Starting phenix.real_space_refine on Sat Sep 12 02:49:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6um2_20816/09_2026/6um2_20816.cif Found real_map, /net/cci-nas-00/data/ceres_data/6um2_20816/09_2026/6um2_20816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6um2_20816/09_2026/6um2_20816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6um2_20816/09_2026/6um2_20816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6um2_20816/09_2026/6um2_20816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6um2_20816/09_2026/6um2_20816.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6um2_20816/09_2026/6um2_20816.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6um2_20816/09_2026/6um2_20816.cif" } resolution = 4.32 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= 0.001 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 107 5.16 5 C 8188 2.51 5 N 2216 2.21 5 O 2583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13094 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1638, 12632 Classifications: {'peptide': 1638} Link IDs: {'PTRANS': 88, 'TRANS': 1549} Chain breaks: 2 Chain: "B" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 364 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.61, per 1000 atoms: 0.20 Number of scatterers: 13094 At special positions: 0 Unit cell: (181.46, 126.42, 130.72, 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 107 16.00 O 2583 8.00 N 2216 7.00 C 8188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, symmetry=0 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 547 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 636 " - pdb=" SG CYS A 672 " distance=2.04 Simple disulfide: pdb=" SG CYS A 680 " - pdb=" SG CYS A 687 " distance=2.02 Simple disulfide: pdb=" SG CYS A 739 " - pdb=" SG CYS A 768 " distance=2.03 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 822 " distance=2.01 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 838 " distance=2.02 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS A 918 " distance=2.02 Simple disulfide: pdb=" SG CYS A 901 " - pdb=" SG CYS A 930 " distance=2.02 Simple disulfide: pdb=" SG CYS A 942 " - pdb=" SG CYS A 978 " distance=2.03 Simple disulfide: pdb=" SG CYS A 984 " - pdb=" SG CYS A 995 " distance=2.03 Simple disulfide: pdb=" SG CYS A1051 " - pdb=" SG CYS A1086 " distance=2.02 Simple disulfide: pdb=" SG CYS A1093 " - pdb=" SG CYS A1134 " distance=2.03 Simple disulfide: pdb=" SG CYS A1143 " - pdb=" SG CYS A1151 " distance=2.03 Simple disulfide: pdb=" SG CYS A1186 " - pdb=" SG CYS A1214 " distance=2.05 Simple disulfide: pdb=" SG CYS A1199 " - pdb=" SG CYS A1226 " distance=2.02 Simple disulfide: pdb=" SG CYS A1236 " - pdb=" SG CYS A1271 " distance=2.04 Simple disulfide: pdb=" SG CYS A1279 " - pdb=" SG CYS A1291 " distance=2.03 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1358 " distance=2.03 Simple disulfide: pdb=" SG CYS A1342 " - pdb=" SG CYS A1370 " distance=2.02 Simple disulfide: pdb=" SG CYS A1378 " - pdb=" SG CYS A1417 " distance=2.05 Simple disulfide: pdb=" SG CYS A1429 " - pdb=" SG CYS A1436 " distance=2.02 Simple disulfide: pdb=" SG CYS A1470 " - pdb=" SG CYS A1503 " distance=2.02 Simple disulfide: pdb=" SG CYS A1485 " - pdb=" SG CYS A1515 " distance=2.02 Simple disulfide: pdb=" SG CYS A1525 " - pdb=" SG CYS A1562 " distance=2.06 Simple disulfide: pdb=" SG CYS A1568 " - pdb=" SG CYS A1575 " distance=2.03 Simple disulfide: pdb=" SG CYS A1607 " - pdb=" SG CYS A1643 " distance=2.03 Simple disulfide: pdb=" SG CYS A1623 " - pdb=" SG CYS A1655 " distance=2.02 Simple disulfide: pdb=" SG CYS A1661 " - pdb=" SG CYS A1704 " distance=2.06 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1722 " distance=2.02 Simple disulfide: pdb=" SG CYS A1759 " - pdb=" SG CYS A1792 " distance=2.05 Simple disulfide: pdb=" SG CYS A1775 " - pdb=" SG CYS A1804 " distance=2.03 Simple disulfide: pdb=" SG CYS A1813 " - pdb=" SG CYS A1848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1859 " - pdb=" SG CYS A1865 " distance=2.02 Simple disulfide: pdb=" SG CYS A1902 " - pdb=" SG CYS A1984 " distance=2.04 Simple disulfide: pdb=" SG CYS A1912 " - pdb=" SG CYS A1936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1926 " - pdb=" SG CYS A1951 " distance=2.05 Simple disulfide: pdb=" SG CYS A1966 " - pdb=" SG CYS A1996 " distance=2.02 Simple disulfide: pdb=" SG CYS A2003 " - pdb=" SG CYS A2038 " distance=2.04 Simple disulfide: pdb=" SG CYS A2048 " - pdb=" SG CYS A2055 " distance=2.06 Simple disulfide: pdb=" SG CYS A2091 " - pdb=" SG CYS A2122 " distance=2.02 Simple disulfide: pdb=" SG CYS A2105 " - pdb=" SG CYS A2134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 47 " distance=2.04 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 60 " distance=2.01 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 51 " distance=2.04 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=1, symmetry=0 Links applied NAG-ASN " NAG A2505 " - " ASN A1030 " " NAG A2506 " - " ASN A1665 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 625.1 milliseconds 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 34 sheets defined 3.8% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 649 through 653 removed outlier: 3.705A pdb=" N THR A 653 " --> pdb=" O THR A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 768 removed outlier: 3.562A pdb=" N CYS A 768 " --> pdb=" O SER A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 938 removed outlier: 4.131A pdb=" N ASP A 937 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 959 Processing helix chain 'A' and resid 1223 through 1226 Processing helix chain 'A' and resid 1825 through 1830 removed outlier: 4.296A pdb=" N SER A1828 " --> pdb=" O ASN A1825 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A1830 " --> pdb=" O SER A1827 " (cutoff:3.500A) Processing helix chain 'A' and resid 1877 through 1881 removed outlier: 3.572A pdb=" N MET A1881 " --> pdb=" O LEU A1878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2134 removed outlier: 4.249A pdb=" N CYS A2134 " --> pdb=" O ARG A2131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2131 through 2134' Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.041A pdb=" N THR B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLN B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N CYS B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 25 removed outlier: 3.734A pdb=" N GLY B 25 " --> pdb=" O GLY B 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 22 through 25' Processing helix chain 'B' and resid 42 through 47 removed outlier: 3.790A pdb=" N CYS B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA2, first strand: chain 'A' and resid 548 through 549 Processing sheet with id=AA3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.770A pdb=" N GLU A 617 " --> pdb=" O THR A 607 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A 607 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 619 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 605 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 631 through 632 removed outlier: 3.544A pdb=" N THR A 631 " --> pdb=" O TYR A 708 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 713 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU A 753 " --> pdb=" O THR A 757 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ASN A 759 " --> pdb=" O GLN A 751 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 665 through 669 removed outlier: 3.521A pdb=" N VAL A 689 " --> pdb=" O GLU A 666 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLY A 700 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS A 687 " --> pdb=" O ASN A 698 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN A 698 " --> pdb=" O CYS A 687 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL A 689 " --> pdb=" O SER A 696 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N SER A 696 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 806 removed outlier: 3.618A pdb=" N TRP A 802 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 815 " --> pdb=" O ASP A 806 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 837 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 858 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 856 " --> pdb=" O GLN A 839 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 864 through 865 removed outlier: 4.761A pdb=" N GLY A 864 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU A 876 " --> pdb=" O GLY A 864 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA9, first strand: chain 'A' and resid 898 through 899 removed outlier: 6.462A pdb=" N HIS A 898 " --> pdb=" O TRP A 924 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER A 921 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER A 913 " --> pdb=" O SER A 921 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 943 through 946 removed outlier: 3.820A pdb=" N ILE A 944 " --> pdb=" O PHE A 953 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 953 " --> pdb=" O ILE A 944 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 964 through 965 removed outlier: 3.669A pdb=" N TYR A 964 " --> pdb=" O PHE A 975 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE A 975 " --> pdb=" O TYR A 964 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1019 through 1021 removed outlier: 3.821A pdb=" N GLN A1020 " --> pdb=" O THR A1028 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1115 through 1117 removed outlier: 3.502A pdb=" N TRP A1115 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A1131 " --> pdb=" O TRP A1115 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A1117 " --> pdb=" O PHE A1129 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE A1129 " --> pdb=" O ALA A1117 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A1151 " --> pdb=" O TYR A1130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1177 through 1180 removed outlier: 7.560A pdb=" N ARG A1194 " --> pdb=" O PHE A1218 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N TRP A1220 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASN A1196 " --> pdb=" O TRP A1220 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR A1222 " --> pdb=" O ASN A1196 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU A1198 " --> pdb=" O THR A1222 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A1215 " --> pdb=" O GLN A1211 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN A1211 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL A1217 " --> pdb=" O GLN A1209 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1230 through 1232 removed outlier: 3.601A pdb=" N TYR A1313 " --> pdb=" O ALA A1231 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A1338 " --> pdb=" O MET A1320 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A1361 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG A1365 " --> pdb=" O ALA A1348 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA A1348 " --> pdb=" O ARG A1365 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1257 through 1259 removed outlier: 3.618A pdb=" N TYR A1266 " --> pdb=" O VAL A1259 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR A1265 " --> pdb=" O GLU A1293 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A1267 " --> pdb=" O CYS A1291 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1411 through 1414 removed outlier: 3.681A pdb=" N VAL A1444 " --> pdb=" O LEU A1437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1462 through 1464 removed outlier: 3.848A pdb=" N TYR A1505 " --> pdb=" O SER A1478 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A1508 " --> pdb=" O MET A1495 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1526 through 1528 Processing sheet with id=AC2, first strand: chain 'A' and resid 1548 through 1550 Processing sheet with id=AC3, first strand: chain 'A' and resid 1584 through 1585 removed outlier: 3.809A pdb=" N GLU A1602 " --> pdb=" O LYS A1585 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A1598 " --> pdb=" O THR A1591 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR A1591 " --> pdb=" O GLN A1598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1584 through 1585 removed outlier: 3.809A pdb=" N GLU A1602 " --> pdb=" O LYS A1585 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A1597 " --> pdb=" O PHE A1621 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A1617 " --> pdb=" O TYR A1601 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A1618 " --> pdb=" O LEU A1645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1664 through 1665 Processing sheet with id=AC6, first strand: chain 'A' and resid 1682 through 1684 removed outlier: 6.613A pdb=" N VAL A1721 " --> pdb=" O ILE A1733 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A1723 " --> pdb=" O ILE A1731 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A1731 " --> pdb=" O LYS A1723 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A1754 " --> pdb=" O ARG A1735 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A1794 " --> pdb=" O THR A1768 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N HIS A1774 " --> pdb=" O THR A1800 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1682 through 1684 removed outlier: 6.613A pdb=" N VAL A1721 " --> pdb=" O ILE A1733 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A1723 " --> pdb=" O ILE A1731 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A1731 " --> pdb=" O LYS A1723 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A1754 " --> pdb=" O ARG A1735 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A1794 " --> pdb=" O THR A1768 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP A1793 " --> pdb=" O THR A1789 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR A1789 " --> pdb=" O ASP A1793 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A1795 " --> pdb=" O LEU A1787 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1837 through 1838 removed outlier: 3.861A pdb=" N HIS A1841 " --> pdb=" O ARG A1838 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1844 through 1845 Processing sheet with id=AD1, first strand: chain 'A' and resid 1882 through 1886 removed outlier: 3.825A pdb=" N SER A1960 " --> pdb=" O TYR A1896 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR A1959 " --> pdb=" O VAL A1986 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N PHE A1988 " --> pdb=" O THR A1959 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A1961 " --> pdb=" O PHE A1988 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU A1985 " --> pdb=" O GLU A1980 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU A1980 " --> pdb=" O GLU A1985 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1987 " --> pdb=" O PHE A1978 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1916 through 1918 Processing sheet with id=AD3, first strand: chain 'A' and resid 1935 through 1937 removed outlier: 3.941A pdb=" N CYS A1936 " --> pdb=" O GLY A1949 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A1949 " --> pdb=" O CYS A1936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 2025 through 2028 removed outlier: 4.056A pdb=" N PHE A2026 " --> pdb=" O TYR A2033 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2054 through 2056 removed outlier: 3.567A pdb=" N GLN A2064 " --> pdb=" O LYS A2056 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2074 through 2076 Processing sheet with id=AD7, first strand: chain 'A' and resid 2098 through 2105 removed outlier: 3.656A pdb=" N PHE A2126 " --> pdb=" O VAL A2100 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A2104 " --> pdb=" O TRP A2128 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER A2130 " --> pdb=" O THR A2104 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 456 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: 3.18 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2814 1.33 - 1.45: 3074 1.45 - 1.57: 7390 1.57 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 13397 Sorted by residual: bond pdb=" N ILE A 855 " pdb=" CA ILE A 855 " ideal model delta sigma weight residual 1.458 1.497 -0.039 9.00e-03 1.23e+04 1.86e+01 bond pdb=" N VAL A1724 " pdb=" CA VAL A1724 " ideal model delta sigma weight residual 1.460 1.492 -0.031 7.30e-03 1.88e+04 1.83e+01 bond pdb=" N ILE A 561 " pdb=" CA ILE A 561 " ideal model delta sigma weight residual 1.459 1.495 -0.037 9.10e-03 1.21e+04 1.63e+01 bond pdb=" N CYS A 636 " pdb=" CA CYS A 636 " ideal model delta sigma weight residual 1.458 1.492 -0.034 9.00e-03 1.23e+04 1.43e+01 bond pdb=" N VAL A 677 " pdb=" CA VAL A 677 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.11e-02 8.12e+03 1.37e+01 ... (remaining 13392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 16569 2.87 - 5.74: 1516 5.74 - 8.61: 97 8.61 - 11.49: 16 11.49 - 14.36: 5 Bond angle restraints: 18203 Sorted by residual: angle pdb=" C VAL A1791 " pdb=" CA VAL A1791 " pdb=" CB VAL A1791 " ideal model delta sigma weight residual 112.02 123.50 -11.48 1.31e+00 5.83e-01 7.68e+01 angle pdb=" C ILE A 897 " pdb=" CA ILE A 897 " pdb=" CB ILE A 897 " ideal model delta sigma weight residual 110.41 119.73 -9.32 1.14e+00 7.69e-01 6.69e+01 angle pdb=" N VAL A1791 " pdb=" CA VAL A1791 " pdb=" C VAL A1791 " ideal model delta sigma weight residual 110.53 103.20 7.33 9.40e-01 1.13e+00 6.08e+01 angle pdb=" C ASN A1520 " pdb=" CA ASN A1520 " pdb=" CB ASN A1520 " ideal model delta sigma weight residual 109.72 122.63 -12.91 1.66e+00 3.63e-01 6.05e+01 angle pdb=" N VAL A1977 " pdb=" CA VAL A1977 " pdb=" C VAL A1977 " ideal model delta sigma weight residual 107.37 118.79 -11.42 1.48e+00 4.57e-01 5.95e+01 ... (remaining 18198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 6848 17.18 - 34.35: 976 34.35 - 51.53: 188 51.53 - 68.71: 27 68.71 - 85.88: 13 Dihedral angle restraints: 8052 sinusoidal: 3199 harmonic: 4853 Sorted by residual: dihedral pdb=" CB CYS A2003 " pdb=" SG CYS A2003 " pdb=" SG CYS A2038 " pdb=" CB CYS A2038 " ideal model delta sinusoidal sigma weight residual -86.00 -0.12 -85.88 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CA CYS A1279 " pdb=" C CYS A1279 " pdb=" N PRO A1280 " pdb=" CA PRO A1280 " ideal model delta harmonic sigma weight residual 180.00 132.99 47.01 0 5.00e+00 4.00e-02 8.84e+01 dihedral pdb=" CB CYS A1378 " pdb=" SG CYS A1378 " pdb=" SG CYS A1417 " pdb=" CB CYS A1417 " ideal model delta sinusoidal sigma weight residual 93.00 8.91 84.09 1 1.00e+01 1.00e-02 8.61e+01 ... (remaining 8049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1871 0.154 - 0.308: 138 0.308 - 0.462: 4 0.462 - 0.616: 1 0.616 - 0.770: 2 Chirality restraints: 2016 Sorted by residual: chirality pdb=" C1 NAG A2506 " pdb=" ND2 ASN A1665 " pdb=" C2 NAG A2506 " pdb=" O5 NAG A2506 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA CYS A 942 " pdb=" N CYS A 942 " pdb=" C CYS A 942 " pdb=" CB CYS A 942 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CA CYS A 775 " pdb=" N CYS A 775 " pdb=" C CYS A 775 " pdb=" CB CYS A 775 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 2013 not shown) Planarity restraints: 2375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 638 " -0.017 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C VAL A 638 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL A 638 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE A 639 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 897 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ILE A 897 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE A 897 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS A 898 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 914 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C LEU A 914 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU A 914 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 915 " 0.017 2.00e-02 2.50e+03 ... (remaining 2372 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 21 2.39 - 3.02: 6911 3.02 - 3.65: 18539 3.65 - 4.27: 26132 4.27 - 4.90: 42740 Nonbonded interactions: 94343 Sorted by model distance: nonbonded pdb=" CG1 VAL B 20 " pdb=" OE2 GLU B 57 " model vdw 1.764 3.460 nonbonded pdb=" ND2 ASN A 879 " pdb=" C1 NAG A2503 " model vdw 2.033 3.550 nonbonded pdb=" O GLU A1314 " pdb=" OD1 ASN A1315 " model vdw 2.135 3.040 nonbonded pdb=" O ASN A 879 " pdb=" OD1 ASN A 879 " model vdw 2.192 3.040 nonbonded pdb=" OG1 THR A 662 " pdb=" O TYR A 665 " model vdw 2.250 3.040 ... (remaining 94338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.520 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 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 : 0.013 0.075 13447 Z= 0.964 Angle : 1.783 14.356 18303 Z= 1.235 Chirality : 0.092 0.770 2016 Planarity : 0.006 0.069 2373 Dihedral : 15.370 82.228 4813 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.74 % Favored : 92.90 % Rotamer: Outliers : 0.41 % Allowed : 12.32 % Favored : 87.27 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.41 % Twisted General : 0.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.93 (0.16), residues: 1676 helix: -4.93 (0.36), residues: 13 sheet: -2.74 (0.24), residues: 377 loop : -3.75 (0.13), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1190 TYR 0.026 0.003 TYR A1031 PHE 0.026 0.003 PHE A1875 TRP 0.023 0.003 TRP A1400 HIS 0.012 0.002 HIS A1677 Details of bonding type rmsd/Z covalent geometry : bond 0.01287 / 0.96 (13397) covalent geometry : angle 1.77801 / 1.24 (18203) SS BOND : bond 0.01181 / 0.84 ( 47) SS BOND : angle 2.17638 / 1.27 ( 94) hydrogen bonds : bond 0.30258 / 20.35 ( 177) hydrogen bonds : angle 12.14511 / 8.15 ( 456) Misc. bond : bond 0.07508 / 3.95 ( 1) link_NAG-ASN : bond 0.01149 / 0.55 ( 2) link_NAG-ASN : angle 5.41091 / 3.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 857 ASN cc_start: 0.7664 (m-40) cc_final: 0.7392 (m110) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.1225 time to fit residues: 15.7596 Evaluate side-chains 53 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 948 ASN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1329 HIS ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1631 ASN ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1747 ASN A1766 ASN A1946 HIS ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2039 GLN ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.098720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077297 restraints weight = 50676.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076883 restraints weight = 50360.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.077698 restraints weight = 46644.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.077810 restraints weight = 31729.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078456 restraints weight = 28138.457| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13447 Z= 0.232 Angle : 0.854 11.241 18303 Z= 0.450 Chirality : 0.051 0.327 2016 Planarity : 0.006 0.072 2373 Dihedral : 8.085 42.281 1836 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.86 % Favored : 89.02 % Rotamer: Outliers : 0.21 % Allowed : 7.50 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.17), residues: 1676 helix: -4.71 (0.44), residues: 21 sheet: -2.47 (0.24), residues: 416 loop : -3.48 (0.14), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 790 TYR 0.018 0.002 TYR A1360 PHE 0.033 0.003 PHE A1794 TRP 0.014 0.002 TRP A1400 HIS 0.011 0.001 HIS A1764 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (13397) covalent geometry : angle 0.84215 / 0.45 (18203) SS BOND : bond 0.00627 / 0.41 ( 47) SS BOND : angle 1.74097 / 1.08 ( 94) hydrogen bonds : bond 0.05324 / 3.65 ( 177) hydrogen bonds : angle 8.67477 / 5.88 ( 456) Misc. bond : bond 0.00844 / 0.44 ( 1) link_NAG-ASN : bond 0.01114 / 0.53 ( 2) link_NAG-ASN : angle 4.87774 / 2.77 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 964 TYR cc_start: 0.7544 (t80) cc_final: 0.7180 (t80) REVERT: A 1320 MET cc_start: 0.8395 (mtt) cc_final: 0.8172 (mtm) REVERT: A 1576 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: B 14 VAL cc_start: 0.8767 (m) cc_final: 0.8496 (p) outliers start: 3 outliers final: 0 residues processed: 73 average time/residue: 0.1177 time to fit residues: 12.7570 Evaluate side-chains 45 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 153 optimal weight: 40.0000 chunk 127 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 31 optimal weight: 0.0040 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 642 GLN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1301 GLN ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1957 HIS A2028 HIS ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.099711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.078779 restraints weight = 51133.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.078828 restraints weight = 53643.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.079798 restraints weight = 47316.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.080033 restraints weight = 30464.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.081061 restraints weight = 27460.362| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13447 Z= 0.173 Angle : 0.771 10.881 18303 Z= 0.404 Chirality : 0.049 0.287 2016 Planarity : 0.005 0.077 2373 Dihedral : 7.351 38.106 1836 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.50 % Favored : 89.44 % Rotamer: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.18), residues: 1676 helix: -3.73 (0.79), residues: 19 sheet: -2.08 (0.25), residues: 395 loop : -3.32 (0.15), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1395 TYR 0.017 0.001 TYR A 723 PHE 0.017 0.002 PHE A1824 TRP 0.049 0.002 TRP A 762 HIS 0.005 0.001 HIS A1144 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (13397) covalent geometry : angle 0.76151 / 0.40 (18203) SS BOND : bond 0.00510 / 0.33 ( 47) SS BOND : angle 1.40469 / 0.86 ( 94) hydrogen bonds : bond 0.04737 / 3.22 ( 177) hydrogen bonds : angle 7.99754 / 5.42 ( 456) Misc. bond : bond 0.00742 / 0.39 ( 1) link_NAG-ASN : bond 0.00936 / 0.45 ( 2) link_NAG-ASN : angle 4.61170 / 2.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.489 Fit side-chains REVERT: A 492 ARG cc_start: 0.7257 (pmt-80) cc_final: 0.6614 (ptm160) REVERT: A 857 ASN cc_start: 0.7519 (m-40) cc_final: 0.6960 (m-40) REVERT: A 964 TYR cc_start: 0.7468 (t80) cc_final: 0.7211 (t80) REVERT: A 1320 MET cc_start: 0.8343 (mtt) cc_final: 0.8132 (mtm) REVERT: A 1624 ARG cc_start: 0.8249 (tpt-90) cc_final: 0.7027 (ttt90) REVERT: B 14 VAL cc_start: 0.8879 (m) cc_final: 0.8651 (p) outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 0.1151 time to fit residues: 13.1781 Evaluate side-chains 49 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 78 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 GLN A 668 HIS ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.097510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.076602 restraints weight = 51287.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077247 restraints weight = 55064.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.077706 restraints weight = 48672.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.078038 restraints weight = 31877.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.078735 restraints weight = 28290.524| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 13447 Z= 0.250 Angle : 0.824 13.005 18303 Z= 0.430 Chirality : 0.050 0.299 2016 Planarity : 0.006 0.092 2373 Dihedral : 7.452 40.476 1836 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.77 % Favored : 87.11 % Rotamer: Outliers : 0.14 % Allowed : 6.13 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.18), residues: 1676 helix: -4.09 (0.63), residues: 20 sheet: -2.06 (0.25), residues: 389 loop : -3.33 (0.15), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1395 TYR 0.014 0.002 TYR A 763 PHE 0.021 0.003 PHE A1916 TRP 0.023 0.002 TRP A 762 HIS 0.006 0.001 HIS A1144 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.25 (13397) covalent geometry : angle 0.81406 / 0.43 (18203) SS BOND : bond 0.00622 / 0.42 ( 47) SS BOND : angle 1.55015 / 0.92 ( 94) hydrogen bonds : bond 0.04769 / 3.22 ( 177) hydrogen bonds : angle 7.97507 / 5.41 ( 456) Misc. bond : bond 0.00529 / 0.28 ( 1) link_NAG-ASN : bond 0.00990 / 0.47 ( 2) link_NAG-ASN : angle 4.66849 / 2.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 855 ILE cc_start: 0.8466 (pt) cc_final: 0.8169 (tt) REVERT: A 857 ASN cc_start: 0.7558 (m-40) cc_final: 0.7308 (m-40) REVERT: A 964 TYR cc_start: 0.7600 (t80) cc_final: 0.7306 (t80) REVERT: A 1320 MET cc_start: 0.8308 (mtt) cc_final: 0.8104 (mtm) REVERT: A 1576 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6184 (m-80) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 0.1239 time to fit residues: 13.2694 Evaluate side-chains 41 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 65 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 152 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 HIS ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.099855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079065 restraints weight = 50931.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.078760 restraints weight = 52353.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.079520 restraints weight = 48805.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.079785 restraints weight = 31765.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.080948 restraints weight = 28192.934| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13447 Z= 0.134 Angle : 0.734 11.669 18303 Z= 0.382 Chirality : 0.048 0.286 2016 Planarity : 0.005 0.087 2373 Dihedral : 6.880 38.034 1836 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.44 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.18), residues: 1676 helix: -3.76 (0.66), residues: 20 sheet: -1.85 (0.26), residues: 388 loop : -3.19 (0.15), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1395 TYR 0.017 0.001 TYR A 723 PHE 0.011 0.001 PHE A1753 TRP 0.017 0.002 TRP A 924 HIS 0.004 0.001 HIS A1953 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13397) covalent geometry : angle 0.72399 / 0.38 (18203) SS BOND : bond 0.00488 / 0.35 ( 47) SS BOND : angle 1.37023 / 0.86 ( 94) hydrogen bonds : bond 0.03894 / 2.57 ( 177) hydrogen bonds : angle 7.35748 / 4.99 ( 456) Misc. bond : bond 0.00501 / 0.26 ( 1) link_NAG-ASN : bond 0.00959 / 0.46 ( 2) link_NAG-ASN : angle 4.67255 / 2.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 925 ASN cc_start: 0.8503 (t0) cc_final: 0.8195 (t0) REVERT: A 1320 MET cc_start: 0.8320 (mtt) cc_final: 0.8116 (mtm) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1158 time to fit residues: 11.9552 Evaluate side-chains 42 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 909 HIS ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.100485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.079432 restraints weight = 50486.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.080202 restraints weight = 47018.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080552 restraints weight = 42137.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.080873 restraints weight = 27550.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.081666 restraints weight = 24234.992| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13447 Z= 0.129 Angle : 0.704 10.786 18303 Z= 0.364 Chirality : 0.047 0.287 2016 Planarity : 0.005 0.073 2373 Dihedral : 6.520 39.191 1836 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.62 % Favored : 89.32 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.86 (0.18), residues: 1676 helix: -3.39 (0.82), residues: 20 sheet: -1.81 (0.26), residues: 398 loop : -3.07 (0.15), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1931 TYR 0.015 0.001 TYR A 723 PHE 0.015 0.001 PHE A1753 TRP 0.014 0.001 TRP A 916 HIS 0.003 0.001 HIS A1953 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (13397) covalent geometry : angle 0.69596 / 0.36 (18203) SS BOND : bond 0.00413 / 0.28 ( 47) SS BOND : angle 1.19316 / 0.73 ( 94) hydrogen bonds : bond 0.03604 / 2.37 ( 177) hydrogen bonds : angle 6.94094 / 4.72 ( 456) Misc. bond : bond 0.00514 / 0.27 ( 1) link_NAG-ASN : bond 0.00946 / 0.45 ( 2) link_NAG-ASN : angle 4.45088 / 2.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 925 ASN cc_start: 0.8375 (t0) cc_final: 0.8111 (t0) REVERT: B 14 VAL cc_start: 0.8836 (m) cc_final: 0.8613 (p) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1114 time to fit residues: 12.0719 Evaluate side-chains 47 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 4 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 56 optimal weight: 0.0370 chunk 153 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 141 optimal weight: 0.2980 chunk 19 optimal weight: 30.0000 overall best weight: 2.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 801 ASN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.099117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.078448 restraints weight = 50807.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078641 restraints weight = 57590.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.079289 restraints weight = 49875.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079591 restraints weight = 32796.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.080579 restraints weight = 28538.455| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13447 Z= 0.182 Angle : 0.752 12.341 18303 Z= 0.387 Chirality : 0.048 0.289 2016 Planarity : 0.005 0.074 2373 Dihedral : 6.648 35.605 1836 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.05 % Favored : 87.95 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.18), residues: 1676 helix: -3.58 (0.81), residues: 20 sheet: -1.77 (0.26), residues: 400 loop : -3.06 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1931 TYR 0.013 0.001 TYR A 763 PHE 0.018 0.002 PHE A1380 TRP 0.051 0.003 TRP A 762 HIS 0.004 0.001 HIS A1144 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (13397) covalent geometry : angle 0.74333 / 0.38 (18203) SS BOND : bond 0.00466 / 0.31 ( 47) SS BOND : angle 1.39876 / 0.83 ( 94) hydrogen bonds : bond 0.04046 / 2.71 ( 177) hydrogen bonds : angle 6.97235 / 4.74 ( 456) Misc. bond : bond 0.00756 / 0.40 ( 1) link_NAG-ASN : bond 0.00937 / 0.45 ( 2) link_NAG-ASN : angle 4.31611 / 2.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.479 Fit side-chains REVERT: A 925 ASN cc_start: 0.8398 (t0) cc_final: 0.8171 (t0) REVERT: A 1781 MET cc_start: 0.8074 (mmm) cc_final: 0.7790 (mmm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1103 time to fit residues: 10.5643 Evaluate side-chains 40 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 151 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 87 optimal weight: 0.7980 chunk 152 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 925 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 HIS ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.099264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.076904 restraints weight = 50263.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.076790 restraints weight = 39048.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.077331 restraints weight = 32004.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.077599 restraints weight = 25294.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077666 restraints weight = 23232.852| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 13447 Z= 0.182 Angle : 0.758 11.480 18303 Z= 0.394 Chirality : 0.048 0.289 2016 Planarity : 0.005 0.072 2373 Dihedral : 6.636 37.223 1836 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.83 (0.18), residues: 1676 helix: -3.76 (0.76), residues: 20 sheet: -1.81 (0.26), residues: 401 loop : -3.03 (0.15), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1395 TYR 0.020 0.001 TYR A1767 PHE 0.058 0.002 PHE A1978 TRP 0.040 0.003 TRP A 762 HIS 0.013 0.001 HIS A 668 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (13397) covalent geometry : angle 0.74865 / 0.39 (18203) SS BOND : bond 0.00463 / 0.31 ( 47) SS BOND : angle 1.50852 / 0.92 ( 94) hydrogen bonds : bond 0.03947 / 2.70 ( 177) hydrogen bonds : angle 6.96695 / 4.72 ( 456) Misc. bond : bond 0.00604 / 0.32 ( 1) link_NAG-ASN : bond 0.00962 / 0.46 ( 2) link_NAG-ASN : angle 4.35753 / 2.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.435 Fit side-chains REVERT: A 925 ASN cc_start: 0.8486 (t0) cc_final: 0.8216 (t0) REVERT: A 926 THR cc_start: 0.8078 (m) cc_final: 0.7820 (m) REVERT: A 964 TYR cc_start: 0.7770 (t80) cc_final: 0.7521 (t80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1027 time to fit residues: 10.1067 Evaluate side-chains 42 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 160 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 119 optimal weight: 0.0030 chunk 47 optimal weight: 7.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 925 ASN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.099187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.078316 restraints weight = 50897.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.079151 restraints weight = 51786.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.079339 restraints weight = 46865.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.079756 restraints weight = 30074.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.080507 restraints weight = 25915.087| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13447 Z= 0.170 Angle : 0.749 14.879 18303 Z= 0.386 Chirality : 0.048 0.290 2016 Planarity : 0.005 0.072 2373 Dihedral : 6.584 35.691 1836 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.18), residues: 1676 helix: -3.73 (0.76), residues: 20 sheet: -1.79 (0.26), residues: 396 loop : -2.98 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1641 TYR 0.016 0.001 TYR A1767 PHE 0.020 0.002 PHE A1380 TRP 0.040 0.002 TRP A 762 HIS 0.009 0.001 HIS A 668 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (13397) covalent geometry : angle 0.74031 / 0.38 (18203) SS BOND : bond 0.00439 / 0.29 ( 47) SS BOND : angle 1.39332 / 0.84 ( 94) hydrogen bonds : bond 0.03932 / 2.65 ( 177) hydrogen bonds : angle 6.84313 / 4.63 ( 456) Misc. bond : bond 0.00735 / 0.39 ( 1) link_NAG-ASN : bond 0.00918 / 0.44 ( 2) link_NAG-ASN : angle 4.22408 / 2.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.489 Fit side-chains REVERT: A 925 ASN cc_start: 0.8448 (t0) cc_final: 0.8214 (t0) REVERT: A 926 THR cc_start: 0.8028 (m) cc_final: 0.7828 (m) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1050 time to fit residues: 9.6585 Evaluate side-chains 41 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 22 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 114 optimal weight: 0.1980 chunk 150 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.099332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.078367 restraints weight = 50811.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.078731 restraints weight = 51994.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.079519 restraints weight = 44087.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.079710 restraints weight = 29714.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080555 restraints weight = 26381.597| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13447 Z= 0.161 Angle : 0.741 14.119 18303 Z= 0.382 Chirality : 0.048 0.293 2016 Planarity : 0.005 0.074 2373 Dihedral : 6.540 35.607 1836 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.18), residues: 1676 helix: -3.64 (0.83), residues: 20 sheet: -1.85 (0.26), residues: 383 loop : -2.91 (0.15), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1931 TYR 0.012 0.001 TYR A1767 PHE 0.020 0.002 PHE A1380 TRP 0.074 0.003 TRP A1509 HIS 0.007 0.001 HIS A 668 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (13397) covalent geometry : angle 0.73305 / 0.38 (18203) SS BOND : bond 0.00443 / 0.30 ( 47) SS BOND : angle 1.29315 / 0.77 ( 94) hydrogen bonds : bond 0.03849 / 2.64 ( 177) hydrogen bonds : angle 6.74102 / 4.55 ( 456) Misc. bond : bond 0.00781 / 0.41 ( 1) link_NAG-ASN : bond 0.00921 / 0.44 ( 2) link_NAG-ASN : angle 4.18794 / 2.39 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.420 Fit side-chains REVERT: A 925 ASN cc_start: 0.8411 (t0) cc_final: 0.8195 (t0) REVERT: A 964 TYR cc_start: 0.7590 (t80) cc_final: 0.7096 (t80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1024 time to fit residues: 9.4804 Evaluate side-chains 42 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 155 optimal weight: 40.0000 chunk 98 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 47 optimal weight: 0.0000 chunk 112 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 948 ASN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1941 ASN ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.101466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.080414 restraints weight = 50038.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.080484 restraints weight = 48458.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.081065 restraints weight = 45235.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.081344 restraints weight = 30760.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082077 restraints weight = 26374.557| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13447 Z= 0.117 Angle : 0.706 19.618 18303 Z= 0.363 Chirality : 0.047 0.291 2016 Planarity : 0.005 0.075 2373 Dihedral : 6.117 35.540 1836 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.18), residues: 1676 helix: -3.58 (0.71), residues: 26 sheet: -1.78 (0.26), residues: 395 loop : -2.84 (0.15), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 731 TYR 0.011 0.001 TYR A1373 PHE 0.023 0.001 PHE A1380 TRP 0.050 0.002 TRP A1509 HIS 0.005 0.001 HIS A 668 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13397) covalent geometry : angle 0.70056 / 0.36 (18203) SS BOND : bond 0.00327 / 0.22 ( 47) SS BOND : angle 1.05802 / 0.65 ( 94) hydrogen bonds : bond 0.03546 / 2.36 ( 177) hydrogen bonds : angle 6.39125 / 4.31 ( 456) Misc. bond : bond 0.01033 / 0.54 ( 1) link_NAG-ASN : bond 0.00865 / 0.41 ( 2) link_NAG-ASN : angle 4.01596 / 2.27 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.35 seconds wall clock time: 33 minutes 20.94 seconds (2000.94 seconds total)