 " " NAG E 1 " - " ASN A 674 " " NAG F 1 " - " ASN A 916 " " NAG G 1 " - " ASN A1222 " " NAG H 1 " - " ASN A1290 " " NAG I 1 " - " ASN A1355 " " NAG J 1 " - " ASN A1565 " " NAG K 1 " - " ASN A1639 " " NAG L 1 " - " ASN A1737 " " NAG M 1 " - " ASN A1804 " Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3304 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 22 sheets defined 25.3% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 75 through 82 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 356 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.733A pdb=" N THR A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.564A pdb=" N LYS A 587 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 616 removed outlier: 4.341A pdb=" N ILE A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Proline residue: A 608 - end of helix Processing helix chain 'A' and resid 633 through 645 Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 670 through 686 Processing helix chain 'A' and resid 686 through 701 Processing helix chain 'A' and resid 707 through 711 Processing helix chain 'A' and resid 796 through 801 Processing helix chain 'A' and resid 926 through 930 Processing helix chain 'A' and resid 941 through 948 Processing helix chain 'A' and resid 990 through 995 Processing helix chain 'A' and resid 1188 through 1201 Processing helix chain 'A' and resid 1207 through 1212 Processing helix chain 'A' and resid 1222 through 1236 removed outlier: 3.835A pdb=" N ILE A1226 " --> pdb=" O ASN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 removed outlier: 3.705A pdb=" N GLN A1253 " --> pdb=" O MET A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1263 Processing helix chain 'A' and resid 1264 through 1275 Processing helix chain 'A' and resid 1295 through 1305 removed outlier: 3.540A pdb=" N THR A1299 " --> pdb=" O TYR A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1343 Processing helix chain 'A' and resid 1354 through 1370 Processing helix chain 'A' and resid 1405 through 1410 Processing helix chain 'A' and resid 1419 through 1423 removed outlier: 3.572A pdb=" N GLY A1423 " --> pdb=" O ARG A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1449 Processing helix chain 'A' and resid 1451 through 1469 removed outlier: 4.056A pdb=" N ARG A1458 " --> pdb=" O TRP A1454 " (cutoff:3.500A) Proline residue: A1459 - end of helix Processing helix chain 'A' and resid 1482 through 1486 Processing helix chain 'A' and resid 1499 through 1514 removed outlier: 3.531A pdb=" N ILE A1505 " --> pdb=" O LEU A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1543 Processing helix chain 'A' and resid 1560 through 1564 removed outlier: 3.998A pdb=" N TRP A1564 " --> pdb=" O PRO A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1597 Proline residue: A1584 - end of helix Processing helix chain 'A' and resid 1603 through 1607 Processing helix chain 'A' and resid 1611 through 1617 removed outlier: 3.541A pdb=" N ASP A1616 " --> pdb=" O VAL A1613 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1617 " --> pdb=" O THR A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1697 Processing helix chain 'A' and resid 1806 through 1809 removed outlier: 3.909A pdb=" N ASN A1809 " --> pdb=" O THR A1806 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1806 through 1809' Processing helix chain 'A' and resid 1811 through 1813 No H-bonds generated for 'chain 'A' and resid 1811 through 1813' Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 113 removed outlier: 4.350A pdb=" N GLN A 121 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 119 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL A 112 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLY A 117 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 288 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR A 271 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N PHE A 272 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 182 through 187 removed outlier: 6.811A pdb=" N ILE A 193 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP A 206 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 195 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 214 Processing sheet with id=AA5, first strand: chain 'A' and resid 621 through 622 removed outlier: 7.116A pdb=" N HIS A 591 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 576 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N TRP A 592 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR A 578 " --> pdb=" O TRP A 592 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE A 493 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 414 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TRP A 494 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 416 " --> pdb=" O TRP A 494 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 349 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N HIS A 348 " --> pdb=" O ASN A 652 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ASN A 654 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER A 350 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A 653 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.676A pdb=" N GLY A 461 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 705 through 706 Processing sheet with id=AA8, first strand: chain 'A' and resid 743 through 748 Processing sheet with id=AA9, first strand: chain 'A' and resid 786 through 791 removed outlier: 6.350A pdb=" N LEU A 805 " --> pdb=" O PHE A 866 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 868 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 786 through 791 removed outlier: 6.350A pdb=" N LEU A 805 " --> pdb=" O PHE A 866 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 868 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 817 through 823 removed outlier: 6.266A pdb=" N LEU A 839 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR A 918 " --> pdb=" O VAL A 882 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 882 " --> pdb=" O THR A 918 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 920 " --> pdb=" O VAL A 880 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL A 880 " --> pdb=" O GLU A 920 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 951 through 952 Processing sheet with id=AB4, first strand: chain 'A' and resid 970 through 978 removed outlier: 4.411A pdb=" N VAL A 975 " --> pdb=" O THR A 983 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR A 983 " --> pdb=" O VAL A 975 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TYR A 977 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY A 981 " --> pdb=" O TYR A 977 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET A1016 " --> pdb=" O HIS A1012 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A1139 " --> pdb=" O GLY A1100 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLY A1100 " --> pdb=" O TYR A1139 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET A1141 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU A1098 " --> pdb=" O MET A1141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1050 through 1055 removed outlier: 6.546A pdb=" N ARG A1065 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL A1071 " --> pdb=" O ARG A1065 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 3.553A pdb=" N PHE A1086 " --> pdb=" O ASN A1083 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1519 through 1520 removed outlier: 6.914A pdb=" N HIS A1489 " --> pdb=" O GLY A1520 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE A1474 " --> pdb=" O GLY A1488 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N TRP A1490 " --> pdb=" O ILE A1474 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N SER A1476 " --> pdb=" O TRP A1490 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A1383 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1281 " --> pdb=" O GLY A1383 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A1282 " --> pdb=" O SER A1245 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN A1214 " --> pdb=" O ASN A1550 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1287 through 1288 Processing sheet with id=AB9, first strand: chain 'A' and resid 1434 through 1436 Processing sheet with id=AC1, first strand: chain 'A' and resid 1601 through 1602 removed outlier: 4.124A pdb=" N ASN A1675 " --> pdb=" O SER A1630 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP A1649 " --> pdb=" O ILE A1658 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1639 through 1644 Processing sheet with id=AC3, first strand: chain 'A' and resid 1682 through 1687 removed outlier: 5.856A pdb=" N AMET A1701 " --> pdb=" O LEU A1763 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR A1765 " --> pdb=" O AMET A1701 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1713 through 1719 removed outlier: 6.662A pdb=" N LEU A1735 " --> pdb=" O ILE A1750 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER A1816 " --> pdb=" O SER A1747 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A1778 " --> pdb=" O THR A1821 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.64 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2890 1.33 - 1.45: 4074 1.45 - 1.57: 8026 1.57 - 1.69: 0 1.69 - 1.82: 95 Bond restraints: 15085 Sorted by residual: bond pdb=" C ALYS A1427 " pdb=" N THR A1428 " ideal model delta sigma weight residual 1.328 1.273 0.056 1.23e-02 6.61e+03 2.04e+01 bond pdb=" CA GLY A1433 " pdb=" C GLY A1433 " ideal model delta sigma weight residual 1.514 1.461 0.053 1.41e-02 5.03e+03 1.43e+01 bond pdb=" N VAL A1040 " pdb=" CA VAL A1040 " ideal model delta sigma weight residual 1.457 1.490 -0.033 9.00e-03 1.23e+04 1.31e+01 bond pdb=" N ILE A1238 " pdb=" CA ILE A1238 " ideal model delta sigma weight residual 1.460 1.487 -0.027 7.60e-03 1.73e+04 1.26e+01 bond pdb=" N VAL A 704 " pdb=" CA VAL A 704 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.21e+01 ... (remaining 15080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 18513 2.43 - 4.85: 1874 4.85 - 7.28: 177 7.28 - 9.70: 20 9.70 - 12.13: 4 Bond angle restraints: 20588 Sorted by residual: angle pdb=" CA PRO A 523 " pdb=" C PRO A 523 " pdb=" O PRO A 523 " ideal model delta sigma weight residual 121.38 114.02 7.36 7.70e-01 1.69e+00 9.14e+01 angle pdb=" CA ASN A 424 " pdb=" CB ASN A 424 " pdb=" CG ASN A 424 " ideal model delta sigma weight residual 112.60 119.90 -7.30 1.00e+00 1.00e+00 5.33e+01 angle pdb=" C TYR A1134 " pdb=" N GLY A1135 " pdb=" CA GLY A1135 " ideal model delta sigma weight residual 122.17 116.02 6.15 8.90e-01 1.26e+00 4.78e+01 angle pdb=" CA TYR A1240 " pdb=" CB TYR A1240 " pdb=" CG TYR A1240 " ideal model delta sigma weight residual 113.90 126.03 -12.13 1.80e+00 3.09e-01 4.54e+01 angle pdb=" CA PRO A 523 " pdb=" C PRO A 523 " pdb=" N ARG A 524 " ideal model delta sigma weight residual 116.45 121.97 -5.52 8.50e-01 1.38e+00 4.22e+01 ... (remaining 20583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 8757 25.88 - 51.76: 415 51.76 - 77.64: 102 77.64 - 103.52: 9 103.52 - 129.40: 1 Dihedral angle restraints: 9284 sinusoidal: 4110 harmonic: 5174 Sorted by residual: dihedral pdb=" CA SER A1400 " pdb=" C SER A1400 " pdb=" N PRO A1401 " pdb=" CA PRO A1401 " ideal model delta harmonic sigma weight residual 180.00 50.60 129.40 0 5.00e+00 4.00e-02 6.70e+02 dihedral pdb=" CD ARG A 388 " pdb=" NE ARG A 388 " pdb=" CZ ARG A 388 " pdb=" NH1 ARG A 388 " ideal model delta sinusoidal sigma weight residual 0.00 77.50 -77.50 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CD ARG A 524 " pdb=" NE ARG A 524 " pdb=" CZ ARG A 524 " pdb=" NH1 ARG A 524 " ideal model delta sinusoidal sigma weight residual 0.00 -72.26 72.26 1 1.00e+01 1.00e-02 6.67e+01 ... (remaining 9281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1421 0.075 - 0.150: 679 0.150 - 0.225: 162 0.225 - 0.300: 17 0.300 - 0.375: 5 Chirality restraints: 2284 Sorted by residual: chirality pdb=" C1 GLC C 2 " pdb=" O4 BGC C 1 " pdb=" C2 GLC C 2 " pdb=" O5 GLC C 2 " both_signs ideal model delta sigma weight residual False 2.40 2.04 0.36 2.00e-02 2.50e+03 3.31e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-02 2.50e+03 2.12e+02 chirality pdb=" C1 GLC B 3 " pdb=" O4 GLC B 2 " pdb=" C2 GLC B 3 " pdb=" O5 GLC B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.65e+02 ... (remaining 2281 not shown) Planarity restraints: 2643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.281 2.00e-02 2.50e+03 2.37e-01 7.03e+02 pdb=" C7 NAG L 1 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.406 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.228 2.00e-02 2.50e+03 1.95e-01 4.75e+02 pdb=" C7 NAG I 1 " 0.049 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.027 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.324 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1901 " -0.159 2.00e-02 2.50e+03 1.34e-01 2.26e+02 pdb=" C7 NAG A1901 " 0.035 2.00e-02 2.50e+03 pdb=" C8 NAG A1901 " 0.035 2.00e-02 2.50e+03 pdb=" N2 NAG A1901 " 0.216 2.00e-02 2.50e+03 pdb=" O7 NAG A1901 " -0.127 2.00e-02 2.50e+03 ... (remaining 2640 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1275 2.74 - 3.28: 13696 3.28 - 3.82: 25002 3.82 - 4.36: 33800 4.36 - 4.90: 54064 Nonbonded interactions: 127837 Sorted by model distance: nonbonded pdb=" OD1 ASP A 380 " pdb=" O6B AC1 B 4 " model vdw 2.205 3.040 nonbonded pdb=" OD2 ASP A 715 " pdb=" OH TYR A 747 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP A 662 " pdb=" OG SER A 665 " model vdw 2.268 3.040 nonbonded pdb=" O5 BGC B 1 " pdb=" O6 BGC B 1 " model vdw 2.292 2.432 nonbonded pdb=" O ASP A 425 " pdb=" OD1 ASP A 425 " model vdw 2.308 3.040 ... (remaining 127832 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'G' selection = chain 'K' } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.540 Find NCS groups from input model: 0.110 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:5.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.012 0.572 15121 Z= 0.781 Angle : 1.568 16.296 20690 Z= 1.027 Chirality : 0.086 0.375 2284 Planarity : 0.025 0.478 2631 Dihedral : 15.395 129.399 5962 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.24 % Favored : 95.36 % Rotamer: Outliers : 5.93 % Allowed : 7.61 % Favored : 86.46 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % 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: -1.06 (0.18), residues: 1775 helix: -0.45 (0.25), residues: 370 sheet: 0.54 (0.25), residues: 430 loop : -1.41 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG A1048 TYR 0.073 0.006 TYR A1682 PHE 0.061 0.007 PHE A1544 TRP 0.035 0.005 TRP A1209 HIS 0.022 0.003 HIS A 542 Details of bonding type rmsd covalent geometry : bond 0.01066 (15085) covalent geometry : angle 1.51718 (20588) SS BOND : bond 0.28309 ( 6) SS BOND : angle 6.54577 ( 12) hydrogen bonds : bond 0.20301 ( 546) hydrogen bonds : angle 7.81867 ( 1447) glycosidic custom : bond 0.04875 ( 2) glycosidic custom : angle 6.94304 ( 6) link_ALPHA1-4 : bond 0.04891 ( 4) link_ALPHA1-4 : angle 6.37859 ( 12) link_BETA1-4 : bond 0.04486 ( 10) link_BETA1-4 : angle 7.46054 ( 30) link_BETA1-6 : bond 0.03485 ( 2) link_BETA1-6 : angle 4.10390 ( 6) link_NAG-ASN : bond 0.00627 ( 12) link_NAG-ASN : angle 3.30473 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 174 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6699 (mt-10) cc_final: 0.6073 (mp0) REVERT: A 115 ASN cc_start: 0.5762 (p0) cc_final: 0.5491 (p0) REVERT: A 159 GLN cc_start: 0.6958 (mt0) cc_final: 0.6663 (mt0) REVERT: A 185 MET cc_start: 0.7001 (ttt) cc_final: 0.6791 (ttp) REVERT: A 189 GLN cc_start: 0.6838 (tt0) cc_final: 0.6487 (tt0) REVERT: A 194 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6750 (ttmt) REVERT: A 334 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7403 (tp) REVERT: A 384 MET cc_start: 0.7891 (mtt) cc_final: 0.7546 (mtt) REVERT: A 405 GLN cc_start: 0.5495 (mm-40) cc_final: 0.5002 (mm-40) REVERT: A 449 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.6021 (p0) REVERT: A 472 LYS cc_start: 0.6703 (mtmm) cc_final: 0.6347 (mtmm) REVERT: A 525 ILE cc_start: 0.6834 (OUTLIER) cc_final: 0.6411 (pp) REVERT: A 571 ASN cc_start: 0.6545 (m-40) cc_final: 0.6340 (m110) REVERT: A 659 LYS cc_start: 0.6922 (ttpp) cc_final: 0.6602 (tttp) REVERT: A 771 MET cc_start: 0.7882 (ttm) cc_final: 0.7427 (ttm) REVERT: A 825 ASP cc_start: 0.6868 (t0) cc_final: 0.6584 (t0) REVERT: A 850 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: A 868 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7056 (pt0) REVERT: A 881 ILE cc_start: 0.7419 (mt) cc_final: 0.7200 (mp) REVERT: A 886 ASP cc_start: 0.7620 (t0) cc_final: 0.6940 (m-30) REVERT: A 918 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7974 (t) REVERT: A 958 PRO cc_start: 0.7017 (Cg_exo) cc_final: 0.6806 (Cg_endo) REVERT: A 991 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.7043 (m) REVERT: A 1014 GLU cc_start: 0.7197 (pm20) cc_final: 0.6523 (pm20) REVERT: A 1036 ASN cc_start: 0.7362 (t0) cc_final: 0.6946 (t0) REVERT: A 1042 SER cc_start: 0.6402 (OUTLIER) cc_final: 0.6201 (p) REVERT: A 1076 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: A 1131 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7552 (mtt) REVERT: A 1145 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6570 (mm-30) REVERT: A 1223 ASP cc_start: 0.6954 (p0) cc_final: 0.6645 (p0) REVERT: A 1240 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7871 (p90) REVERT: A 1251 GLU cc_start: 0.6887 (tt0) cc_final: 0.6414 (tp30) REVERT: A 1255 ASP cc_start: 0.7544 (m-30) cc_final: 0.7122 (m-30) REVERT: A 1305 ASP cc_start: 0.7603 (t70) cc_final: 0.7349 (t0) REVERT: A 1341 GLU cc_start: 0.7562 (tt0) cc_final: 0.6916 (mp0) REVERT: A 1342 GLN cc_start: 0.8086 (mt0) cc_final: 0.7819 (mt0) REVERT: A 1405 ASP cc_start: 0.7153 (t0) cc_final: 0.6664 (t0) REVERT: A 1406 SER cc_start: 0.6809 (OUTLIER) cc_final: 0.6415 (m) REVERT: A 1407 SER cc_start: 0.7541 (OUTLIER) cc_final: 0.7150 (t) REVERT: A 1421 ASN cc_start: 0.7584 (p0) cc_final: 0.7300 (p0) REVERT: A 1714 GLU cc_start: 0.7177 (mp0) cc_final: 0.6202 (tm-30) REVERT: A 1726 ASP cc_start: 0.7762 (m-30) cc_final: 0.7274 (m-30) REVERT: A 1730 GLN cc_start: 0.7468 (mt0) cc_final: 0.7118 (mt0) REVERT: A 1742 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7657 (mm-40) REVERT: A 1748 HIS cc_start: 0.6937 (m-70) cc_final: 0.6314 (m170) outliers start: 92 outliers final: 17 residues processed: 242 average time/residue: 0.5235 time to fit residues: 139.7073 Evaluate side-chains 168 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 299 GLN Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 850 ASP Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 991 SER Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1042 SER Chi-restraints excluded: chain A residue 1055 LYS Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1240 TYR Chi-restraints excluded: chain A residue 1313 ASP Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1407 SER Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1566 ASP Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1782 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 855 GLN A 890 GLN A1027 ASN A1165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.102784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.080565 restraints weight = 40159.084| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.98 r_work: 0.2470 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15121 Z= 0.129 Angle : 0.666 9.168 20690 Z= 0.342 Chirality : 0.046 0.237 2284 Planarity : 0.005 0.072 2631 Dihedral : 8.109 63.662 2708 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.71 % Favored : 97.17 % Rotamer: Outliers : 1.87 % Allowed : 11.54 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.20), residues: 1775 helix: 0.81 (0.27), residues: 362 sheet: 0.68 (0.25), residues: 453 loop : -0.81 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 926 TYR 0.015 0.002 TYR A1461 PHE 0.020 0.002 PHE A1019 TRP 0.016 0.001 TRP A 727 HIS 0.005 0.001 HIS A 550 Details of bonding type rmsd covalent geometry : bond 0.00276 (15085) covalent geometry : angle 0.64404 (20588) SS BOND : bond 0.00328 ( 6) SS BOND : angle 1.50187 ( 12) hydrogen bonds : bond 0.04944 ( 546) hydrogen bonds : angle 5.81851 ( 1447) glycosidic custom : bond 0.00028 ( 2) glycosidic custom : angle 0.85789 ( 6) link_ALPHA1-4 : bond 0.00586 ( 4) link_ALPHA1-4 : angle 1.41769 ( 12) link_BETA1-4 : bond 0.00580 ( 10) link_BETA1-4 : angle 2.52461 ( 30) link_BETA1-6 : bond 0.00461 ( 2) link_BETA1-6 : angle 1.20933 ( 6) link_NAG-ASN : bond 0.00506 ( 12) link_NAG-ASN : angle 3.26153 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7318 (mp0) REVERT: A 81 GLN cc_start: 0.7908 (tt0) cc_final: 0.7127 (tp40) REVERT: A 108 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6349 (tp30) REVERT: A 159 GLN cc_start: 0.7641 (mt0) cc_final: 0.7398 (mt0) REVERT: A 185 MET cc_start: 0.8082 (ttt) cc_final: 0.7867 (ttp) REVERT: A 202 ARG cc_start: 0.7662 (tpp-160) cc_final: 0.7414 (tpp-160) REVERT: A 384 MET cc_start: 0.9031 (mtt) cc_final: 0.8778 (mtt) REVERT: A 405 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6845 (mm-40) REVERT: A 406 ASP cc_start: 0.7998 (t70) cc_final: 0.7623 (t0) REVERT: A 571 ASN cc_start: 0.7001 (m-40) cc_final: 0.6777 (m110) REVERT: A 659 LYS cc_start: 0.7624 (ttpp) cc_final: 0.7397 (tttp) REVERT: A 771 MET cc_start: 0.8609 (ttm) cc_final: 0.8297 (ttm) REVERT: A 831 THR cc_start: 0.7963 (p) cc_final: 0.7675 (p) REVERT: A 868 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8029 (pt0) REVERT: A 886 ASP cc_start: 0.8056 (t0) cc_final: 0.7549 (m-30) REVERT: A 1014 GLU cc_start: 0.8052 (pm20) cc_final: 0.7696 (pm20) REVERT: A 1036 ASN cc_start: 0.8698 (t0) cc_final: 0.8436 (t0) REVERT: A 1076 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8908 (tt0) REVERT: A 1089 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8448 (tp) REVERT: A 1341 GLU cc_start: 0.8116 (tt0) cc_final: 0.7617 (mp0) REVERT: A 1342 GLN cc_start: 0.8688 (mt0) cc_final: 0.8470 (mt0) REVERT: A 1406 SER cc_start: 0.8288 (p) cc_final: 0.7995 (m) REVERT: A 1421 ASN cc_start: 0.8440 (p0) cc_final: 0.8190 (p0) REVERT: A 1674 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8385 (tp) REVERT: A 1714 GLU cc_start: 0.8179 (mp0) cc_final: 0.7830 (mm-30) REVERT: A 1742 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8099 (mm-40) outliers start: 29 outliers final: 7 residues processed: 172 average time/residue: 0.5710 time to fit residues: 107.8565 Evaluate side-chains 131 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1313 ASP Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1782 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 104 optimal weight: 9.9990 chunk 9 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN A 890 GLN A1027 ASN A1165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.099722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.076136 restraints weight = 25725.615| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 1.94 r_work: 0.2484 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2390 r_free = 0.2390 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2390 r_free = 0.2390 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15121 Z= 0.219 Angle : 0.730 10.051 20690 Z= 0.377 Chirality : 0.051 0.281 2284 Planarity : 0.006 0.072 2631 Dihedral : 7.069 61.693 2666 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.55 % Rotamer: Outliers : 1.87 % Allowed : 11.80 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.19), residues: 1775 helix: 0.70 (0.27), residues: 363 sheet: 0.74 (0.25), residues: 455 loop : -0.89 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1217 TYR 0.023 0.002 TYR A 679 PHE 0.025 0.002 PHE A1019 TRP 0.014 0.002 TRP A1322 HIS 0.007 0.002 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00514 (15085) covalent geometry : angle 0.71090 (20588) SS BOND : bond 0.00506 ( 6) SS BOND : angle 2.28591 ( 12) hydrogen bonds : bond 0.05918 ( 546) hydrogen bonds : angle 5.78494 ( 1447) glycosidic custom : bond 0.00193 ( 2) glycosidic custom : angle 1.32623 ( 6) link_ALPHA1-4 : bond 0.00478 ( 4) link_ALPHA1-4 : angle 1.65444 ( 12) link_BETA1-4 : bond 0.00512 ( 10) link_BETA1-4 : angle 2.27663 ( 30) link_BETA1-6 : bond 0.00329 ( 2) link_BETA1-6 : angle 1.47722 ( 6) link_NAG-ASN : bond 0.00766 ( 12) link_NAG-ASN : angle 3.05378 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7316 (mp0) REVERT: A 81 GLN cc_start: 0.7974 (tt0) cc_final: 0.7152 (tp40) REVERT: A 159 GLN cc_start: 0.7735 (mt0) cc_final: 0.7403 (mt0) REVERT: A 185 MET cc_start: 0.8159 (ttt) cc_final: 0.7958 (ttp) REVERT: A 405 GLN cc_start: 0.7381 (mm-40) cc_final: 0.6945 (mm-40) REVERT: A 525 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7703 (pp) REVERT: A 771 MET cc_start: 0.8594 (ttm) cc_final: 0.8392 (ttm) REVERT: A 868 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7882 (pt0) REVERT: A 879 ASN cc_start: 0.8269 (m110) cc_final: 0.8044 (m-40) REVERT: A 886 ASP cc_start: 0.8124 (t0) cc_final: 0.7544 (m-30) REVERT: A 910 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7788 (mm-30) REVERT: A 1014 GLU cc_start: 0.8163 (pm20) cc_final: 0.7900 (pm20) REVERT: A 1036 ASN cc_start: 0.8736 (t0) cc_final: 0.8435 (t0) REVERT: A 1341 GLU cc_start: 0.8204 (tt0) cc_final: 0.7619 (mp0) REVERT: A 1406 SER cc_start: 0.8316 (p) cc_final: 0.8035 (t) REVERT: A 1421 ASN cc_start: 0.8434 (p0) cc_final: 0.8102 (p0) REVERT: A 1674 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8495 (tp) outliers start: 29 outliers final: 12 residues processed: 137 average time/residue: 0.5703 time to fit residues: 86.7632 Evaluate side-chains 121 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1313 ASP Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1744 THR Chi-restraints excluded: chain A residue 1768 ILE Chi-restraints excluded: chain A residue 1782 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 138 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 160 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 571 ASN A 884 GLN A 890 GLN A1027 ASN A1165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.077630 restraints weight = 39484.112| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.92 r_work: 0.2433 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2306 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2319 r_free = 0.2319 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2319 r_free = 0.2319 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15121 Z= 0.151 Angle : 0.641 9.367 20690 Z= 0.331 Chirality : 0.047 0.255 2284 Planarity : 0.005 0.077 2631 Dihedral : 6.687 59.399 2663 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 1.55 % Allowed : 12.06 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1775 helix: 0.93 (0.27), residues: 363 sheet: 0.57 (0.25), residues: 472 loop : -0.83 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 524 TYR 0.018 0.002 TYR A 840 PHE 0.024 0.002 PHE A1019 TRP 0.013 0.001 TRP A1360 HIS 0.005 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00347 (15085) covalent geometry : angle 0.62450 (20588) SS BOND : bond 0.00252 ( 6) SS BOND : angle 1.60881 ( 12) hydrogen bonds : bond 0.04882 ( 546) hydrogen bonds : angle 5.56647 ( 1447) glycosidic custom : bond 0.00132 ( 2) glycosidic custom : angle 0.99318 ( 6) link_ALPHA1-4 : bond 0.00449 ( 4) link_ALPHA1-4 : angle 1.45135 ( 12) link_BETA1-4 : bond 0.00457 ( 10) link_BETA1-4 : angle 1.87444 ( 30) link_BETA1-6 : bond 0.00392 ( 2) link_BETA1-6 : angle 1.27871 ( 6) link_NAG-ASN : bond 0.00568 ( 12) link_NAG-ASN : angle 2.83897 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7391 (mp0) REVERT: A 81 GLN cc_start: 0.8003 (tt0) cc_final: 0.7183 (tp40) REVERT: A 159 GLN cc_start: 0.7760 (mt0) cc_final: 0.7379 (mt0) REVERT: A 299 GLN cc_start: 0.8328 (pt0) cc_final: 0.8107 (pt0) REVERT: A 359 ASN cc_start: 0.7912 (m110) cc_final: 0.7622 (m110) REVERT: A 405 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6921 (mm-40) REVERT: A 406 ASP cc_start: 0.8375 (t0) cc_final: 0.8147 (t0) REVERT: A 525 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7660 (pp) REVERT: A 868 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7958 (pt0) REVERT: A 879 ASN cc_start: 0.8293 (m110) cc_final: 0.8078 (m-40) REVERT: A 886 ASP cc_start: 0.8192 (t0) cc_final: 0.7617 (m-30) REVERT: A 910 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: A 1014 GLU cc_start: 0.8287 (pm20) cc_final: 0.8049 (pm20) REVERT: A 1036 ASN cc_start: 0.8840 (t0) cc_final: 0.8553 (t0) REVERT: A 1341 GLU cc_start: 0.8286 (tt0) cc_final: 0.7667 (mp0) REVERT: A 1406 SER cc_start: 0.8201 (p) cc_final: 0.7979 (t) REVERT: A 1674 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8435 (tp) REVERT: A 1786 GLU cc_start: 0.5908 (mt-10) cc_final: 0.5644 (mp0) outliers start: 24 outliers final: 13 residues processed: 140 average time/residue: 0.5051 time to fit residues: 78.9845 Evaluate side-chains 125 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 884 GLN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1313 ASP Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1744 THR Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1817 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 123 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 571 ASN A 890 GLN A1165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.099583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.076423 restraints weight = 36037.537| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.61 r_work: 0.2447 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2320 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2313 r_free = 0.2313 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2313 r_free = 0.2313 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15121 Z= 0.201 Angle : 0.684 9.579 20690 Z= 0.353 Chirality : 0.049 0.265 2284 Planarity : 0.005 0.077 2631 Dihedral : 6.688 58.297 2663 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 1.74 % Allowed : 11.61 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.20), residues: 1775 helix: 0.84 (0.27), residues: 363 sheet: 0.55 (0.25), residues: 465 loop : -0.89 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 524 TYR 0.021 0.002 TYR A 679 PHE 0.025 0.002 PHE A1019 TRP 0.012 0.001 TRP A1360 HIS 0.006 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00476 (15085) covalent geometry : angle 0.66769 (20588) SS BOND : bond 0.00263 ( 6) SS BOND : angle 1.71633 ( 12) hydrogen bonds : bond 0.05430 ( 546) hydrogen bonds : angle 5.65826 ( 1447) glycosidic custom : bond 0.00173 ( 2) glycosidic custom : angle 1.24453 ( 6) link_ALPHA1-4 : bond 0.00435 ( 4) link_ALPHA1-4 : angle 1.54882 ( 12) link_BETA1-4 : bond 0.00484 ( 10) link_BETA1-4 : angle 1.92950 ( 30) link_BETA1-6 : bond 0.00377 ( 2) link_BETA1-6 : angle 1.39142 ( 6) link_NAG-ASN : bond 0.00681 ( 12) link_NAG-ASN : angle 2.93062 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7391 (mp0) REVERT: A 81 GLN cc_start: 0.7968 (tt0) cc_final: 0.7721 (tt0) REVERT: A 159 GLN cc_start: 0.7765 (mt0) cc_final: 0.7390 (mt0) REVERT: A 405 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7058 (mm-40) REVERT: A 437 ARG cc_start: 0.8432 (mtm-85) cc_final: 0.8218 (mtm-85) REVERT: A 525 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7676 (pp) REVERT: A 868 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7958 (pt0) REVERT: A 886 ASP cc_start: 0.8145 (t0) cc_final: 0.7541 (m-30) REVERT: A 910 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: A 1014 GLU cc_start: 0.8256 (pm20) cc_final: 0.8047 (pm20) REVERT: A 1036 ASN cc_start: 0.8834 (t0) cc_final: 0.8550 (t0) REVERT: A 1341 GLU cc_start: 0.8269 (tt0) cc_final: 0.7662 (mp0) REVERT: A 1406 SER cc_start: 0.8194 (p) cc_final: 0.7992 (t) REVERT: A 1674 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 1786 GLU cc_start: 0.6036 (mt-10) cc_final: 0.5777 (mp0) outliers start: 27 outliers final: 16 residues processed: 132 average time/residue: 0.5167 time to fit residues: 75.7454 Evaluate side-chains 129 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1313 ASP Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1744 THR Chi-restraints excluded: chain A residue 1781 ILE Chi-restraints excluded: chain A residue 1782 SER Chi-restraints excluded: chain A residue 1817 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 25 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 299 GLN A 571 ASN A 890 GLN A1165 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.077516 restraints weight = 38929.817| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.87 r_work: 0.2441 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2312 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2315 r_free = 0.2315 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2315 r_free = 0.2315 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15121 Z= 0.152 Angle : 0.631 9.348 20690 Z= 0.325 Chirality : 0.047 0.254 2284 Planarity : 0.005 0.076 2631 Dihedral : 6.446 59.230 2663 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.95 % Rotamer: Outliers : 1.48 % Allowed : 11.80 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1775 helix: 1.02 (0.27), residues: 363 sheet: 0.57 (0.25), residues: 465 loop : -0.84 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 524 TYR 0.019 0.002 TYR A 840 PHE 0.024 0.002 PHE A1019 TRP 0.013 0.001 TRP A1360 HIS 0.004 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00351 (15085) covalent geometry : angle 0.61548 (20588) SS BOND : bond 0.00207 ( 6) SS BOND : angle 1.38527 ( 12) hydrogen bonds : bond 0.04790 ( 546) hydrogen bonds : angle 5.51642 ( 1447) glycosidic custom : bond 0.00158 ( 2) glycosidic custom : angle 0.99923 ( 6) link_ALPHA1-4 : bond 0.00455 ( 4) link_ALPHA1-4 : angle 1.41833 ( 12) link_BETA1-4 : bond 0.00452 ( 10) link_BETA1-4 : angle 1.75027 ( 30) link_BETA1-6 : bond 0.00405 ( 2) link_BETA1-6 : angle 1.29503 ( 6) link_NAG-ASN : bond 0.00563 ( 12) link_NAG-ASN : angle 2.82123 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7339 (mp0) REVERT: A 81 GLN cc_start: 0.7961 (tt0) cc_final: 0.7743 (tt0) REVERT: A 159 GLN cc_start: 0.7732 (mt0) cc_final: 0.7372 (mt0) REVERT: A 299 GLN cc_start: 0.8326 (pt0) cc_final: 0.8126 (pt0) REVERT: A 334 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8769 (tp) REVERT: A 405 GLN cc_start: 0.7411 (mm-40) cc_final: 0.7028 (mm-40) REVERT: A 437 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8180 (mtm-85) REVERT: A 525 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7648 (pp) REVERT: A 571 ASN cc_start: 0.7301 (m-40) cc_final: 0.6127 (t0) REVERT: A 868 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7926 (pt0) REVERT: A 886 ASP cc_start: 0.8168 (t0) cc_final: 0.7563 (m-30) REVERT: A 910 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: A 1014 GLU cc_start: 0.8260 (pm20) cc_final: 0.8060 (pm20) REVERT: A 1036 ASN cc_start: 0.8844 (t0) cc_final: 0.8564 (t0) REVERT: A 1341 GLU cc_start: 0.8248 (tt0) cc_final: 0.7600 (mp0) REVERT: A 1406 SER cc_start: 0.8197 (p) cc_final: 0.7990 (t) REVERT: A 1674 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8442 (tp) REVERT: A 1786 GLU cc_start: 0.6020 (mt-10) cc_final: 0.5701 (mp0) outliers start: 23 outliers final: 13 residues processed: 131 average time/residue: 0.5652 time to fit residues: 82.0694 Evaluate side-chains 128 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1744 THR Chi-restraints excluded: chain A residue 1781 ILE Chi-restraints excluded: chain A residue 1817 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 408 HIS A 890 GLN A1165 GLN A1807 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.077392 restraints weight = 36721.464| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.69 r_work: 0.2461 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2332 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2332 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2332 r_free = 0.2332 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2332 r_free = 0.2332 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15121 Z= 0.152 Angle : 0.631 9.412 20690 Z= 0.325 Chirality : 0.047 0.257 2284 Planarity : 0.005 0.078 2631 Dihedral : 6.307 59.190 2660 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 1.55 % Allowed : 11.67 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1775 helix: 1.08 (0.27), residues: 363 sheet: 0.57 (0.25), residues: 465 loop : -0.82 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 524 TYR 0.018 0.002 TYR A 679 PHE 0.024 0.002 PHE A1019 TRP 0.013 0.001 TRP A1360 HIS 0.004 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00351 (15085) covalent geometry : angle 0.61534 (20588) SS BOND : bond 0.00211 ( 6) SS BOND : angle 1.36958 ( 12) hydrogen bonds : bond 0.04787 ( 546) hydrogen bonds : angle 5.48776 ( 1447) glycosidic custom : bond 0.00159 ( 2) glycosidic custom : angle 1.04307 ( 6) link_ALPHA1-4 : bond 0.00448 ( 4) link_ALPHA1-4 : angle 1.39090 ( 12) link_BETA1-4 : bond 0.00438 ( 10) link_BETA1-4 : angle 1.71878 ( 30) link_BETA1-6 : bond 0.00371 ( 2) link_BETA1-6 : angle 1.30567 ( 6) link_NAG-ASN : bond 0.00562 ( 12) link_NAG-ASN : angle 2.81643 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7367 (mp0) REVERT: A 81 GLN cc_start: 0.7985 (tt0) cc_final: 0.7734 (tt0) REVERT: A 159 GLN cc_start: 0.7757 (mt0) cc_final: 0.7377 (mt0) REVERT: A 299 GLN cc_start: 0.8305 (pt0) cc_final: 0.8100 (pt0) REVERT: A 334 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8779 (tp) REVERT: A 405 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7000 (mm-40) REVERT: A 437 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8190 (mtm-85) REVERT: A 525 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7656 (pp) REVERT: A 571 ASN cc_start: 0.7243 (m-40) cc_final: 0.6064 (t0) REVERT: A 868 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7900 (pt0) REVERT: A 884 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: A 886 ASP cc_start: 0.8194 (t0) cc_final: 0.7582 (m-30) REVERT: A 910 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7981 (mm-30) REVERT: A 918 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8732 (t) REVERT: A 1014 GLU cc_start: 0.8303 (pm20) cc_final: 0.8086 (pm20) REVERT: A 1036 ASN cc_start: 0.8834 (t0) cc_final: 0.8553 (t0) REVERT: A 1341 GLU cc_start: 0.8240 (tt0) cc_final: 0.7638 (mp0) REVERT: A 1674 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8458 (tp) REVERT: A 1786 GLU cc_start: 0.6006 (mt-10) cc_final: 0.5684 (mp0) outliers start: 23 outliers final: 12 residues processed: 135 average time/residue: 0.5594 time to fit residues: 83.8535 Evaluate side-chains 128 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 884 GLN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1744 THR Chi-restraints excluded: chain A residue 1781 ILE Chi-restraints excluded: chain A residue 1817 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 127 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 393 ASN A 408 HIS A 890 GLN A1165 GLN A1807 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.077556 restraints weight = 35919.321| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.66 r_work: 0.2500 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2341 r_free = 0.2341 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2341 r_free = 0.2341 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15121 Z= 0.160 Angle : 0.637 9.402 20690 Z= 0.328 Chirality : 0.047 0.259 2284 Planarity : 0.005 0.075 2631 Dihedral : 6.309 59.089 2660 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.05 % Favored : 96.83 % Rotamer: Outliers : 1.55 % Allowed : 11.86 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1775 helix: 1.08 (0.27), residues: 363 sheet: 0.55 (0.25), residues: 465 loop : -0.81 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 524 TYR 0.018 0.002 TYR A 679 PHE 0.024 0.002 PHE A1019 TRP 0.013 0.001 TRP A1360 HIS 0.005 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00371 (15085) covalent geometry : angle 0.62123 (20588) SS BOND : bond 0.00215 ( 6) SS BOND : angle 1.39099 ( 12) hydrogen bonds : bond 0.04880 ( 546) hydrogen bonds : angle 5.51047 ( 1447) glycosidic custom : bond 0.00170 ( 2) glycosidic custom : angle 1.07444 ( 6) link_ALPHA1-4 : bond 0.00457 ( 4) link_ALPHA1-4 : angle 1.40484 ( 12) link_BETA1-4 : bond 0.00440 ( 10) link_BETA1-4 : angle 1.69594 ( 30) link_BETA1-6 : bond 0.00400 ( 2) link_BETA1-6 : angle 1.31981 ( 6) link_NAG-ASN : bond 0.00574 ( 12) link_NAG-ASN : angle 2.84975 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7367 (mp0) REVERT: A 81 GLN cc_start: 0.8019 (tt0) cc_final: 0.7743 (tt0) REVERT: A 159 GLN cc_start: 0.7790 (mt0) cc_final: 0.7419 (mt0) REVERT: A 405 GLN cc_start: 0.7427 (mm-40) cc_final: 0.7016 (mm-40) REVERT: A 437 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8195 (mtm-85) REVERT: A 525 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7717 (pp) REVERT: A 571 ASN cc_start: 0.7255 (m-40) cc_final: 0.6087 (t0) REVERT: A 868 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7882 (pt0) REVERT: A 884 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7583 (tt0) REVERT: A 886 ASP cc_start: 0.8156 (t0) cc_final: 0.7559 (m-30) REVERT: A 910 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: A 1014 GLU cc_start: 0.8284 (pm20) cc_final: 0.8069 (pm20) REVERT: A 1036 ASN cc_start: 0.8799 (t0) cc_final: 0.8519 (t0) REVERT: A 1341 GLU cc_start: 0.8215 (tt0) cc_final: 0.7606 (mp0) REVERT: A 1674 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8455 (tp) REVERT: A 1786 GLU cc_start: 0.6008 (mt-10) cc_final: 0.5734 (mp0) outliers start: 23 outliers final: 14 residues processed: 134 average time/residue: 0.5178 time to fit residues: 77.2747 Evaluate side-chains 127 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 884 GLN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1744 THR Chi-restraints excluded: chain A residue 1781 ILE Chi-restraints excluded: chain A residue 1817 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 140 optimal weight: 4.9990 chunk 28 optimal weight: 0.0060 chunk 121 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 119 optimal weight: 0.3980 chunk 85 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 overall best weight: 3.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 299 GLN A 408 HIS A 890 GLN A1165 GLN A1807 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.077567 restraints weight = 43328.104| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 3.18 r_work: 0.2406 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2426 r_free = 0.2426 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15121 Z= 0.169 Angle : 0.647 9.387 20690 Z= 0.334 Chirality : 0.047 0.261 2284 Planarity : 0.005 0.072 2631 Dihedral : 6.336 58.831 2659 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 1.68 % Allowed : 11.86 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1775 helix: 1.06 (0.27), residues: 362 sheet: 0.59 (0.25), residues: 453 loop : -0.84 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 524 TYR 0.019 0.002 TYR A 679 PHE 0.024 0.002 PHE A1019 TRP 0.013 0.001 TRP A1360 HIS 0.005 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00394 (15085) covalent geometry : angle 0.63129 (20588) SS BOND : bond 0.00217 ( 6) SS BOND : angle 1.42137 ( 12) hydrogen bonds : bond 0.04981 ( 546) hydrogen bonds : angle 5.53507 ( 1447) glycosidic custom : bond 0.00176 ( 2) glycosidic custom : angle 1.13147 ( 6) link_ALPHA1-4 : bond 0.00456 ( 4) link_ALPHA1-4 : angle 1.42795 ( 12) link_BETA1-4 : bond 0.00442 ( 10) link_BETA1-4 : angle 1.69226 ( 30) link_BETA1-6 : bond 0.00389 ( 2) link_BETA1-6 : angle 1.33193 ( 6) link_NAG-ASN : bond 0.00588 ( 12) link_NAG-ASN : angle 2.90451 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7261 (mp0) REVERT: A 81 GLN cc_start: 0.7978 (tt0) cc_final: 0.7689 (tt0) REVERT: A 159 GLN cc_start: 0.7744 (mt0) cc_final: 0.7384 (mt0) REVERT: A 405 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6931 (mm-40) REVERT: A 437 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.8160 (mtm-85) REVERT: A 525 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7648 (pp) REVERT: A 571 ASN cc_start: 0.7201 (m-40) cc_final: 0.6042 (t0) REVERT: A 720 ASP cc_start: 0.8374 (p0) cc_final: 0.8168 (p0) REVERT: A 868 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7767 (pt0) REVERT: A 884 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: A 886 ASP cc_start: 0.8067 (t0) cc_final: 0.7465 (m-30) REVERT: A 910 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7692 (mm-30) REVERT: A 1014 GLU cc_start: 0.8104 (pm20) cc_final: 0.7890 (pm20) REVERT: A 1036 ASN cc_start: 0.8738 (t0) cc_final: 0.8450 (t0) REVERT: A 1341 GLU cc_start: 0.8047 (tt0) cc_final: 0.7541 (mp0) REVERT: A 1674 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8461 (tp) outliers start: 25 outliers final: 18 residues processed: 136 average time/residue: 0.5245 time to fit residues: 79.6316 Evaluate side-chains 134 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 884 GLN Chi-restraints excluded: chain A residue 910 GLU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1241 ASP Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1483 SER Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1744 THR Chi-restraints excluded: chain A residue 1771 VAL Chi-restraints excluded: chain A residue 1781 ILE Chi-restraints excluded: chain A residue 1817 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 68 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 299 GLN A 408 HIS A 890 GLN A1165 GLN A1807 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.102955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.080028 restraints weight = 40453.101| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.92 r_work: 0.2473 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2346 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2357 r_free = 0.2357 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2357 r_free = 0.2357 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15121 Z= 0.106 Angle : 0.578 9.309 20690 Z= 0.297 Chirality : 0.044 0.246 2284 Planarity : 0.004 0.071 2631 Dihedral : 5.972 58.864 2659 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.29 % Rotamer: Outliers : 1.10 % Allowed : 12.25 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1775 helix: 1.33 (0.28), residues: 362 sheet: 0.54 (0.25), residues: 470 loop : -0.72 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 524 TYR 0.017 0.001 TYR A 840 PHE 0.022 0.001 PHE A1019 TRP 0.015 0.001 TRP A1360 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00230 (15085) covalent geometry : angle 0.56364 (20588) SS BOND : bond 0.00188 ( 6) SS BOND : angle 0.97368 ( 12) hydrogen bonds : bond 0.03948 ( 546) hydrogen bonds : angle 5.28769 ( 1447) glycosidic custom : bond 0.00109 ( 2) glycosidic custom : angle 0.82444 ( 6) link_ALPHA1-4 : bond 0.00402 ( 4) link_ALPHA1-4 : angle 1.23163 ( 12) link_BETA1-4 : bond 0.00421 ( 10) link_BETA1-4 : angle 1.51450 ( 30) link_BETA1-6 : bond 0.00419 ( 2) link_BETA1-6 : angle 1.22222 ( 6) link_NAG-ASN : bond 0.00475 ( 12) link_NAG-ASN : angle 2.66937 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3550 Ramachandran restraints generated. 1775 Oldfield, 0 Emsley, 1775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7324 (mp0) REVERT: A 81 GLN cc_start: 0.8011 (tt0) cc_final: 0.7744 (tt0) REVERT: A 159 GLN cc_start: 0.7780 (mt0) cc_final: 0.7400 (mt0) REVERT: A 299 GLN cc_start: 0.8272 (pt0) cc_final: 0.8018 (pt0) REVERT: A 405 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6993 (mm-40) REVERT: A 437 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8120 (mtm-85) REVERT: A 525 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7640 (pp) REVERT: A 571 ASN cc_start: 0.7338 (m-40) cc_final: 0.6151 (t0) REVERT: A 868 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7877 (pt0) REVERT: A 886 ASP cc_start: 0.8204 (t0) cc_final: 0.7698 (m-30) REVERT: A 1014 GLU cc_start: 0.8330 (pm20) cc_final: 0.8118 (pm20) REVERT: A 1036 ASN cc_start: 0.8846 (t0) cc_final: 0.8584 (t0) REVERT: A 1341 GLU cc_start: 0.8248 (tt0) cc_final: 0.7621 (mp0) outliers start: 16 outliers final: 9 residues processed: 137 average time/residue: 0.5376 time to fit residues: 82.0039 Evaluate side-chains 124 residues out of total 1547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 424 ASN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1406 SER Chi-restraints excluded: chain A residue 1744 THR Chi-restraints excluded: chain A residue 1771 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 59 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 408 HIS A 890 GLN A1165 GLN A1807 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.099822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.076602 restraints weight = 33837.396| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.53 r_work: 0.2463 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2338 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2350 r_free = 0.2350 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2350 r_free = 0.2350 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15121 Z= 0.194 Angle : 0.673 9.513 20690 Z= 0.346 Chirality : 0.049 0.269 2284 Planarity : 0.005 0.072 2631 Dihedral : 6.300 58.548 2657 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 0.97 % Allowed : 12.44 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.48 % Cis-general : 0.18 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.20), residues: 1775 helix: 1.08 (0.27), residues: 362 sheet: 0.58 (0.25), residues: 453 loop : -0.82 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 524 TYR 0.021 0.002 TYR A 679 PHE 0.025 0.002 PHE A1019 TRP 0.012 0.001 TRP A1360 HIS 0.006 0.001 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00461 (15085) covalent geometry : angle 0.65687 (20588) SS BOND : bond 0.00243 ( 6) SS BOND : angle 1.53479 ( 12) hydrogen bonds : bond 0.05226 ( 546) hydrogen bonds : angle 5.56188 ( 1447) glycosidic custom : bond 0.00203 ( 2) glycosidic custom : angle 1.26341 ( 6) link_ALPHA1-4 : bond 0.00468 ( 4) link_ALPHA1-4 : angle 1.46832 ( 12) link_BETA1-4 : bond 0.00455 ( 10) link_BETA1-4 : angle 1.70878 ( 30) link_BETA1-6 : bond 0.00369 ( 2) link_BETA1-6 : angle 1.36494 ( 6) link_NAG-ASN : bond 0.00621 ( 12) link_NAG-ASN : angle 2.95639 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4824.46 seconds wall clock time: 82 minutes 54.78 seconds (4974.78 seconds total)