Starting phenix.real_space_refine on Wed Mar 4 22:42:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lkp_23409/03_2026/7lkp_23409.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lkp_23409/03_2026/7lkp_23409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lkp_23409/03_2026/7lkp_23409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lkp_23409/03_2026/7lkp_23409.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lkp_23409/03_2026/7lkp_23409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lkp_23409/03_2026/7lkp_23409.map" } resolution = 3.27 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= -0.001 sd= 0.062 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 84 5.16 5 C 10278 2.51 5 N 2564 2.21 5 O 2863 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s 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: 15789 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1941, 15274 Classifications: {'peptide': 1941} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 102, 'TRANS': 1838} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4, 'TRP:plan': 1, 'PHE:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 3, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 415 Unusual residues: {'AJP': 1, 'CLR': 7, 'NAG': 6, 'POV': 7} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'POV:plan-1': 4, 'POV:plan-2': 7, 'POV:plan-3': 7} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 3.45, per 1000 atoms: 0.22 Number of scatterers: 15789 At special positions: 0 Unit cell: (85.49, 99.91, 210.12, 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 84 16.00 O 2863 8.00 N 2564 7.00 C 10278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=2.04 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.02 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=4, symmetry=0 Links applied BETA1-3 " BMA C 3 " - " BMA C 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A2301 " - " ASN A 444 " " NAG A2302 " - " ASN A 504 " " NAG A2303 " - " ASN A1469 " " NAG A2304 " - " ASN A1588 " " NAG A2305 " - " ASN A1662 " " NAG A2306 " - " ASN A 98 " " NAG B 1 " - " ASN A 415 " " NAG C 1 " - " ASN A1529 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 599.4 milliseconds 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3632 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 11 sheets defined 56.8% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 3.864A pdb=" N LYS A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 45 removed outlier: 3.548A pdb=" N VAL A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 118 through 137 Processing helix chain 'A' and resid 274 through 290 Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 300 through 306 removed outlier: 4.131A pdb=" N MET A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.770A pdb=" N MET A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.705A pdb=" N ASN A 343 " --> pdb=" O TYR A 340 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN A 344 " --> pdb=" O GLU A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 340 through 344' Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 367 through 378 removed outlier: 3.522A pdb=" N ASN A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'A' and resid 415 through 444 removed outlier: 3.819A pdb=" N GLU A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 461 through 468 removed outlier: 3.785A pdb=" N LEU A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 498 through 518 Processing helix chain 'A' and resid 530 through 543 removed outlier: 3.660A pdb=" N SER A 540 " --> pdb=" O GLN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 624 removed outlier: 3.543A pdb=" N LEU A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 662 removed outlier: 4.300A pdb=" N ILE A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Proline residue: A 656 - end of helix Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.963A pdb=" N SER A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 690 Processing helix chain 'A' and resid 693 through 722 removed outlier: 3.587A pdb=" N TRP A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 729 through 755 removed outlier: 3.776A pdb=" N THR A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 774 removed outlier: 4.690A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 779 removed outlier: 3.987A pdb=" N LEU A 778 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 794 Processing helix chain 'A' and resid 797 through 815 removed outlier: 4.064A pdb=" N TYR A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN A 815 " --> pdb=" O ARG A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 Processing helix chain 'A' and resid 970 through 977 Processing helix chain 'A' and resid 999 through 1004 Processing helix chain 'A' and resid 1019 through 1032 removed outlier: 3.658A pdb=" N LYS A1031 " --> pdb=" O TYR A1027 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1050 Processing helix chain 'A' and resid 1051 through 1055 Processing helix chain 'A' and resid 1063 through 1075 Processing helix chain 'A' and resid 1076 through 1080 removed outlier: 4.132A pdb=" N ASP A1079 " --> pdb=" O PHE A1076 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A1080 " --> pdb=" O VAL A1077 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1076 through 1080' Processing helix chain 'A' and resid 1093 through 1107 Processing helix chain 'A' and resid 1120 through 1126 Processing helix chain 'A' and resid 1143 through 1149 Processing helix chain 'A' and resid 1205 through 1216 Processing helix chain 'A' and resid 1239 through 1253 Processing helix chain 'A' and resid 1268 through 1277 removed outlier: 3.660A pdb=" N ILE A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1367 Processing helix chain 'A' and resid 1369 through 1390 removed outlier: 4.123A pdb=" N PHE A1373 " --> pdb=" O SER A1369 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1380 - end of helix Processing helix chain 'A' and resid 1406 through 1411 Processing helix chain 'A' and resid 1424 through 1436 Processing helix chain 'A' and resid 1467 through 1477 removed outlier: 3.647A pdb=" N THR A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A1477 " --> pdb=" O LEU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1544 removed outlier: 3.576A pdb=" N PHE A1533 " --> pdb=" O ASN A1529 " (cutoff:3.500A) Proline residue: A1539 - end of helix Processing helix chain 'A' and resid 1572 through 1587 Processing helix chain 'A' and resid 1592 through 1599 Processing helix chain 'A' and resid 1601 through 1608 Processing helix chain 'A' and resid 1625 through 1641 removed outlier: 3.617A pdb=" N SER A1629 " --> pdb=" O HIS A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1664 through 1707 removed outlier: 4.360A pdb=" N LEU A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR A1675 " --> pdb=" O ILE A1671 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL A1693 " --> pdb=" O SER A1689 " (cutoff:3.500A) Proline residue: A1694 - end of helix removed outlier: 3.763A pdb=" N PHE A1697 " --> pdb=" O VAL A1693 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1717 Processing helix chain 'A' and resid 1719 through 1749 Processing helix chain 'A' and resid 1751 through 1756 removed outlier: 3.631A pdb=" N SER A1756 " --> pdb=" O LYS A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1779 Proline residue: A1776 - end of helix Processing helix chain 'A' and resid 1780 through 1785 removed outlier: 4.016A pdb=" N LEU A1784 " --> pdb=" O PRO A1780 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A1785 " --> pdb=" O ALA A1781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1780 through 1785' Processing helix chain 'A' and resid 1790 through 1816 removed outlier: 4.274A pdb=" N THR A1810 " --> pdb=" O SER A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1822 through 1833 Processing helix chain 'A' and resid 1836 through 1862 removed outlier: 3.859A pdb=" N CYS A1840 " --> pdb=" O PHE A1836 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A1841 " --> pdb=" O PRO A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1876 through 1899 Processing helix chain 'A' and resid 1918 through 1930 removed outlier: 3.658A pdb=" N ALA A1922 " --> pdb=" O ASP A1918 " (cutoff:3.500A) Processing helix chain 'A' and resid 1977 through 1987 removed outlier: 3.546A pdb=" N GLY A1987 " --> pdb=" O LYS A1983 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2013 Processing helix chain 'A' and resid 2028 through 2041 removed outlier: 3.901A pdb=" N LEU A2033 " --> pdb=" O GLY A2029 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2045 No H-bonds generated for 'chain 'A' and resid 2043 through 2045' Processing helix chain 'A' and resid 2046 through 2058 removed outlier: 3.699A pdb=" N LEU A2058 " --> pdb=" O SER A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2072 through 2085 Processing helix chain 'A' and resid 2105 through 2120 removed outlier: 3.604A pdb=" N GLY A2120 " --> pdb=" O ILE A2116 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2137 removed outlier: 3.715A pdb=" N CYS A2133 " --> pdb=" O SER A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2161 Processing helix chain 'A' and resid 2178 through 2180 No H-bonds generated for 'chain 'A' and resid 2178 through 2180' Processing helix chain 'A' and resid 2181 through 2193 removed outlier: 4.463A pdb=" N VAL A2185 " --> pdb=" O ASP A2181 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A2186 " --> pdb=" O LEU A2182 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN A2187 " --> pdb=" O ASN A2183 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A2188 " --> pdb=" O PRO A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2214 through 2225 removed outlier: 4.209A pdb=" N ILE A2218 " --> pdb=" O SER A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2253 removed outlier: 3.654A pdb=" N VAL A2244 " --> pdb=" O THR A2240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.821A pdb=" N TYR A 633 " --> pdb=" O VAL A1617 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE A1619 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLN A 635 " --> pdb=" O PHE A1619 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR A1414 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ILE A1560 " --> pdb=" O TYR A1414 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE A1416 " --> pdb=" O ILE A1560 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 527 removed outlier: 6.370A pdb=" N ILE A 398 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 953 through 954 removed outlier: 6.924A pdb=" N PHE A 953 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 988 " --> pdb=" O CYS A 930 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 986 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 989 " --> pdb=" O ARG A 992 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1006 through 1007 removed outlier: 6.700A pdb=" N GLY A1006 " --> pdb=" O ILE A1084 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL A1083 " --> pdb=" O ILE A1114 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N SER A1116 " --> pdb=" O VAL A1083 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A1130 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER A1141 " --> pdb=" O ILE A1130 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A1132 " --> pdb=" O TYR A1139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1223 through 1225 removed outlier: 3.512A pdb=" N ILE A1225 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A1261 " --> pdb=" O VAL A1160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1953 through 1958 removed outlier: 5.567A pdb=" N ASP A1956 " --> pdb=" O LYS A1945 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS A1945 " --> pdb=" O ASP A1956 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A1938 " --> pdb=" O VAL A1962 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1953 through 1958 removed outlier: 5.567A pdb=" N ASP A1956 " --> pdb=" O LYS A1945 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LYS A1945 " --> pdb=" O ASP A1956 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A1943 " --> pdb=" O SER A1993 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A1993 " --> pdb=" O LEU A1943 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2014 through 2016 removed outlier: 6.045A pdb=" N GLY A2015 " --> pdb=" O LEU A2093 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2140 through 2143 Processing sheet with id=AB2, first strand: chain 'A' and resid 2197 through 2202 removed outlier: 7.350A pdb=" N GLN A2207 " --> pdb=" O ARG A2199 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG A2201 " --> pdb=" O MET A2205 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N MET A2205 " --> pdb=" O ARG A2201 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A2233 " --> pdb=" O LYS A2170 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2280 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: 3.39 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3011 1.33 - 1.45: 3953 1.45 - 1.58: 9090 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 16189 Sorted by residual: bond pdb=" C29 POV A2317 " pdb="C210 POV A2317 " ideal model delta sigma weight residual 1.333 1.518 -0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C TYR A 326 " pdb=" N PRO A 327 " ideal model delta sigma weight residual 1.330 1.374 -0.044 1.25e-02 6.40e+03 1.27e+01 bond pdb=" N SER A 281 " pdb=" CA SER A 281 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.04e-02 9.25e+03 9.67e+00 ... (remaining 16184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 21815 3.86 - 7.71: 197 7.71 - 11.57: 14 11.57 - 15.43: 0 15.43 - 19.29: 2 Bond angle restraints: 22028 Sorted by residual: angle pdb=" N PRO A 492 " pdb=" CA PRO A 492 " pdb=" CB PRO A 492 " ideal model delta sigma weight residual 103.25 110.61 -7.36 1.05e+00 9.07e-01 4.91e+01 angle pdb=" C SER A 281 " pdb=" N PRO A 282 " pdb=" CA PRO A 282 " ideal model delta sigma weight residual 119.05 126.62 -7.57 1.11e+00 8.12e-01 4.65e+01 angle pdb=" C28 POV A2317 " pdb=" C29 POV A2317 " pdb="C210 POV A2317 " ideal model delta sigma weight residual 127.79 108.50 19.29 3.00e+00 1.11e-01 4.13e+01 angle pdb=" C29 POV A2317 " pdb="C210 POV A2317 " pdb="C211 POV A2317 " ideal model delta sigma weight residual 127.67 108.42 19.25 3.00e+00 1.11e-01 4.12e+01 angle pdb=" C TYR A 326 " pdb=" N PRO A 327 " pdb=" CA PRO A 327 " ideal model delta sigma weight residual 120.21 125.76 -5.55 9.60e-01 1.09e+00 3.34e+01 ... (remaining 22023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.31: 9716 34.31 - 68.62: 354 68.62 - 102.92: 117 102.92 - 137.23: 68 137.23 - 171.54: 12 Dihedral angle restraints: 10267 sinusoidal: 4643 harmonic: 5624 Sorted by residual: dihedral pdb=" CB CYS A 370 " pdb=" SG CYS A 370 " pdb=" SG CYS A 519 " pdb=" CB CYS A 519 " ideal model delta sinusoidal sigma weight residual 93.00 169.86 -76.86 1 1.00e+01 1.00e-02 7.42e+01 dihedral pdb=" CB CYS A1444 " pdb=" SG CYS A1444 " pdb=" SG CYS A1455 " pdb=" CB CYS A1455 " ideal model delta sinusoidal sigma weight residual 93.00 151.60 -58.60 1 1.00e+01 1.00e-02 4.60e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 81 " pdb=" CB CYS A 81 " ideal model delta sinusoidal sigma weight residual -86.00 -142.66 56.66 1 1.00e+01 1.00e-02 4.32e+01 ... (remaining 10264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.186: 2532 1.186 - 2.372: 0 2.372 - 3.559: 0 3.559 - 4.745: 6 4.745 - 5.931: 23 Chirality restraints: 2561 Sorted by residual: chirality pdb=" C12 AJP A2310 " pdb=" C07 AJP A2310 " pdb=" C11 AJP A2310 " pdb=" C13 AJP A2310 " both_signs ideal model delta sigma weight residual False 3.01 -2.92 5.93 2.00e-01 2.50e+01 8.79e+02 chirality pdb=" C20 AJP A2310 " pdb=" C15 AJP A2310 " pdb=" C19 AJP A2310 " pdb=" C21 AJP A2310 " both_signs ideal model delta sigma weight residual False 2.96 -2.88 5.83 2.00e-01 2.50e+01 8.51e+02 chirality pdb=" C07 AJP A2310 " pdb=" C06 AJP A2310 " pdb=" C08 AJP A2310 " pdb=" C12 AJP A2310 " both_signs ideal model delta sigma weight residual False -2.73 2.69 -5.42 2.00e-01 2.50e+01 7.34e+02 ... (remaining 2558 not shown) Planarity restraints: 2722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A2317 " -0.126 2.00e-02 2.50e+03 1.26e-01 1.59e+02 pdb=" C29 POV A2317 " 0.126 2.00e-02 2.50e+03 pdb="C210 POV A2317 " 0.126 2.00e-02 2.50e+03 pdb="C211 POV A2317 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.005 2.00e-02 2.50e+03 2.61e-02 8.51e+00 pdb=" CG ASN A 98 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " -0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG A2306 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A1494 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" CD GLU A1494 " 0.048 2.00e-02 2.50e+03 pdb=" OE1 GLU A1494 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU A1494 " -0.017 2.00e-02 2.50e+03 ... (remaining 2719 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 118 2.54 - 3.13: 12927 3.13 - 3.72: 23964 3.72 - 4.31: 31336 4.31 - 4.90: 53275 Nonbonded interactions: 121620 Sorted by model distance: nonbonded pdb=" NE2 GLN A1475 " pdb=" CD LYS A1476 " model vdw 1.954 3.520 nonbonded pdb=" CG LYS A2172 " pdb=" OE2 GLU A2232 " model vdw 1.992 3.440 nonbonded pdb=" OD2 ASP A1731 " pdb=" OH TYR A1779 " model vdw 2.075 3.040 nonbonded pdb=" CD1 LEU A2178 " pdb=" N LEU A2179 " model vdw 2.086 3.540 nonbonded pdb=" OD1 ASN A 965 " pdb=" OG1 THR A 970 " model vdw 2.110 3.040 ... (remaining 121615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.040 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 : 0.008 0.540 16213 Z= 0.684 Angle : 1.004 19.286 22082 Z= 0.569 Chirality : 0.534 5.931 2561 Planarity : 0.005 0.126 2714 Dihedral : 23.570 171.539 6617 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.67 % Favored : 94.28 % Rotamer: Outliers : 0.60 % Allowed : 1.99 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 1923 helix: 0.84 (0.16), residues: 1045 sheet: -1.90 (0.39), residues: 172 loop : -2.49 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 537 TYR 0.017 0.002 TYR A 360 PHE 0.027 0.002 PHE A1417 TRP 0.032 0.002 TRP A 439 HIS 0.006 0.001 HIS A 289 Details of bonding type rmsd covalent geometry : bond 0.00624 (16189) covalent geometry : angle 0.98827 (22028) SS BOND : bond 0.00509 ( 6) SS BOND : angle 3.00169 ( 12) hydrogen bonds : bond 0.15273 ( 777) hydrogen bonds : angle 6.10707 ( 2280) Misc. bond : bond 0.36355 ( 4) link_BETA1-3 : bond 0.00435 ( 1) link_BETA1-3 : angle 1.03012 ( 3) link_BETA1-4 : bond 0.00599 ( 4) link_BETA1-4 : angle 2.35731 ( 12) link_BETA1-6 : bond 0.00410 ( 1) link_BETA1-6 : angle 1.57900 ( 3) link_NAG-ASN : bond 0.00953 ( 8) link_NAG-ASN : angle 4.87016 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 283 time to evaluate : 0.592 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. REVERT: A 28 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6876 (mm-30) REVERT: A 290 ARG cc_start: 0.7434 (tpp80) cc_final: 0.6950 (mtt180) REVERT: A 304 MET cc_start: 0.8023 (ppp) cc_final: 0.7482 (ptt) REVERT: A 530 ASP cc_start: 0.7878 (p0) cc_final: 0.7629 (p0) REVERT: A 556 MET cc_start: 0.7950 (ptm) cc_final: 0.7503 (ptp) REVERT: A 596 ASP cc_start: 0.8431 (t0) cc_final: 0.8017 (t0) REVERT: A 757 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7871 (mmtm) REVERT: A 811 ARG cc_start: 0.7372 (ttm-80) cc_final: 0.6751 (ttm-80) REVERT: A 919 GLU cc_start: 0.7940 (tt0) cc_final: 0.7736 (tt0) REVERT: A 933 ASN cc_start: 0.8126 (m-40) cc_final: 0.7647 (m110) REVERT: A 948 ARG cc_start: 0.6806 (tpt170) cc_final: 0.6015 (tpm170) REVERT: A 992 ARG cc_start: 0.7169 (mpp80) cc_final: 0.6788 (mtm110) REVERT: A 1003 GLN cc_start: 0.7948 (tt0) cc_final: 0.7607 (tm-30) REVERT: A 1041 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 1238 PHE cc_start: 0.7457 (t80) cc_final: 0.7193 (t80) REVERT: A 1241 ARG cc_start: 0.8008 (mmp-170) cc_final: 0.7798 (ttm-80) REVERT: A 1243 TYR cc_start: 0.7358 (m-80) cc_final: 0.7130 (m-10) REVERT: A 1489 ARG cc_start: 0.7441 (ptp90) cc_final: 0.7229 (ptp90) REVERT: A 1587 MET cc_start: 0.8497 (mmm) cc_final: 0.8115 (ptm) REVERT: A 1596 ARG cc_start: 0.7755 (mmt180) cc_final: 0.7543 (mmt-90) REVERT: A 1824 ARG cc_start: 0.7336 (mtt180) cc_final: 0.7132 (ttt-90) REVERT: A 1942 GLU cc_start: 0.8259 (mp0) cc_final: 0.8045 (mp0) REVERT: A 2160 LYS cc_start: 0.8302 (ttpp) cc_final: 0.8024 (ttpt) REVERT: A 2206 LEU cc_start: 0.8618 (pt) cc_final: 0.8387 (pt) REVERT: A 2208 PHE cc_start: 0.6929 (m-80) cc_final: 0.6184 (m-80) REVERT: A 2232 GLU cc_start: 0.7630 (mp0) cc_final: 0.7236 (mp0) outliers start: 10 outliers final: 4 residues processed: 291 average time/residue: 0.1322 time to fit residues: 55.9037 Evaluate side-chains 213 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 209 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1240 HIS Chi-restraints excluded: chain A residue 1826 ASN Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2182 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A1029 GLN ** A1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1240 HIS A1356 GLN ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1621 ASN A1899 HIS A2006 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.150366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109321 restraints weight = 20287.760| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.22 r_work: 0.3103 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16213 Z= 0.171 Angle : 0.998 35.910 22082 Z= 0.423 Chirality : 0.082 2.213 2561 Planarity : 0.005 0.060 2714 Dihedral : 16.825 179.766 3048 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 1.39 % Allowed : 11.41 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.19), residues: 1923 helix: 1.05 (0.16), residues: 1053 sheet: -1.58 (0.39), residues: 173 loop : -2.30 (0.21), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 572 TYR 0.018 0.002 TYR A 954 PHE 0.022 0.002 PHE A 718 TRP 0.018 0.001 TRP A 439 HIS 0.007 0.001 HIS A1899 Details of bonding type rmsd covalent geometry : bond 0.00381 (16189) covalent geometry : angle 0.98468 (22028) SS BOND : bond 0.00521 ( 6) SS BOND : angle 2.92787 ( 12) hydrogen bonds : bond 0.05173 ( 777) hydrogen bonds : angle 4.71901 ( 2280) Misc. bond : bond 0.00273 ( 4) link_BETA1-3 : bond 0.00913 ( 1) link_BETA1-3 : angle 2.03193 ( 3) link_BETA1-4 : bond 0.00332 ( 4) link_BETA1-4 : angle 2.99914 ( 12) link_BETA1-6 : bond 0.00777 ( 1) link_BETA1-6 : angle 2.90679 ( 3) link_NAG-ASN : bond 0.00801 ( 8) link_NAG-ASN : angle 4.02498 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.483 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. REVERT: A 290 ARG cc_start: 0.7204 (tpp80) cc_final: 0.6501 (mtt180) REVERT: A 304 MET cc_start: 0.7911 (ppp) cc_final: 0.7560 (ptt) REVERT: A 420 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 530 ASP cc_start: 0.7643 (p0) cc_final: 0.7360 (p0) REVERT: A 544 GLU cc_start: 0.8294 (tt0) cc_final: 0.7805 (tp30) REVERT: A 669 MET cc_start: 0.7359 (mmm) cc_final: 0.7116 (mmm) REVERT: A 811 ARG cc_start: 0.7154 (ttm-80) cc_final: 0.6463 (ttm-80) REVERT: A 925 TRP cc_start: 0.7339 (m-90) cc_final: 0.6979 (m-90) REVERT: A 933 ASN cc_start: 0.7787 (m-40) cc_final: 0.7473 (m110) REVERT: A 948 ARG cc_start: 0.6708 (tpt170) cc_final: 0.6147 (tpm170) REVERT: A 992 ARG cc_start: 0.6385 (mpp80) cc_final: 0.5788 (mtm110) REVERT: A 1003 GLN cc_start: 0.8254 (tt0) cc_final: 0.7595 (tm-30) REVERT: A 1041 GLU cc_start: 0.7296 (tm-30) cc_final: 0.7086 (tm-30) REVERT: A 1045 MET cc_start: 0.7288 (tmm) cc_final: 0.7006 (tmm) REVERT: A 1223 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6534 (tm-30) REVERT: A 1243 TYR cc_start: 0.7241 (m-80) cc_final: 0.6786 (m-80) REVERT: A 1425 GLU cc_start: 0.7893 (pm20) cc_final: 0.7286 (tm-30) REVERT: A 1489 ARG cc_start: 0.7051 (ptp90) cc_final: 0.6654 (ptt-90) REVERT: A 1831 LYS cc_start: 0.7260 (mmmt) cc_final: 0.6935 (mttm) REVERT: A 1927 ARG cc_start: 0.6648 (ttt180) cc_final: 0.6258 (ttt180) REVERT: A 1942 GLU cc_start: 0.8454 (mp0) cc_final: 0.7945 (mp0) REVERT: A 2006 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.6043 (p0) REVERT: A 2205 MET cc_start: 0.7508 (ptm) cc_final: 0.6936 (ttm) REVERT: A 2208 PHE cc_start: 0.6636 (m-80) cc_final: 0.5725 (m-80) REVERT: A 2232 GLU cc_start: 0.8161 (mp0) cc_final: 0.7904 (mp0) outliers start: 23 outliers final: 16 residues processed: 236 average time/residue: 0.1131 time to fit residues: 40.8085 Evaluate side-chains 221 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 872 TYR Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1240 HIS Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2006 ASN Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2202 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 59 optimal weight: 0.9990 chunk 147 optimal weight: 0.5980 chunk 15 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 110 GLN A 338 ASN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 GLN ** A1214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105956 restraints weight = 20209.976| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.95 r_work: 0.3122 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16213 Z= 0.150 Angle : 0.916 35.050 22082 Z= 0.386 Chirality : 0.079 2.147 2561 Planarity : 0.004 0.064 2714 Dihedral : 14.440 175.615 3044 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.32 % Favored : 95.63 % Rotamer: Outliers : 2.29 % Allowed : 14.67 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.19), residues: 1923 helix: 1.19 (0.16), residues: 1060 sheet: -1.45 (0.39), residues: 173 loop : -2.28 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1368 TYR 0.013 0.001 TYR A 400 PHE 0.028 0.001 PHE A 503 TRP 0.013 0.001 TRP A 605 HIS 0.004 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00342 (16189) covalent geometry : angle 0.90202 (22028) SS BOND : bond 0.00477 ( 6) SS BOND : angle 2.77097 ( 12) hydrogen bonds : bond 0.04727 ( 777) hydrogen bonds : angle 4.41282 ( 2280) Misc. bond : bond 0.00125 ( 4) link_BETA1-3 : bond 0.00896 ( 1) link_BETA1-3 : angle 2.21182 ( 3) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 3.08730 ( 12) link_BETA1-6 : bond 0.01022 ( 1) link_BETA1-6 : angle 2.86981 ( 3) link_NAG-ASN : bond 0.00714 ( 8) link_NAG-ASN : angle 3.82471 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.550 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. REVERT: A 290 ARG cc_start: 0.7188 (tpp80) cc_final: 0.6566 (mmt180) REVERT: A 304 MET cc_start: 0.8026 (ppp) cc_final: 0.7637 (ptt) REVERT: A 434 VAL cc_start: 0.7122 (OUTLIER) cc_final: 0.6918 (p) REVERT: A 530 ASP cc_start: 0.7527 (p0) cc_final: 0.7260 (p0) REVERT: A 600 ASP cc_start: 0.8796 (m-30) cc_final: 0.8567 (m-30) REVERT: A 669 MET cc_start: 0.7430 (mmm) cc_final: 0.7221 (mmm) REVERT: A 811 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6484 (ttm-80) REVERT: A 925 TRP cc_start: 0.7329 (m-90) cc_final: 0.6886 (m-90) REVERT: A 933 ASN cc_start: 0.7875 (m-40) cc_final: 0.7507 (m110) REVERT: A 948 ARG cc_start: 0.6524 (tpt170) cc_final: 0.5632 (tpm170) REVERT: A 992 ARG cc_start: 0.6245 (mpp80) cc_final: 0.5632 (mtm110) REVERT: A 1002 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6770 (tpm170) REVERT: A 1003 GLN cc_start: 0.8222 (tt0) cc_final: 0.7616 (tm-30) REVERT: A 1041 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6970 (tm-30) REVERT: A 1052 HIS cc_start: 0.8214 (t70) cc_final: 0.7949 (t-90) REVERT: A 1223 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6577 (tm-30) REVERT: A 1243 TYR cc_start: 0.7427 (m-80) cc_final: 0.6957 (m-80) REVERT: A 1489 ARG cc_start: 0.6850 (ptp90) cc_final: 0.6389 (ptt-90) REVERT: A 1555 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.6325 (mp10) REVERT: A 1587 MET cc_start: 0.8643 (mmm) cc_final: 0.8024 (ttm) REVERT: A 1831 LYS cc_start: 0.7370 (mmmt) cc_final: 0.7014 (mttm) REVERT: A 1927 ARG cc_start: 0.6591 (ttt180) cc_final: 0.6212 (ttt180) REVERT: A 1942 GLU cc_start: 0.8330 (mp0) cc_final: 0.7862 (mp0) REVERT: A 2006 ASN cc_start: 0.7346 (p0) cc_final: 0.6158 (p0) REVERT: A 2178 LEU cc_start: 0.3800 (OUTLIER) cc_final: 0.3549 (pp) REVERT: A 2190 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7956 (pt0) REVERT: A 2232 GLU cc_start: 0.8188 (mp0) cc_final: 0.7893 (mp0) outliers start: 38 outliers final: 27 residues processed: 232 average time/residue: 0.1188 time to fit residues: 41.8351 Evaluate side-chains 234 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 872 TYR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1240 HIS Chi-restraints excluded: chain A residue 1555 GLN Chi-restraints excluded: chain A residue 1692 PHE Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2171 ILE Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2202 HIS Chi-restraints excluded: chain A residue 2240 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 18 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 167 optimal weight: 0.0970 chunk 124 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 68 optimal weight: 7.9990 chunk 140 optimal weight: 0.4980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 338 ASN A 413 ASN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1053 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1214 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.151480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110576 restraints weight = 20063.881| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.97 r_work: 0.3129 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16213 Z= 0.131 Angle : 0.877 34.528 22082 Z= 0.366 Chirality : 0.077 2.075 2561 Planarity : 0.004 0.062 2714 Dihedral : 13.493 176.428 3044 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 2.23 % Allowed : 16.91 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1923 helix: 1.32 (0.16), residues: 1064 sheet: -1.32 (0.39), residues: 173 loop : -2.19 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 537 TYR 0.012 0.001 TYR A 400 PHE 0.023 0.001 PHE A 718 TRP 0.013 0.001 TRP A 605 HIS 0.003 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00293 (16189) covalent geometry : angle 0.86460 (22028) SS BOND : bond 0.00723 ( 6) SS BOND : angle 2.54698 ( 12) hydrogen bonds : bond 0.04332 ( 777) hydrogen bonds : angle 4.23766 ( 2280) Misc. bond : bond 0.00091 ( 4) link_BETA1-3 : bond 0.00691 ( 1) link_BETA1-3 : angle 1.98139 ( 3) link_BETA1-4 : bond 0.00526 ( 4) link_BETA1-4 : angle 2.68151 ( 12) link_BETA1-6 : bond 0.00974 ( 1) link_BETA1-6 : angle 2.53151 ( 3) link_NAG-ASN : bond 0.00736 ( 8) link_NAG-ASN : angle 3.67851 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 0.402 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 286 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: A 290 ARG cc_start: 0.7172 (tpp80) cc_final: 0.6420 (mmt180) REVERT: A 304 MET cc_start: 0.8084 (ppp) cc_final: 0.7643 (ptt) REVERT: A 420 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7128 (mm-30) REVERT: A 530 ASP cc_start: 0.7362 (p0) cc_final: 0.7109 (p0) REVERT: A 808 TYR cc_start: 0.7215 (m-10) cc_final: 0.6890 (m-10) REVERT: A 811 ARG cc_start: 0.7032 (ttm-80) cc_final: 0.6254 (ttm-80) REVERT: A 925 TRP cc_start: 0.7299 (m-90) cc_final: 0.6896 (m-10) REVERT: A 933 ASN cc_start: 0.7861 (m-40) cc_final: 0.7367 (m-40) REVERT: A 948 ARG cc_start: 0.6431 (tpt170) cc_final: 0.5513 (tpm170) REVERT: A 992 ARG cc_start: 0.6131 (mpp80) cc_final: 0.5512 (mtm110) REVERT: A 1003 GLN cc_start: 0.8309 (tt0) cc_final: 0.7563 (tm-30) REVERT: A 1041 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6867 (tm-30) REVERT: A 1045 MET cc_start: 0.7275 (tmm) cc_final: 0.7046 (tmm) REVERT: A 1052 HIS cc_start: 0.8116 (t70) cc_final: 0.7890 (t-90) REVERT: A 1243 TYR cc_start: 0.7420 (m-80) cc_final: 0.6936 (m-80) REVERT: A 1489 ARG cc_start: 0.6621 (ptp90) cc_final: 0.6337 (ptp90) REVERT: A 1555 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.6266 (mp10) REVERT: A 1587 MET cc_start: 0.8605 (mmm) cc_final: 0.7970 (ttp) REVERT: A 1712 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6525 (tt) REVERT: A 1779 TYR cc_start: 0.6526 (OUTLIER) cc_final: 0.6039 (m-10) REVERT: A 1831 LYS cc_start: 0.7383 (mmmt) cc_final: 0.7061 (mttm) REVERT: A 1885 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6384 (mt-10) REVERT: A 1927 ARG cc_start: 0.6555 (ttt180) cc_final: 0.6209 (ttt180) REVERT: A 1942 GLU cc_start: 0.8279 (mp0) cc_final: 0.7753 (mp0) REVERT: A 2178 LEU cc_start: 0.3812 (OUTLIER) cc_final: 0.3553 (pp) REVERT: A 2221 LEU cc_start: 0.6512 (mt) cc_final: 0.6290 (mt) REVERT: A 2232 GLU cc_start: 0.8258 (mp0) cc_final: 0.7875 (mp0) outliers start: 37 outliers final: 27 residues processed: 226 average time/residue: 0.1180 time to fit residues: 40.4156 Evaluate side-chains 234 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 872 TYR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1240 HIS Chi-restraints excluded: chain A residue 1555 GLN Chi-restraints excluded: chain A residue 1692 PHE Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2171 ILE Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2202 HIS Chi-restraints excluded: chain A residue 2240 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 131 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 15 optimal weight: 0.0970 chunk 14 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 0.0770 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 GLN ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110977 restraints weight = 19871.726| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.21 r_work: 0.3120 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16213 Z= 0.121 Angle : 0.854 34.465 22082 Z= 0.355 Chirality : 0.077 2.061 2561 Planarity : 0.004 0.064 2714 Dihedral : 13.120 176.148 3044 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.11 % Favored : 95.84 % Rotamer: Outliers : 2.36 % Allowed : 18.78 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1923 helix: 1.44 (0.16), residues: 1059 sheet: -1.17 (0.40), residues: 171 loop : -2.13 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.013 0.001 TYR A 400 PHE 0.024 0.001 PHE A 718 TRP 0.013 0.001 TRP A 605 HIS 0.003 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00266 (16189) covalent geometry : angle 0.84292 (22028) SS BOND : bond 0.00372 ( 6) SS BOND : angle 2.41190 ( 12) hydrogen bonds : bond 0.04079 ( 777) hydrogen bonds : angle 4.11655 ( 2280) Misc. bond : bond 0.00083 ( 4) link_BETA1-3 : bond 0.00727 ( 1) link_BETA1-3 : angle 1.95755 ( 3) link_BETA1-4 : bond 0.00375 ( 4) link_BETA1-4 : angle 2.15027 ( 12) link_BETA1-6 : bond 0.00778 ( 1) link_BETA1-6 : angle 1.91409 ( 3) link_NAG-ASN : bond 0.00693 ( 8) link_NAG-ASN : angle 3.47101 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.669 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 290 ARG cc_start: 0.7179 (tpp80) cc_final: 0.6400 (mmt180) REVERT: A 304 MET cc_start: 0.7937 (ppp) cc_final: 0.7627 (ptt) REVERT: A 530 ASP cc_start: 0.7414 (p0) cc_final: 0.7125 (p0) REVERT: A 808 TYR cc_start: 0.7262 (m-10) cc_final: 0.6932 (m-10) REVERT: A 811 ARG cc_start: 0.7122 (ttm-80) cc_final: 0.6381 (ttm-80) REVERT: A 925 TRP cc_start: 0.7218 (m-90) cc_final: 0.6626 (m-90) REVERT: A 992 ARG cc_start: 0.6086 (mpp80) cc_final: 0.5560 (mtm110) REVERT: A 1003 GLN cc_start: 0.8359 (tt0) cc_final: 0.7555 (tm-30) REVERT: A 1041 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6864 (tm-30) REVERT: A 1045 MET cc_start: 0.7308 (tmm) cc_final: 0.6621 (tmm) REVERT: A 1135 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8079 (pp30) REVERT: A 1243 TYR cc_start: 0.7492 (m-80) cc_final: 0.7043 (m-10) REVERT: A 1489 ARG cc_start: 0.6550 (ptp90) cc_final: 0.6286 (ptp90) REVERT: A 1587 MET cc_start: 0.8602 (mmm) cc_final: 0.7966 (ttp) REVERT: A 1712 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6666 (tt) REVERT: A 1779 TYR cc_start: 0.6599 (OUTLIER) cc_final: 0.6079 (m-10) REVERT: A 1824 ARG cc_start: 0.7421 (mtt180) cc_final: 0.7037 (ttt-90) REVERT: A 1885 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6502 (mt-10) REVERT: A 1927 ARG cc_start: 0.6527 (ttt180) cc_final: 0.6239 (ttt180) REVERT: A 1942 GLU cc_start: 0.8204 (mp0) cc_final: 0.7692 (mp0) REVERT: A 2178 LEU cc_start: 0.3970 (OUTLIER) cc_final: 0.3697 (pp) REVERT: A 2232 GLU cc_start: 0.8268 (mp0) cc_final: 0.7876 (mp0) outliers start: 39 outliers final: 28 residues processed: 228 average time/residue: 0.1144 time to fit residues: 39.6952 Evaluate side-chains 224 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 872 TYR Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1240 HIS Chi-restraints excluded: chain A residue 1692 PHE Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1784 LEU Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2171 ILE Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2202 HIS Chi-restraints excluded: chain A residue 2240 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 141 optimal weight: 0.6980 chunk 192 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 92 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 146 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110064 restraints weight = 20209.183| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.04 r_work: 0.3135 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16213 Z= 0.125 Angle : 0.845 34.608 22082 Z= 0.351 Chirality : 0.076 2.041 2561 Planarity : 0.004 0.063 2714 Dihedral : 12.927 176.239 3044 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 2.90 % Allowed : 19.20 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 1923 helix: 1.49 (0.16), residues: 1060 sheet: -1.10 (0.39), residues: 181 loop : -2.06 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.012 0.001 TYR A 400 PHE 0.025 0.001 PHE A 718 TRP 0.013 0.001 TRP A 605 HIS 0.003 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00280 (16189) covalent geometry : angle 0.83561 (22028) SS BOND : bond 0.00534 ( 6) SS BOND : angle 2.34441 ( 12) hydrogen bonds : bond 0.04003 ( 777) hydrogen bonds : angle 4.03207 ( 2280) Misc. bond : bond 0.00081 ( 4) link_BETA1-3 : bond 0.00700 ( 1) link_BETA1-3 : angle 2.12144 ( 3) link_BETA1-4 : bond 0.00332 ( 4) link_BETA1-4 : angle 2.01230 ( 12) link_BETA1-6 : bond 0.00867 ( 1) link_BETA1-6 : angle 1.52785 ( 3) link_NAG-ASN : bond 0.00647 ( 8) link_NAG-ASN : angle 3.29999 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.614 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 304 MET cc_start: 0.7995 (ppp) cc_final: 0.7716 (ptt) REVERT: A 316 MET cc_start: 0.6843 (mmp) cc_final: 0.5837 (ttt) REVERT: A 420 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 811 ARG cc_start: 0.6982 (ttm-80) cc_final: 0.6251 (ttm-80) REVERT: A 925 TRP cc_start: 0.7173 (m-90) cc_final: 0.6605 (m-90) REVERT: A 964 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.6757 (t-90) REVERT: A 992 ARG cc_start: 0.6009 (mpp80) cc_final: 0.5538 (mtm110) REVERT: A 1003 GLN cc_start: 0.8311 (tt0) cc_final: 0.7518 (tm-30) REVERT: A 1041 GLU cc_start: 0.7107 (tm-30) cc_final: 0.6833 (tm-30) REVERT: A 1045 MET cc_start: 0.7295 (tmm) cc_final: 0.6634 (tmm) REVERT: A 1239 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7124 (mptp) REVERT: A 1243 TYR cc_start: 0.7440 (m-80) cc_final: 0.6989 (m-10) REVERT: A 1489 ARG cc_start: 0.6325 (ptp90) cc_final: 0.6091 (ptp90) REVERT: A 1555 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6418 (mp10) REVERT: A 1587 MET cc_start: 0.8505 (mmm) cc_final: 0.7878 (ttp) REVERT: A 1596 ARG cc_start: 0.7360 (mmt180) cc_final: 0.7155 (mmt-90) REVERT: A 1712 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6733 (tt) REVERT: A 1772 TRP cc_start: 0.8020 (OUTLIER) cc_final: 0.7316 (t-100) REVERT: A 1779 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.5966 (m-10) REVERT: A 1824 ARG cc_start: 0.7434 (mtt180) cc_final: 0.7046 (ttt-90) REVERT: A 1885 GLU cc_start: 0.6801 (mt-10) cc_final: 0.6471 (mt-10) REVERT: A 1927 ARG cc_start: 0.6503 (ttt180) cc_final: 0.6242 (ttt180) REVERT: A 1942 GLU cc_start: 0.8161 (mp0) cc_final: 0.7639 (mp0) REVERT: A 2014 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7942 (ptt) REVERT: A 2221 LEU cc_start: 0.6427 (mt) cc_final: 0.6183 (mt) REVERT: A 2232 GLU cc_start: 0.8336 (mp0) cc_final: 0.7786 (mp0) outliers start: 48 outliers final: 29 residues processed: 227 average time/residue: 0.1173 time to fit residues: 40.5920 Evaluate side-chains 225 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 872 TYR Chi-restraints excluded: chain A residue 964 HIS Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1115 MET Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1240 HIS Chi-restraints excluded: chain A residue 1555 GLN Chi-restraints excluded: chain A residue 1692 PHE Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1772 TRP Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1784 LEU Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2171 ILE Chi-restraints excluded: chain A residue 2202 HIS Chi-restraints excluded: chain A residue 2240 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 74 optimal weight: 0.5980 chunk 15 optimal weight: 0.0670 chunk 28 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 12 optimal weight: 8.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 GLN ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.153104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111295 restraints weight = 19765.400| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.06 r_work: 0.3146 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16213 Z= 0.116 Angle : 0.839 34.516 22082 Z= 0.346 Chirality : 0.076 2.041 2561 Planarity : 0.004 0.067 2714 Dihedral : 12.835 176.253 3044 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.06 % Favored : 95.89 % Rotamer: Outliers : 2.66 % Allowed : 19.75 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.20), residues: 1923 helix: 1.58 (0.16), residues: 1058 sheet: -1.01 (0.39), residues: 181 loop : -2.02 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 290 TYR 0.012 0.001 TYR A 400 PHE 0.025 0.001 PHE A 718 TRP 0.013 0.001 TRP A 605 HIS 0.003 0.001 HIS A 964 Details of bonding type rmsd covalent geometry : bond 0.00252 (16189) covalent geometry : angle 0.83015 (22028) SS BOND : bond 0.00269 ( 6) SS BOND : angle 2.26011 ( 12) hydrogen bonds : bond 0.03835 ( 777) hydrogen bonds : angle 3.96211 ( 2280) Misc. bond : bond 0.00075 ( 4) link_BETA1-3 : bond 0.00664 ( 1) link_BETA1-3 : angle 2.00200 ( 3) link_BETA1-4 : bond 0.00350 ( 4) link_BETA1-4 : angle 1.94979 ( 12) link_BETA1-6 : bond 0.00783 ( 1) link_BETA1-6 : angle 1.47198 ( 3) link_NAG-ASN : bond 0.00664 ( 8) link_NAG-ASN : angle 3.17607 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.614 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 304 MET cc_start: 0.8084 (ppp) cc_final: 0.7834 (ptt) REVERT: A 599 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: A 600 ASP cc_start: 0.8401 (m-30) cc_final: 0.7833 (m-30) REVERT: A 811 ARG cc_start: 0.7064 (ttm-80) cc_final: 0.6365 (ttm-80) REVERT: A 925 TRP cc_start: 0.7225 (m-90) cc_final: 0.6591 (m-90) REVERT: A 992 ARG cc_start: 0.6027 (mpp80) cc_final: 0.5574 (mtm110) REVERT: A 1003 GLN cc_start: 0.8358 (tt0) cc_final: 0.7554 (tm-30) REVERT: A 1041 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6842 (tm-30) REVERT: A 1045 MET cc_start: 0.7321 (tmm) cc_final: 0.6748 (tmm) REVERT: A 1239 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7096 (mptp) REVERT: A 1243 TYR cc_start: 0.7435 (m-80) cc_final: 0.6957 (m-10) REVERT: A 1489 ARG cc_start: 0.6341 (ptp90) cc_final: 0.6056 (ptp90) REVERT: A 1555 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6524 (mp10) REVERT: A 1587 MET cc_start: 0.8470 (mmm) cc_final: 0.7885 (ttp) REVERT: A 1596 ARG cc_start: 0.7286 (mmt180) cc_final: 0.7073 (mmt-90) REVERT: A 1712 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6825 (tt) REVERT: A 1772 TRP cc_start: 0.8042 (OUTLIER) cc_final: 0.7340 (t-100) REVERT: A 1779 TYR cc_start: 0.6638 (OUTLIER) cc_final: 0.6114 (m-10) REVERT: A 1824 ARG cc_start: 0.7434 (mtt180) cc_final: 0.7055 (ttt-90) REVERT: A 1885 GLU cc_start: 0.6803 (mt-10) cc_final: 0.6504 (mt-10) REVERT: A 1927 ARG cc_start: 0.6427 (ttt180) cc_final: 0.6220 (ttt180) REVERT: A 1942 GLU cc_start: 0.8145 (mp0) cc_final: 0.7636 (mp0) REVERT: A 2014 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7987 (ptt) REVERT: A 2232 GLU cc_start: 0.8322 (mp0) cc_final: 0.7859 (mp0) outliers start: 44 outliers final: 29 residues processed: 214 average time/residue: 0.1201 time to fit residues: 39.0945 Evaluate side-chains 222 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 186 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1555 GLN Chi-restraints excluded: chain A residue 1692 PHE Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1729 LEU Chi-restraints excluded: chain A residue 1772 TRP Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1784 LEU Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2171 ILE Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2202 HIS Chi-restraints excluded: chain A residue 2240 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 148 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 294 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2006 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.147353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101201 restraints weight = 20441.793| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.21 r_work: 0.3061 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16213 Z= 0.146 Angle : 0.856 34.894 22082 Z= 0.357 Chirality : 0.076 2.025 2561 Planarity : 0.004 0.072 2714 Dihedral : 12.801 176.233 3042 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.47 % Favored : 95.48 % Rotamer: Outliers : 2.72 % Allowed : 20.11 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.20), residues: 1923 helix: 1.53 (0.16), residues: 1061 sheet: -1.08 (0.39), residues: 181 loop : -2.03 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.012 0.001 TYR A 400 PHE 0.026 0.001 PHE A 718 TRP 0.012 0.001 TRP A 605 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00343 (16189) covalent geometry : angle 0.84672 (22028) SS BOND : bond 0.00449 ( 6) SS BOND : angle 2.48400 ( 12) hydrogen bonds : bond 0.04135 ( 777) hydrogen bonds : angle 3.98532 ( 2280) Misc. bond : bond 0.00085 ( 4) link_BETA1-3 : bond 0.00648 ( 1) link_BETA1-3 : angle 1.95847 ( 3) link_BETA1-4 : bond 0.00325 ( 4) link_BETA1-4 : angle 1.98515 ( 12) link_BETA1-6 : bond 0.00694 ( 1) link_BETA1-6 : angle 1.42786 ( 3) link_NAG-ASN : bond 0.00598 ( 8) link_NAG-ASN : angle 3.17720 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.564 Fit side-chains TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 304 MET cc_start: 0.8093 (ppp) cc_final: 0.7846 (ptt) REVERT: A 600 ASP cc_start: 0.8368 (m-30) cc_final: 0.7772 (m-30) REVERT: A 811 ARG cc_start: 0.6992 (ttm-80) cc_final: 0.6297 (ttm-80) REVERT: A 925 TRP cc_start: 0.7114 (m-90) cc_final: 0.6574 (m-10) REVERT: A 992 ARG cc_start: 0.6001 (mpp80) cc_final: 0.5444 (mtm110) REVERT: A 1003 GLN cc_start: 0.8326 (tt0) cc_final: 0.7546 (tm-30) REVERT: A 1041 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6811 (tm-30) REVERT: A 1045 MET cc_start: 0.7299 (tmm) cc_final: 0.6729 (tmm) REVERT: A 1239 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7063 (mptp) REVERT: A 1243 TYR cc_start: 0.7409 (m-80) cc_final: 0.6932 (m-10) REVERT: A 1489 ARG cc_start: 0.6355 (ptp90) cc_final: 0.6033 (ptp90) REVERT: A 1555 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.6363 (mp10) REVERT: A 1587 MET cc_start: 0.8476 (mmm) cc_final: 0.7879 (ttp) REVERT: A 1712 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6854 (tt) REVERT: A 1772 TRP cc_start: 0.8056 (OUTLIER) cc_final: 0.7351 (t-100) REVERT: A 1779 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.6068 (m-10) REVERT: A 1824 ARG cc_start: 0.7446 (mtt180) cc_final: 0.7064 (ttt-90) REVERT: A 1885 GLU cc_start: 0.6908 (mt-10) cc_final: 0.6610 (mt-10) REVERT: A 1927 ARG cc_start: 0.6409 (ttt180) cc_final: 0.6186 (ttt180) REVERT: A 1942 GLU cc_start: 0.8185 (mp0) cc_final: 0.7681 (mp0) REVERT: A 2014 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7955 (ptt) REVERT: A 2232 GLU cc_start: 0.8258 (mp0) cc_final: 0.7753 (mp0) outliers start: 45 outliers final: 31 residues processed: 219 average time/residue: 0.1187 time to fit residues: 39.1309 Evaluate side-chains 229 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 192 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 442 PHE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 872 TYR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1555 GLN Chi-restraints excluded: chain A residue 1692 PHE Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1772 TRP Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1784 LEU Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2171 ILE Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2202 HIS Chi-restraints excluded: chain A residue 2240 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 111 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 99 optimal weight: 0.0670 chunk 73 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 148 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1727 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102802 restraints weight = 20350.318| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 3.11 r_work: 0.3097 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16213 Z= 0.122 Angle : 0.852 34.658 22082 Z= 0.354 Chirality : 0.076 2.031 2561 Planarity : 0.004 0.062 2714 Dihedral : 12.763 176.236 3042 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 2.29 % Allowed : 20.89 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1923 helix: 1.62 (0.16), residues: 1059 sheet: -1.00 (0.39), residues: 178 loop : -1.98 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.012 0.001 TYR A 400 PHE 0.024 0.001 PHE A 718 TRP 0.014 0.001 TRP A 605 HIS 0.003 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00270 (16189) covalent geometry : angle 0.84316 (22028) SS BOND : bond 0.00345 ( 6) SS BOND : angle 2.30347 ( 12) hydrogen bonds : bond 0.03858 ( 777) hydrogen bonds : angle 3.91955 ( 2280) Misc. bond : bond 0.00077 ( 4) link_BETA1-3 : bond 0.00632 ( 1) link_BETA1-3 : angle 1.82028 ( 3) link_BETA1-4 : bond 0.00346 ( 4) link_BETA1-4 : angle 1.89126 ( 12) link_BETA1-6 : bond 0.00806 ( 1) link_BETA1-6 : angle 1.48291 ( 3) link_NAG-ASN : bond 0.00732 ( 8) link_NAG-ASN : angle 3.25672 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.557 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 304 MET cc_start: 0.8127 (ppp) cc_final: 0.7852 (ptt) REVERT: A 316 MET cc_start: 0.6752 (mmp) cc_final: 0.5783 (ttt) REVERT: A 599 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: A 600 ASP cc_start: 0.8379 (m-30) cc_final: 0.7780 (m-30) REVERT: A 811 ARG cc_start: 0.7045 (ttm-80) cc_final: 0.6371 (ttm-80) REVERT: A 925 TRP cc_start: 0.7170 (m-90) cc_final: 0.6708 (m-10) REVERT: A 992 ARG cc_start: 0.5850 (mpp80) cc_final: 0.5323 (mtm110) REVERT: A 1003 GLN cc_start: 0.8333 (tt0) cc_final: 0.7552 (tm-30) REVERT: A 1041 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6785 (tm-30) REVERT: A 1045 MET cc_start: 0.7277 (tmm) cc_final: 0.6917 (tmm) REVERT: A 1239 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7073 (mptp) REVERT: A 1243 TYR cc_start: 0.7428 (m-80) cc_final: 0.6920 (m-10) REVERT: A 1489 ARG cc_start: 0.6361 (ptp90) cc_final: 0.6065 (ptp90) REVERT: A 1555 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.6435 (mp10) REVERT: A 1712 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6932 (tt) REVERT: A 1772 TRP cc_start: 0.8085 (OUTLIER) cc_final: 0.7382 (t-100) REVERT: A 1779 TYR cc_start: 0.6687 (OUTLIER) cc_final: 0.6041 (m-10) REVERT: A 1824 ARG cc_start: 0.7446 (mtt180) cc_final: 0.7068 (ttt-90) REVERT: A 1885 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6652 (mt-10) REVERT: A 1927 ARG cc_start: 0.6416 (ttt180) cc_final: 0.6204 (ttt180) REVERT: A 1942 GLU cc_start: 0.8159 (mp0) cc_final: 0.7655 (mp0) REVERT: A 2014 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7977 (ptt) REVERT: A 2232 GLU cc_start: 0.8263 (mp0) cc_final: 0.7758 (mp0) outliers start: 38 outliers final: 27 residues processed: 218 average time/residue: 0.1166 time to fit residues: 38.4255 Evaluate side-chains 221 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 872 TYR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1555 GLN Chi-restraints excluded: chain A residue 1692 PHE Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1729 LEU Chi-restraints excluded: chain A residue 1772 TRP Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1784 LEU Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2171 ILE Chi-restraints excluded: chain A residue 2202 HIS Chi-restraints excluded: chain A residue 2240 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 114 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.147400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101433 restraints weight = 20357.662| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.21 r_work: 0.3071 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16213 Z= 0.144 Angle : 0.863 34.850 22082 Z= 0.360 Chirality : 0.076 2.019 2561 Planarity : 0.004 0.063 2714 Dihedral : 12.749 176.195 3042 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.37 % Favored : 95.58 % Rotamer: Outliers : 2.23 % Allowed : 21.07 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1923 helix: 1.58 (0.16), residues: 1061 sheet: -1.03 (0.39), residues: 179 loop : -1.97 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.012 0.001 TYR A 400 PHE 0.025 0.001 PHE A 718 TRP 0.013 0.001 TRP A 339 HIS 0.003 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00337 (16189) covalent geometry : angle 0.85407 (22028) SS BOND : bond 0.00383 ( 6) SS BOND : angle 2.44540 ( 12) hydrogen bonds : bond 0.04036 ( 777) hydrogen bonds : angle 3.94709 ( 2280) Misc. bond : bond 0.00085 ( 4) link_BETA1-3 : bond 0.00509 ( 1) link_BETA1-3 : angle 1.67951 ( 3) link_BETA1-4 : bond 0.00319 ( 4) link_BETA1-4 : angle 1.92820 ( 12) link_BETA1-6 : bond 0.00603 ( 1) link_BETA1-6 : angle 1.43283 ( 3) link_NAG-ASN : bond 0.00789 ( 8) link_NAG-ASN : angle 3.17038 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.552 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 707 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 304 MET cc_start: 0.8125 (ppp) cc_final: 0.7859 (ptt) REVERT: A 316 MET cc_start: 0.6825 (mmp) cc_final: 0.5944 (ttt) REVERT: A 600 ASP cc_start: 0.8381 (m-30) cc_final: 0.7778 (m-30) REVERT: A 811 ARG cc_start: 0.7077 (ttm-80) cc_final: 0.6445 (ttm-80) REVERT: A 925 TRP cc_start: 0.7161 (m-90) cc_final: 0.6548 (m-90) REVERT: A 992 ARG cc_start: 0.6044 (mpp80) cc_final: 0.5566 (mtm110) REVERT: A 1003 GLN cc_start: 0.8357 (tt0) cc_final: 0.7546 (tm-30) REVERT: A 1041 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6768 (tm-30) REVERT: A 1045 MET cc_start: 0.7271 (tmm) cc_final: 0.6916 (tmm) REVERT: A 1239 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7137 (mptp) REVERT: A 1243 TYR cc_start: 0.7442 (m-80) cc_final: 0.6944 (m-10) REVERT: A 1489 ARG cc_start: 0.6323 (ptp90) cc_final: 0.6076 (ptp90) REVERT: A 1555 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.6431 (mp10) REVERT: A 1712 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6918 (tt) REVERT: A 1772 TRP cc_start: 0.8110 (OUTLIER) cc_final: 0.7312 (t-100) REVERT: A 1779 TYR cc_start: 0.6820 (OUTLIER) cc_final: 0.6179 (m-10) REVERT: A 1824 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7100 (ttt-90) REVERT: A 1885 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6751 (mt-10) REVERT: A 1927 ARG cc_start: 0.6425 (ttt180) cc_final: 0.6224 (ttt180) REVERT: A 1942 GLU cc_start: 0.8194 (mp0) cc_final: 0.7683 (mp0) REVERT: A 2014 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8040 (ptt) REVERT: A 2232 GLU cc_start: 0.8227 (mp0) cc_final: 0.7729 (mp0) outliers start: 37 outliers final: 29 residues processed: 207 average time/residue: 0.1297 time to fit residues: 40.2786 Evaluate side-chains 223 residues out of total 1708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 727 TYR Chi-restraints excluded: chain A residue 787 THR Chi-restraints excluded: chain A residue 791 LYS Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 872 TYR Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1143 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain A residue 1239 LYS Chi-restraints excluded: chain A residue 1555 GLN Chi-restraints excluded: chain A residue 1692 PHE Chi-restraints excluded: chain A residue 1712 LEU Chi-restraints excluded: chain A residue 1772 TRP Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1784 LEU Chi-restraints excluded: chain A residue 1789 SER Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1990 THR Chi-restraints excluded: chain A residue 2014 MET Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2042 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2171 ILE Chi-restraints excluded: chain A residue 2189 PHE Chi-restraints excluded: chain A residue 2202 HIS Chi-restraints excluded: chain A residue 2240 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 153 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 188 optimal weight: 0.4980 chunk 162 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102261 restraints weight = 20327.013| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.09 r_work: 0.3102 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16213 Z= 0.128 Angle : 0.859 34.764 22082 Z= 0.358 Chirality : 0.076 2.021 2561 Planarity : 0.004 0.058 2714 Dihedral : 12.717 176.182 3042 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 2.42 % Allowed : 21.07 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1923 helix: 1.62 (0.16), residues: 1059 sheet: -0.73 (0.41), residues: 170 loop : -1.97 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 948 TYR 0.012 0.001 TYR A 400 PHE 0.027 0.001 PHE A 718 TRP 0.014 0.001 TRP A 605 HIS 0.003 0.001 HIS A1354 Details of bonding type rmsd covalent geometry : bond 0.00292 (16189) covalent geometry : angle 0.85135 (22028) SS BOND : bond 0.00376 ( 6) SS BOND : angle 2.29316 ( 12) hydrogen bonds : bond 0.03881 ( 777) hydrogen bonds : angle 3.90898 ( 2280) Misc. bond : bond 0.00077 ( 4) link_BETA1-3 : bond 0.00593 ( 1) link_BETA1-3 : angle 1.62916 ( 3) link_BETA1-4 : bond 0.00335 ( 4) link_BETA1-4 : angle 1.86434 ( 12) link_BETA1-6 : bond 0.00762 ( 1) link_BETA1-6 : angle 1.43628 ( 3) link_NAG-ASN : bond 0.00764 ( 8) link_NAG-ASN : angle 3.06828 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3597.11 seconds wall clock time: 62 minutes 21.53 seconds (3741.53 seconds total)