Starting phenix.real_space_refine on Wed Mar 4 11:20:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6um2_20816/03_2026/6um2_20816.cif Found real_map, /net/cci-nas-00/data/ceres_data/6um2_20816/03_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_20816/03_2026/6um2_20816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6um2_20816/03_2026/6um2_20816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6um2_20816/03_2026/6um2_20816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6um2_20816/03_2026/6um2_20816.map" } 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-dev-5986/lib/python3.9/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 dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.65, 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: 1.26 Conformation dependent library (CDL) restraints added in 803.8 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: 0.71 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: 3.06 Time building geometry restraints manager: 1.75 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: 6975 17.18 - 34.35: 978 34.35 - 51.53: 198 51.53 - 68.71: 35 68.71 - 85.88: 13 Dihedral angle restraints: 8199 sinusoidal: 3346 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 8196 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: 2.990 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.780 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 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 : 15.414 82.228 4960 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 covalent geometry : bond 0.01287 (13397) covalent geometry : angle 1.77801 (18203) SS BOND : bond 0.01181 ( 47) SS BOND : angle 2.17638 ( 94) hydrogen bonds : bond 0.30258 ( 177) hydrogen bonds : angle 12.14511 ( 456) Misc. bond : bond 0.07508 ( 1) link_NAG-ASN : bond 0.01149 ( 2) link_NAG-ASN : angle 5.41091 ( 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 : 0.469 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: 0.1300 time to fit residues: 16.3592 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 : 0.451 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.098684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.077357 restraints weight = 50719.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076872 restraints weight = 51788.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.077878 restraints weight = 46670.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.077896 restraints weight = 31552.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.078751 restraints weight = 28318.694| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13447 Z= 0.242 Angle : 0.851 11.537 18303 Z= 0.449 Chirality : 0.051 0.339 2016 Planarity : 0.006 0.071 2373 Dihedral : 8.578 52.397 1983 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.98 % Favored : 88.90 % Rotamer: Outliers : 0.21 % Allowed : 7.71 % Favored : 92.09 % 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: -4.69 (0.45), residues: 21 sheet: -2.46 (0.24), residues: 416 loop : -3.48 (0.14), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 790 TYR 0.024 0.002 TYR A1822 PHE 0.036 0.003 PHE A1794 TRP 0.015 0.002 TRP A1400 HIS 0.009 0.001 HIS A1764 Details of bonding type rmsd covalent geometry : bond 0.00530 (13397) covalent geometry : angle 0.83941 (18203) SS BOND : bond 0.00631 ( 47) SS BOND : angle 1.71337 ( 94) hydrogen bonds : bond 0.05235 ( 177) hydrogen bonds : angle 8.65806 ( 456) Misc. bond : bond 0.00936 ( 1) link_NAG-ASN : bond 0.01094 ( 2) link_NAG-ASN : angle 4.92380 ( 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 74 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 964 TYR cc_start: 0.7540 (t80) cc_final: 0.7191 (t80) REVERT: A 1320 MET cc_start: 0.8387 (mtt) cc_final: 0.8164 (mtm) REVERT: A 1576 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6992 (m-10) REVERT: B 14 VAL cc_start: 0.8739 (m) cc_final: 0.8478 (p) outliers start: 3 outliers final: 0 residues processed: 74 average time/residue: 0.1097 time to fit residues: 12.0410 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 : 0.450 ------------------------------------------------------------------------------- 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: 3.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 153 optimal weight: 40.0000 chunk 127 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 3 optimal weight: 0.0370 chunk 126 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3866 r_free = 0.3866 target = 0.099933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077670 restraints weight = 51132.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076678 restraints weight = 43554.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077458 restraints weight = 38513.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.077951 restraints weight = 29586.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.078230 restraints weight = 26621.083| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13447 Z= 0.164 Angle : 0.771 10.667 18303 Z= 0.404 Chirality : 0.049 0.301 2016 Planarity : 0.005 0.090 2373 Dihedral : 7.941 51.611 1983 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.38 % Favored : 89.56 % Rotamer: Outliers : 0.14 % Allowed : 6.47 % Favored : 93.39 % 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: -4.25 (0.18), residues: 1676 helix: -3.81 (0.74), residues: 19 sheet: -2.12 (0.25), residues: 398 loop : -3.33 (0.15), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1395 TYR 0.017 0.001 TYR A 723 PHE 0.017 0.002 PHE A1824 TRP 0.033 0.002 TRP A 762 HIS 0.006 0.001 HIS A1144 Details of bonding type rmsd covalent geometry : bond 0.00371 (13397) covalent geometry : angle 0.76071 (18203) SS BOND : bond 0.00501 ( 47) SS BOND : angle 1.44728 ( 94) hydrogen bonds : bond 0.04744 ( 177) hydrogen bonds : angle 8.05034 ( 456) Misc. bond : bond 0.00830 ( 1) link_NAG-ASN : bond 0.01095 ( 2) link_NAG-ASN : angle 4.80334 ( 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: 2 poor density : 77 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 492 ARG cc_start: 0.7285 (pmt-80) cc_final: 0.6636 (ptm160) REVERT: A 857 ASN cc_start: 0.7452 (m-40) cc_final: 0.6984 (m-40) REVERT: A 964 TYR cc_start: 0.7523 (t80) cc_final: 0.7222 (t80) REVERT: A 1320 MET cc_start: 0.8351 (mtt) cc_final: 0.8116 (mtm) REVERT: A 1624 ARG cc_start: 0.8246 (tpt-90) cc_final: 0.7047 (ttt90) REVERT: B 14 VAL cc_start: 0.8734 (m) cc_final: 0.8498 (p) outliers start: 2 outliers final: 1 residues processed: 77 average time/residue: 0.1091 time to fit residues: 12.3142 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 : 0.464 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 0.0770 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3878 r_free = 0.3878 target = 0.100576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.079477 restraints weight = 50671.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080130 restraints weight = 49085.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.080376 restraints weight = 46332.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.080945 restraints weight = 29059.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.081507 restraints weight = 25435.146| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13447 Z= 0.149 Angle : 0.726 9.980 18303 Z= 0.380 Chirality : 0.048 0.308 2016 Planarity : 0.005 0.081 2373 Dihedral : 7.402 53.599 1983 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.44 % Favored : 89.50 % Rotamer: Outliers : 0.07 % Allowed : 4.13 % Favored : 95.80 % 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: -4.11 (0.18), residues: 1676 helix: -3.66 (0.70), residues: 26 sheet: -1.96 (0.25), residues: 392 loop : -3.24 (0.15), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1242 TYR 0.017 0.001 TYR A1139 PHE 0.014 0.002 PHE B 19 TRP 0.019 0.002 TRP A 762 HIS 0.005 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00340 (13397) covalent geometry : angle 0.71698 (18203) SS BOND : bond 0.00466 ( 47) SS BOND : angle 1.34695 ( 94) hydrogen bonds : bond 0.04183 ( 177) hydrogen bonds : angle 7.53882 ( 456) Misc. bond : bond 0.00699 ( 1) link_NAG-ASN : bond 0.00942 ( 2) link_NAG-ASN : angle 4.60264 ( 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 80 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.514 Fit side-chains REVERT: A 857 ASN cc_start: 0.7375 (m-40) cc_final: 0.6859 (m-40) REVERT: A 1320 MET cc_start: 0.8307 (mtt) cc_final: 0.8073 (mtm) REVERT: A 1589 ARG cc_start: 0.8032 (tpt170) cc_final: 0.7792 (mmm160) REVERT: B 14 VAL cc_start: 0.8869 (m) cc_final: 0.8614 (p) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.1250 time to fit residues: 14.4934 Evaluate side-chains 45 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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: 30.0000 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.097954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077360 restraints weight = 51554.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.077219 restraints weight = 62883.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.078394 restraints weight = 50774.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.078521 restraints weight = 33386.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.079417 restraints weight = 29740.679| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13447 Z= 0.227 Angle : 0.807 17.375 18303 Z= 0.416 Chirality : 0.049 0.313 2016 Planarity : 0.006 0.075 2373 Dihedral : 7.655 59.913 1983 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.41 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % 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: -4.07 (0.18), residues: 1676 helix: -3.93 (0.72), residues: 20 sheet: -1.89 (0.25), residues: 398 loop : -3.24 (0.15), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1395 TYR 0.017 0.002 TYR A 907 PHE 0.020 0.002 PHE A1916 TRP 0.033 0.002 TRP A1798 HIS 0.005 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00512 (13397) covalent geometry : angle 0.79676 (18203) SS BOND : bond 0.00571 ( 47) SS BOND : angle 1.58820 ( 94) hydrogen bonds : bond 0.04611 ( 177) hydrogen bonds : angle 7.53557 ( 456) Misc. bond : bond 0.01137 ( 1) link_NAG-ASN : bond 0.01057 ( 2) link_NAG-ASN : angle 4.76135 ( 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 66 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.497 Fit side-chains REVERT: A 855 ILE cc_start: 0.8615 (pt) cc_final: 0.8110 (mp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1159 time to fit residues: 11.4141 Evaluate side-chains 43 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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: 0.8980 chunk 42 optimal weight: 6.9990 chunk 143 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.100346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.079272 restraints weight = 50327.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.080096 restraints weight = 49446.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.080531 restraints weight = 41617.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.080818 restraints weight = 27452.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081471 restraints weight = 24437.740| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13447 Z= 0.129 Angle : 0.722 13.561 18303 Z= 0.371 Chirality : 0.047 0.305 2016 Planarity : 0.005 0.076 2373 Dihedral : 7.034 51.047 1983 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.08 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: -3.91 (0.18), residues: 1676 helix: -3.87 (0.73), residues: 20 sheet: -1.81 (0.26), residues: 387 loop : -3.10 (0.15), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1395 TYR 0.017 0.001 TYR A 723 PHE 0.016 0.001 PHE A1753 TRP 0.019 0.002 TRP A1798 HIS 0.005 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00293 (13397) covalent geometry : angle 0.71363 (18203) SS BOND : bond 0.00421 ( 47) SS BOND : angle 1.23530 ( 94) hydrogen bonds : bond 0.03858 ( 177) hydrogen bonds : angle 6.96592 ( 456) Misc. bond : bond 0.01150 ( 1) link_NAG-ASN : bond 0.00966 ( 2) link_NAG-ASN : angle 4.62421 ( 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 74 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.470 Fit side-chains REVERT: A 855 ILE cc_start: 0.8502 (pt) cc_final: 0.8035 (mp) REVERT: A 925 ASN cc_start: 0.8345 (t0) cc_final: 0.8064 (t0) REVERT: A 926 THR cc_start: 0.7837 (m) cc_final: 0.7608 (m) REVERT: A 1589 ARG cc_start: 0.8018 (tpt90) cc_final: 0.7691 (mmm160) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1133 time to fit residues: 12.5710 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 : 0.483 ------------------------------------------------------------------------------- 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: 0.9980 chunk 126 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 56 optimal weight: 0.0060 chunk 153 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 141 optimal weight: 0.0970 chunk 19 optimal weight: 20.0000 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.101458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.080242 restraints weight = 50716.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.082094 restraints weight = 45432.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.081877 restraints weight = 39447.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.082191 restraints weight = 25151.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.082619 restraints weight = 22134.114| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 13447 Z= 0.136 Angle : 0.726 11.620 18303 Z= 0.377 Chirality : 0.048 0.307 2016 Planarity : 0.005 0.076 2373 Dihedral : 6.702 41.546 1983 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -3.75 (0.18), residues: 1676 helix: -3.70 (0.79), residues: 19 sheet: -1.69 (0.26), residues: 396 loop : -3.00 (0.15), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1395 TYR 0.016 0.001 TYR A 723 PHE 0.035 0.002 PHE A1978 TRP 0.044 0.002 TRP A 762 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00306 (13397) covalent geometry : angle 0.71897 (18203) SS BOND : bond 0.00351 ( 47) SS BOND : angle 1.16826 ( 94) hydrogen bonds : bond 0.03927 ( 177) hydrogen bonds : angle 6.63936 ( 456) Misc. bond : bond 0.00911 ( 1) link_NAG-ASN : bond 0.00960 ( 2) link_NAG-ASN : angle 4.42184 ( 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 72 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.481 Fit side-chains REVERT: A 492 ARG cc_start: 0.7217 (pmt-80) cc_final: 0.6773 (ptt90) REVERT: A 964 TYR cc_start: 0.7673 (t80) cc_final: 0.7192 (t80) REVERT: A 1589 ARG cc_start: 0.8071 (tpt90) cc_final: 0.7694 (mmm160) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1054 time to fit residues: 11.7905 Evaluate side-chains 48 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 7.9990 chunk 91 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 93 optimal weight: 0.4980 chunk 27 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3829 r_free = 0.3829 target = 0.097893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.077487 restraints weight = 50947.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.077162 restraints weight = 61262.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077915 restraints weight = 49561.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078964 restraints weight = 32013.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.079158 restraints weight = 27813.352| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 13447 Z= 0.264 Angle : 0.827 17.186 18303 Z= 0.427 Chirality : 0.051 0.310 2016 Planarity : 0.006 0.074 2373 Dihedral : 7.271 41.778 1983 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -3.88 (0.18), residues: 1676 helix: -4.34 (0.58), residues: 19 sheet: -1.81 (0.26), residues: 390 loop : -3.06 (0.15), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1493 TYR 0.016 0.002 TYR B 27 PHE 0.057 0.003 PHE A1978 TRP 0.065 0.004 TRP A1509 HIS 0.016 0.002 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00595 (13397) covalent geometry : angle 0.81659 (18203) SS BOND : bond 0.00578 ( 47) SS BOND : angle 1.69049 ( 94) hydrogen bonds : bond 0.04526 ( 177) hydrogen bonds : angle 7.05923 ( 456) Misc. bond : bond 0.00868 ( 1) link_NAG-ASN : bond 0.01066 ( 2) link_NAG-ASN : angle 4.45219 ( 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 59 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.471 Fit side-chains REVERT: A 855 ILE cc_start: 0.8635 (pt) cc_final: 0.8161 (mp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1144 time to fit residues: 10.2589 Evaluate side-chains 32 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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: 20.0000 chunk 17 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1399 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 = 0.3852 r_free = 0.3852 target = 0.099007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.077934 restraints weight = 50927.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.078120 restraints weight = 53702.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.078701 restraints weight = 45465.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079496 restraints weight = 29887.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.079758 restraints weight = 26848.019| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 13447 Z= 0.181 Angle : 0.854 44.872 18303 Z= 0.418 Chirality : 0.049 0.310 2016 Planarity : 0.005 0.075 2373 Dihedral : 7.033 40.016 1983 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -3.81 (0.18), residues: 1676 helix: -4.24 (0.59), residues: 20 sheet: -1.86 (0.26), residues: 384 loop : -2.97 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1641 TYR 0.018 0.001 TYR B 59 PHE 0.034 0.002 PHE A1978 TRP 0.060 0.003 TRP A1509 HIS 0.010 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00414 (13397) covalent geometry : angle 0.84659 (18203) SS BOND : bond 0.00461 ( 47) SS BOND : angle 1.42255 ( 94) hydrogen bonds : bond 0.04231 ( 177) hydrogen bonds : angle 6.86734 ( 456) Misc. bond : bond 0.02251 ( 1) link_NAG-ASN : bond 0.00974 ( 2) link_NAG-ASN : angle 4.43932 ( 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 59 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.429 Fit side-chains REVERT: A 855 ILE cc_start: 0.8575 (pt) cc_final: 0.8119 (mp) REVERT: A 1589 ARG cc_start: 0.8037 (tpt90) cc_final: 0.7706 (mmm160) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1093 time to fit residues: 10.0196 Evaluate side-chains 37 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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: 0.6980 chunk 132 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.099661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.078635 restraints weight = 50649.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.079062 restraints weight = 50846.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.079593 restraints weight = 43598.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.079908 restraints weight = 28537.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080684 restraints weight = 25048.811| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.3752 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= 0.154 Angle : 0.768 22.664 18303 Z= 0.390 Chirality : 0.048 0.310 2016 Planarity : 0.005 0.076 2373 Dihedral : 6.847 38.696 1983 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % 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: -3.71 (0.18), residues: 1676 helix: -4.08 (0.86), residues: 12 sheet: -1.80 (0.26), residues: 381 loop : -2.91 (0.15), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1641 TYR 0.020 0.001 TYR A1767 PHE 0.025 0.002 PHE A1978 TRP 0.057 0.003 TRP A1509 HIS 0.008 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00352 (13397) covalent geometry : angle 0.75981 (18203) SS BOND : bond 0.00427 ( 47) SS BOND : angle 1.30799 ( 94) hydrogen bonds : bond 0.03933 ( 177) hydrogen bonds : angle 6.76167 ( 456) Misc. bond : bond 0.01470 ( 1) link_NAG-ASN : bond 0.00979 ( 2) link_NAG-ASN : angle 4.31947 ( 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 : 0.468 Fit side-chains revert: symmetry clash REVERT: A 855 ILE cc_start: 0.8615 (pt) cc_final: 0.8203 (mp) REVERT: A 1589 ARG cc_start: 0.8051 (tpt90) cc_final: 0.7694 (mmm160) REVERT: A 1781 MET cc_start: 0.8344 (mmm) cc_final: 0.8096 (mmm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1085 time to fit residues: 9.9513 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 : 0.458 ------------------------------------------------------------------------------- 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: 6.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 47 optimal weight: 0.0980 chunk 112 optimal weight: 0.0570 overall best weight: 1.8304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.099587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.078668 restraints weight = 50470.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.078881 restraints weight = 52452.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.079509 restraints weight = 45718.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079796 restraints weight = 30073.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080576 restraints weight = 26426.477| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13447 Z= 0.155 Angle : 0.721 12.437 18303 Z= 0.374 Chirality : 0.048 0.309 2016 Planarity : 0.005 0.076 2373 Dihedral : 6.726 38.049 1983 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -3.65 (0.18), residues: 1676 helix: -3.03 (1.12), residues: 12 sheet: -1.83 (0.26), residues: 383 loop : -2.85 (0.15), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1641 TYR 0.012 0.001 TYR A1373 PHE 0.021 0.002 PHE A1978 TRP 0.047 0.003 TRP A1509 HIS 0.006 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00352 (13397) covalent geometry : angle 0.71338 (18203) SS BOND : bond 0.00426 ( 47) SS BOND : angle 1.23729 ( 94) hydrogen bonds : bond 0.04132 ( 177) hydrogen bonds : angle 6.65563 ( 456) Misc. bond : bond 0.01082 ( 1) link_NAG-ASN : bond 0.00958 ( 2) link_NAG-ASN : angle 4.23053 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.94 seconds wall clock time: 32 minutes 41.45 seconds (1961.45 seconds total)