Starting phenix.real_space_refine on Thu Jul 31 07:24:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6um2_20816/07_2025/6um2_20816.cif Found real_map, /net/cci-nas-00/data/ceres_data/6um2_20816/07_2025/6um2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6um2_20816/07_2025/6um2_20816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6um2_20816/07_2025/6um2_20816.map" model { file = "/net/cci-nas-00/data/ceres_data/6um2_20816/07_2025/6um2_20816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6um2_20816/07_2025/6um2_20816.cif" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.67, per 1000 atoms: 0.66 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: 3.05 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 2.11 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: 6.64 Time building geometry restraints manager: 3.67 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: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 35.770 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.600 ------------------------------------------------------------------------------- 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 : 10.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.003 TRP A1400 HIS 0.012 0.002 HIS A1677 PHE 0.026 0.003 PHE A1875 TYR 0.026 0.003 TYR A1031 ARG 0.004 0.001 ARG A1190 Details of bonding type rmsd link_NAG-ASN : bond 0.01149 ( 2) link_NAG-ASN : angle 5.41091 ( 6) hydrogen bonds : bond 0.30258 ( 177) hydrogen bonds : angle 12.14511 ( 456) SS BOND : bond 0.01181 ( 47) SS BOND : angle 2.17638 ( 94) covalent geometry : bond 0.01287 (13397) covalent geometry : angle 1.77801 (18203) Misc. bond : bond 0.07508 ( 1) *********************** 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 : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 857 ASN cc_start: 0.7664 (m-40) cc_final: 0.7394 (m110) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.3004 time to fit residues: 38.5088 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 : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 759 ASN ** A 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** A1708 ASN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.099393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.077975 restraints weight = 49666.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.077044 restraints weight = 50558.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.077892 restraints weight = 45978.852| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13447 Z= 0.202 Angle : 0.826 11.486 18303 Z= 0.436 Chirality : 0.050 0.342 2016 Planarity : 0.005 0.071 2373 Dihedral : 8.455 51.109 1983 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.44 % Favored : 89.44 % Rotamer: Outliers : 0.28 % Allowed : 7.30 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.17), residues: 1676 helix: -4.56 (0.50), residues: 21 sheet: -2.45 (0.24), residues: 416 loop : -3.45 (0.14), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1400 HIS 0.011 0.001 HIS A1764 PHE 0.033 0.003 PHE A1794 TYR 0.023 0.002 TYR A1822 ARG 0.005 0.000 ARG A 790 Details of bonding type rmsd link_NAG-ASN : bond 0.01094 ( 2) link_NAG-ASN : angle 4.89182 ( 6) hydrogen bonds : bond 0.05128 ( 177) hydrogen bonds : angle 8.52896 ( 456) SS BOND : bond 0.00578 ( 47) SS BOND : angle 1.69803 ( 94) covalent geometry : bond 0.00459 (13397) covalent geometry : angle 0.81491 (18203) Misc. bond : bond 0.00644 ( 1) *********************** 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 78 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 1.401 Fit side-chains REVERT: A 701 ARG cc_start: 0.7485 (mtm180) cc_final: 0.7039 (mpt180) REVERT: A 964 TYR cc_start: 0.7473 (t80) cc_final: 0.7222 (t80) REVERT: A 1624 ARG cc_start: 0.8255 (tpt-90) cc_final: 0.7276 (ttt90) REVERT: B 14 VAL cc_start: 0.8554 (m) cc_final: 0.8329 (p) outliers start: 4 outliers final: 0 residues processed: 78 average time/residue: 0.2625 time to fit residues: 30.9866 Evaluate side-chains 46 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 87 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** A1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1301 GLN ** 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** A1957 HIS A2028 HIS ** A2070 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.098844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.077807 restraints weight = 51222.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.078665 restraints weight = 51588.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078986 restraints weight = 46182.662| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13447 Z= 0.211 Angle : 0.797 12.084 18303 Z= 0.416 Chirality : 0.050 0.298 2016 Planarity : 0.006 0.091 2373 Dihedral : 7.985 50.903 1983 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.86 % Favored : 89.08 % Rotamer: Outliers : 0.07 % Allowed : 7.36 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.18), residues: 1676 helix: -3.55 (0.96), residues: 13 sheet: -2.06 (0.25), residues: 393 loop : -3.34 (0.15), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 762 HIS 0.005 0.001 HIS A1144 PHE 0.021 0.002 PHE A1824 TYR 0.016 0.002 TYR A1139 ARG 0.012 0.001 ARG A1395 Details of bonding type rmsd link_NAG-ASN : bond 0.00952 ( 2) link_NAG-ASN : angle 4.64072 ( 6) hydrogen bonds : bond 0.04936 ( 177) hydrogen bonds : angle 8.03925 ( 456) SS BOND : bond 0.00514 ( 47) SS BOND : angle 1.52989 ( 94) covalent geometry : bond 0.00478 (13397) covalent geometry : angle 0.78744 (18203) Misc. bond : bond 0.00744 ( 1) *********************** 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 75 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 857 ASN cc_start: 0.7592 (m-40) cc_final: 0.7248 (m-40) REVERT: B 14 VAL cc_start: 0.8827 (m) cc_final: 0.8558 (p) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.3070 time to fit residues: 33.7324 Evaluate side-chains 46 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 3 optimal weight: 0.0570 chunk 150 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 overall best weight: 2.1104 ------------------------------------------------------------------------------- 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** A1301 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.099457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.078291 restraints weight = 50027.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.079686 restraints weight = 47540.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079722 restraints weight = 42594.346| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13447 Z= 0.175 Angle : 0.755 11.163 18303 Z= 0.394 Chirality : 0.049 0.310 2016 Planarity : 0.005 0.081 2373 Dihedral : 7.562 54.010 1983 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.58 % Favored : 88.37 % Rotamer: Outliers : 0.07 % Allowed : 4.82 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.18), residues: 1676 helix: -3.66 (0.77), residues: 20 sheet: -1.97 (0.25), residues: 392 loop : -3.27 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 762 HIS 0.005 0.001 HIS A1144 PHE 0.014 0.002 PHE A1824 TYR 0.017 0.001 TYR A 717 ARG 0.007 0.001 ARG A 718 Details of bonding type rmsd link_NAG-ASN : bond 0.00969 ( 2) link_NAG-ASN : angle 4.70195 ( 6) hydrogen bonds : bond 0.04273 ( 177) hydrogen bonds : angle 7.61286 ( 456) SS BOND : bond 0.00561 ( 47) SS BOND : angle 1.37895 ( 94) covalent geometry : bond 0.00391 (13397) covalent geometry : angle 0.74529 (18203) Misc. bond : bond 0.00536 ( 1) *********************** 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: 1 poor density : 74 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 857 ASN cc_start: 0.7473 (m-40) cc_final: 0.7205 (m-40) REVERT: A 1733 ILE cc_start: 0.9454 (pt) cc_final: 0.9253 (pt) REVERT: B 14 VAL cc_start: 0.8889 (m) cc_final: 0.8672 (p) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.3013 time to fit residues: 32.9076 Evaluate side-chains 46 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 78 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 20 optimal weight: 0.0570 chunk 166 optimal weight: 4.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- 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 ** 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 = 0.3866 r_free = 0.3866 target = 0.099795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.078824 restraints weight = 50678.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.078152 restraints weight = 49718.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.078954 restraints weight = 43693.293| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13447 Z= 0.141 Angle : 0.721 10.218 18303 Z= 0.375 Chirality : 0.048 0.303 2016 Planarity : 0.005 0.076 2373 Dihedral : 7.231 58.950 1983 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.86 % Favored : 89.08 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.18), residues: 1676 helix: -3.45 (0.76), residues: 26 sheet: -1.80 (0.26), residues: 385 loop : -3.14 (0.15), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 916 HIS 0.013 0.001 HIS A 668 PHE 0.017 0.002 PHE A1753 TYR 0.017 0.001 TYR A1235 ARG 0.007 0.000 ARG A1395 Details of bonding type rmsd link_NAG-ASN : bond 0.00989 ( 2) link_NAG-ASN : angle 4.67884 ( 6) hydrogen bonds : bond 0.03936 ( 177) hydrogen bonds : angle 7.27665 ( 456) SS BOND : bond 0.00448 ( 47) SS BOND : angle 1.36192 ( 94) covalent geometry : bond 0.00315 (13397) covalent geometry : angle 0.71127 (18203) Misc. bond : bond 0.00414 ( 1) *********************** 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 : 1.524 Fit side-chains revert: symmetry clash REVERT: A 492 ARG cc_start: 0.7246 (pmt-80) cc_final: 0.6712 (ptt90) REVERT: A 925 ASN cc_start: 0.8411 (t0) cc_final: 0.8111 (t0) REVERT: B 14 VAL cc_start: 0.8830 (m) cc_final: 0.8609 (p) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2935 time to fit residues: 29.1609 Evaluate side-chains 46 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 154 optimal weight: 0.0970 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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** 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 = 0.3902 r_free = 0.3902 target = 0.101556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.080190 restraints weight = 51240.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.080776 restraints weight = 46866.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081432 restraints weight = 40902.972| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13447 Z= 0.113 Angle : 0.683 9.936 18303 Z= 0.352 Chirality : 0.047 0.304 2016 Planarity : 0.005 0.075 2373 Dihedral : 6.691 54.434 1983 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.67 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.18), residues: 1676 helix: -3.20 (0.90), residues: 19 sheet: -1.70 (0.26), residues: 397 loop : -3.02 (0.15), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 916 HIS 0.007 0.001 HIS A 668 PHE 0.023 0.001 PHE A1824 TYR 0.017 0.001 TYR A 723 ARG 0.004 0.000 ARG A1395 Details of bonding type rmsd link_NAG-ASN : bond 0.00901 ( 2) link_NAG-ASN : angle 4.41934 ( 6) hydrogen bonds : bond 0.03377 ( 177) hydrogen bonds : angle 6.73695 ( 456) SS BOND : bond 0.00340 ( 47) SS BOND : angle 1.05771 ( 94) covalent geometry : bond 0.00253 (13397) covalent geometry : angle 0.67632 (18203) Misc. bond : bond 0.00689 ( 1) *********************** 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 78 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 ARG cc_start: 0.7291 (pmt-80) cc_final: 0.6706 (ptt90) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2819 time to fit residues: 33.1260 Evaluate side-chains 49 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 123 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 150 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 chunk 143 optimal weight: 0.2980 overall best weight: 3.8588 ------------------------------------------------------------------------------- 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** A1774 HIS ** 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 = 0.3829 r_free = 0.3829 target = 0.097918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077028 restraints weight = 51103.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.079566 restraints weight = 59297.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.079126 restraints weight = 43900.529| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13447 Z= 0.260 Angle : 0.811 14.184 18303 Z= 0.418 Chirality : 0.050 0.305 2016 Planarity : 0.006 0.075 2373 Dihedral : 7.167 45.035 1983 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.18), residues: 1676 helix: -3.52 (0.83), residues: 20 sheet: -1.79 (0.26), residues: 400 loop : -3.08 (0.15), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP A 762 HIS 0.005 0.001 HIS A1711 PHE 0.027 0.003 PHE A1824 TYR 0.015 0.002 TYR B 27 ARG 0.004 0.001 ARG A 790 Details of bonding type rmsd link_NAG-ASN : bond 0.01009 ( 2) link_NAG-ASN : angle 4.51817 ( 6) hydrogen bonds : bond 0.04360 ( 177) hydrogen bonds : angle 7.15236 ( 456) SS BOND : bond 0.00642 ( 47) SS BOND : angle 1.62567 ( 94) covalent geometry : bond 0.00589 (13397) covalent geometry : angle 0.80094 (18203) Misc. bond : bond 0.00983 ( 1) *********************** 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 : 1.369 Fit side-chains revert: symmetry clash REVERT: A 855 ILE cc_start: 0.8665 (pt) cc_final: 0.7849 (mm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.2171 time to fit residues: 22.6473 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 : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 55 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.099640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077464 restraints weight = 50799.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.076622 restraints weight = 46349.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.077429 restraints weight = 37302.179| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3579 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= 0.158 Angle : 0.738 11.450 18303 Z= 0.381 Chirality : 0.048 0.304 2016 Planarity : 0.005 0.074 2373 Dihedral : 6.806 38.661 1983 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.18), residues: 1676 helix: -3.55 (0.85), residues: 20 sheet: -1.78 (0.26), residues: 405 loop : -2.97 (0.15), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 762 HIS 0.005 0.001 HIS A1953 PHE 0.028 0.002 PHE A1824 TYR 0.014 0.001 TYR A1822 ARG 0.003 0.000 ARG A 790 Details of bonding type rmsd link_NAG-ASN : bond 0.00960 ( 2) link_NAG-ASN : angle 4.48989 ( 6) hydrogen bonds : bond 0.03829 ( 177) hydrogen bonds : angle 6.87363 ( 456) SS BOND : bond 0.00435 ( 47) SS BOND : angle 1.44216 ( 94) covalent geometry : bond 0.00360 (13397) covalent geometry : angle 0.72796 (18203) Misc. bond : bond 0.00608 ( 1) *********************** 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 66 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2362 time to fit residues: 25.1763 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 : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 144 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 107 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** 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 = 0.3887 r_free = 0.3887 target = 0.100775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.080069 restraints weight = 50464.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.081439 restraints weight = 57677.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.081619 restraints weight = 50152.042| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13447 Z= 0.129 Angle : 0.738 19.083 18303 Z= 0.380 Chirality : 0.048 0.306 2016 Planarity : 0.005 0.073 2373 Dihedral : 6.545 37.749 1983 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.18), residues: 1676 helix: -3.40 (0.78), residues: 20 sheet: -1.77 (0.26), residues: 397 loop : -2.88 (0.15), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 762 HIS 0.003 0.001 HIS A1953 PHE 0.077 0.002 PHE A1978 TYR 0.016 0.001 TYR A1767 ARG 0.004 0.000 ARG A 731 Details of bonding type rmsd link_NAG-ASN : bond 0.00945 ( 2) link_NAG-ASN : angle 4.27669 ( 6) hydrogen bonds : bond 0.03538 ( 177) hydrogen bonds : angle 6.61678 ( 456) SS BOND : bond 0.00392 ( 47) SS BOND : angle 1.29667 ( 94) covalent geometry : bond 0.00292 (13397) covalent geometry : angle 0.73001 (18203) Misc. bond : bond 0.00946 ( 1) *********************** 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 64 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ARG cc_start: 0.7082 (pmt-80) cc_final: 0.6672 (ptt90) REVERT: A 1781 MET cc_start: 0.8162 (mmm) cc_final: 0.7961 (mmt) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2265 time to fit residues: 23.7371 Evaluate side-chains 44 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 105 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 149 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 160 optimal weight: 40.0000 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** B 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.100777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.078403 restraints weight = 50305.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.077776 restraints weight = 40443.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.078160 restraints weight = 34322.395| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3900 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= 0.136 Angle : 0.710 10.823 18303 Z= 0.365 Chirality : 0.047 0.306 2016 Planarity : 0.005 0.075 2373 Dihedral : 6.380 37.641 1983 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.10 % Favored : 88.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.18), residues: 1676 helix: -3.44 (0.81), residues: 20 sheet: -1.81 (0.26), residues: 393 loop : -2.83 (0.15), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 762 HIS 0.003 0.001 HIS A1953 PHE 0.065 0.002 PHE A1978 TYR 0.015 0.001 TYR A1767 ARG 0.004 0.000 ARG A 731 Details of bonding type rmsd link_NAG-ASN : bond 0.00968 ( 2) link_NAG-ASN : angle 4.16976 ( 6) hydrogen bonds : bond 0.03535 ( 177) hydrogen bonds : angle 6.51777 ( 456) SS BOND : bond 0.00395 ( 47) SS BOND : angle 1.20874 ( 94) covalent geometry : bond 0.00310 (13397) covalent geometry : angle 0.70229 (18203) Misc. bond : bond 0.00487 ( 1) ********************** 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 56 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: A 964 TYR cc_start: 0.7684 (t80) cc_final: 0.7433 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2148 time to fit residues: 20.5003 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 : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 0.0670 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.099898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.079268 restraints weight = 50914.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.079137 restraints weight = 56543.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080262 restraints weight = 48065.352| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3918 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= 0.167 Angle : 0.726 11.712 18303 Z= 0.374 Chirality : 0.048 0.309 2016 Planarity : 0.005 0.075 2373 Dihedral : 6.505 37.634 1983 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.18), residues: 1676 helix: -3.64 (0.71), residues: 26 sheet: -1.87 (0.26), residues: 383 loop : -2.81 (0.15), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 762 HIS 0.004 0.001 HIS A1144 PHE 0.053 0.002 PHE A1978 TYR 0.012 0.001 TYR A1767 ARG 0.003 0.000 ARG A 731 Details of bonding type rmsd link_NAG-ASN : bond 0.00966 ( 2) link_NAG-ASN : angle 4.14930 ( 6) hydrogen bonds : bond 0.03677 ( 177) hydrogen bonds : angle 6.72685 ( 456) SS BOND : bond 0.00427 ( 47) SS BOND : angle 1.30067 ( 94) covalent geometry : bond 0.00381 (13397) covalent geometry : angle 0.71832 (18203) Misc. bond : bond 0.00687 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3829.53 seconds wall clock time: 67 minutes 33.66 seconds (4053.66 seconds total)