Starting phenix.real_space_refine on Mon Sep 14 15:05:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7elb_31179/09_2026/7elb_31179_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7elb_31179/09_2026/7elb_31179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7elb_31179/09_2026/7elb_31179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7elb_31179/09_2026/7elb_31179.map" model { file = "/net/cci-nas-00/data/ceres_data/7elb_31179/09_2026/7elb_31179_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7elb_31179/09_2026/7elb_31179_neut.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 8 6.06 5 S 206 5.16 5 C 19756 2.51 5 N 5182 2.21 5 O 5858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31012 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1937, 15094 Classifications: {'peptide': 1937} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 56, 'TRANS': 1880} Chain breaks: 18 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 448 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 11, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 15, 'HIS:plan': 3, 'PHE:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 257 Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MN': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 284 145.402 137.655 73.723 1.00145.16 S ATOM 2195 SG CYS A 287 146.588 138.413 69.997 1.00148.88 S ATOM 3474 SG CYS A 470 147.358 140.873 73.058 1.00171.01 S ATOM 11412 SG CYS A1650 89.959 130.417 80.520 1.00119.28 S ATOM 11425 SG CYS A1652 89.093 129.011 83.562 1.00125.98 S ATOM 11444 SG CYS A1655 93.137 129.302 81.393 1.00104.84 S ATOM 11516 SG CYS A1664 89.698 126.991 80.887 1.00 95.84 S ATOM 15155 SG CYS B 39 150.675 106.231 98.956 1.00150.30 S ATOM 15176 SG CYS B 42 153.037 107.294 96.452 1.00142.09 S ATOM 15310 SG CYS B 58 153.150 107.267 101.022 1.00172.54 S ATOM 15335 SG CYS B 61 151.219 109.639 99.400 1.00160.00 S ATOM 15258 SG CYS B 52 143.184 104.537 105.863 1.00186.87 S ATOM 15425 SG CYS B 72 142.335 107.219 103.928 1.00174.10 S ATOM 15449 SG CYS B 75 140.309 104.499 103.986 1.00161.30 S Restraints were copied for chains: C, D Time building chain proxies: 26.73, per 1000 atoms: 0.86 Number of scatterers: 31012 At special positions: 0 Unit cell: (182.52, 170.64, 140.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 Mn 2 24.99 S 206 16.00 O 5858 8.00 N 5182 7.00 C 19756 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 60 " distance=2.05 Simple disulfide: pdb=" SG CYS A1691 " - pdb=" SG CYS A1776 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 60 " distance=2.05 Simple disulfide: pdb=" SG CYS C1691 " - pdb=" SG CYS C1776 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" ND1 HIS A 472 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 284 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 470 " pdb="ZN ZN A2302 " - pdb=" SG CYS A 287 " pdb=" ZN A2303 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1650 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1664 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1652 " pdb="ZN ZN A2303 " - pdb=" SG CYS A1655 " pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 58 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 39 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb=" ZN B 102 " pdb="ZN ZN B 102 " - pdb=" NE2 HIS B 55 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 52 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 102 " - pdb=" SG CYS B 72 " pdb=" ZN C2302 " pdb="ZN ZN C2302 " - pdb=" ND1 HIS C 472 " pdb="ZN ZN C2302 " - pdb=" SG CYS C 284 " pdb="ZN ZN C2302 " - pdb=" SG CYS C 470 " pdb="ZN ZN C2302 " - pdb=" SG CYS C 287 " pdb=" ZN C2303 " pdb="ZN ZN C2303 " - pdb=" SG CYS C1650 " pdb="ZN ZN C2303 " - pdb=" SG CYS C1664 " pdb="ZN ZN C2303 " - pdb=" SG CYS C1652 " pdb="ZN ZN C2303 " - pdb=" SG CYS C1655 " pdb=" ZN D 101 " pdb="ZN ZN D 101 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 101 " - pdb=" SG CYS D 58 " pdb="ZN ZN D 101 " - pdb=" SG CYS D 39 " pdb="ZN ZN D 101 " - pdb=" SG CYS D 42 " pdb=" ZN D 102 " pdb="ZN ZN D 102 " - pdb=" NE2 HIS D 55 " pdb="ZN ZN D 102 " - pdb=" SG CYS D 52 " pdb="ZN ZN D 102 " - pdb=" SG CYS D 75 " pdb="ZN ZN D 102 " - pdb=" SG CYS D 72 " Number of angles added : 36 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7552 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 22 sheets defined 49.4% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.759A pdb=" N LYS A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.729A pdb=" N GLY A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 28 " --> pdb=" O HIS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 57 removed outlier: 4.160A pdb=" N LEU A 39 " --> pdb=" O PRO A 35 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N THR A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 108 through 125 removed outlier: 3.830A pdb=" N SER A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 156 through 171 Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.980A pdb=" N GLN A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 232 through 248 removed outlier: 3.862A pdb=" N ASP A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 274 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.675A pdb=" N ASN A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 303 Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.729A pdb=" N GLY A 339 " --> pdb=" O ASN A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 365 Processing helix chain 'A' and resid 389 through 391 No H-bonds generated for 'chain 'A' and resid 389 through 391' Processing helix chain 'A' and resid 396 through 405 removed outlier: 3.519A pdb=" N LYS A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.683A pdb=" N LEU A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 481 through 502 Processing helix chain 'A' and resid 574 through 578 removed outlier: 3.587A pdb=" N ARG A 577 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 578 " --> pdb=" O PRO A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 574 through 578' Processing helix chain 'A' and resid 579 through 583 removed outlier: 3.595A pdb=" N VAL A 582 " --> pdb=" O PHE A 579 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 583' Processing helix chain 'A' and resid 586 through 598 Processing helix chain 'A' and resid 605 through 622 Proline residue: A 611 - end of helix Processing helix chain 'A' and resid 625 through 644 removed outlier: 3.735A pdb=" N GLN A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 644 " --> pdb=" O MET A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 removed outlier: 4.098A pdb=" N VAL A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 Processing helix chain 'A' and resid 702 through 705 Processing helix chain 'A' and resid 712 through 732 Proline residue: A 727 - end of helix Processing helix chain 'A' and resid 745 through 760 Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.670A pdb=" N ARG A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 852 Processing helix chain 'A' and resid 863 through 874 removed outlier: 3.753A pdb=" N TYR A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 874 " --> pdb=" O LEU A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 896 removed outlier: 4.114A pdb=" N ALA A 896 " --> pdb=" O LEU A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 921 Processing helix chain 'A' and resid 963 through 968 removed outlier: 4.482A pdb=" N VAL A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 968 " --> pdb=" O LEU A 964 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 963 through 968' Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.763A pdb=" N VAL A 974 " --> pdb=" O ASP A 971 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 975 " --> pdb=" O PRO A 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 975' Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.864A pdb=" N VAL A 979 " --> pdb=" O PRO A 976 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 980 " --> pdb=" O PRO A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 980' Processing helix chain 'A' and resid 981 through 989 removed outlier: 3.820A pdb=" N ASP A 985 " --> pdb=" O LYS A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 3.715A pdb=" N ASP A1021 " --> pdb=" O SER A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1035 Processing helix chain 'A' and resid 1135 through 1156 Processing helix chain 'A' and resid 1163 through 1181 Processing helix chain 'A' and resid 1197 through 1208 removed outlier: 3.853A pdb=" N PHE A1201 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1233 removed outlier: 3.635A pdb=" N HIS A1233 " --> pdb=" O LYS A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1249 Processing helix chain 'A' and resid 1264 through 1273 Processing helix chain 'A' and resid 1295 through 1319 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1395 through 1405 removed outlier: 3.711A pdb=" N PHE A1399 " --> pdb=" O LEU A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1428 Processing helix chain 'A' and resid 1435 through 1450 Processing helix chain 'A' and resid 1472 through 1485 removed outlier: 3.786A pdb=" N PHE A1485 " --> pdb=" O ILE A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1507 Processing helix chain 'A' and resid 1513 through 1520 removed outlier: 3.573A pdb=" N ASN A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1537 through 1545 removed outlier: 3.549A pdb=" N LEU A1545 " --> pdb=" O VAL A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1590 removed outlier: 3.930A pdb=" N LYS A1583 " --> pdb=" O PRO A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1625 Processing helix chain 'A' and resid 1639 through 1645 removed outlier: 3.613A pdb=" N VAL A1643 " --> pdb=" O TYR A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 3.663A pdb=" N ASN A1669 " --> pdb=" O ASN A1666 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1694 removed outlier: 3.595A pdb=" N GLY A1694 " --> pdb=" O ALA A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1744 Processing helix chain 'A' and resid 1744 through 1750 Processing helix chain 'A' and resid 1758 through 1764 removed outlier: 3.743A pdb=" N SER A1762 " --> pdb=" O ASP A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1783 removed outlier: 3.594A pdb=" N MET A1781 " --> pdb=" O ILE A1777 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A1782 " --> pdb=" O ALA A1778 " (cutoff:3.500A) Processing helix chain 'A' and resid 1788 through 1793 removed outlier: 3.729A pdb=" N LEU A1793 " --> pdb=" O ILE A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1809 Processing helix chain 'A' and resid 1826 through 1843 removed outlier: 3.605A pdb=" N ILE A1830 " --> pdb=" O SER A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1860 through 1864 removed outlier: 4.308A pdb=" N VAL A1863 " --> pdb=" O PHE A1860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1875 through 1884 removed outlier: 3.580A pdb=" N VAL A1884 " --> pdb=" O PHE A1880 " (cutoff:3.500A) Processing helix chain 'A' and resid 1919 through 1924 removed outlier: 4.604A pdb=" N LEU A1924 " --> pdb=" O ASP A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1941 Processing helix chain 'A' and resid 2003 through 2015 removed outlier: 3.501A pdb=" N ALA A2015 " --> pdb=" O VAL A2011 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2037 Processing helix chain 'A' and resid 2101 through 2109 Processing helix chain 'A' and resid 2113 through 2129 removed outlier: 3.582A pdb=" N VAL A2117 " --> pdb=" O ASP A2113 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP A2125 " --> pdb=" O LEU A2121 " (cutoff:3.500A) Proline residue: A2126 - end of helix Processing helix chain 'A' and resid 2139 through 2146 Processing helix chain 'A' and resid 2150 through 2157 removed outlier: 4.280A pdb=" N ILE A2157 " --> pdb=" O LEU A2153 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.605A pdb=" N HIS B 62 " --> pdb=" O CYS B 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 12 removed outlier: 3.758A pdb=" N LYS C 9 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.731A pdb=" N GLY C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 28 " --> pdb=" O HIS C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 57 removed outlier: 4.162A pdb=" N LEU C 39 " --> pdb=" O PRO C 35 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 108 through 125 removed outlier: 3.829A pdb=" N SER C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 156 through 171 Processing helix chain 'C' and resid 181 through 190 removed outlier: 3.981A pdb=" N GLN C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 188 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 223 Processing helix chain 'C' and resid 232 through 248 removed outlier: 3.862A pdb=" N ASP C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 274 Processing helix chain 'C' and resid 284 through 289 removed outlier: 3.675A pdb=" N ASN C 288 " --> pdb=" O CYS C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 303 Processing helix chain 'C' and resid 322 through 339 removed outlier: 3.729A pdb=" N GLY C 339 " --> pdb=" O ASN C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 365 Processing helix chain 'C' and resid 389 through 391 No H-bonds generated for 'chain 'C' and resid 389 through 391' Processing helix chain 'C' and resid 396 through 405 removed outlier: 3.519A pdb=" N LYS C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 420 Processing helix chain 'C' and resid 440 through 451 removed outlier: 3.683A pdb=" N LEU C 444 " --> pdb=" O ASP C 440 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 451 " --> pdb=" O ILE C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 481 through 502 Processing helix chain 'C' and resid 574 through 578 removed outlier: 3.588A pdb=" N ARG C 577 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE C 578 " --> pdb=" O PRO C 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 574 through 578' Processing helix chain 'C' and resid 579 through 583 removed outlier: 3.595A pdb=" N VAL C 582 " --> pdb=" O PHE C 579 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE C 583 " --> pdb=" O LEU C 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 579 through 583' Processing helix chain 'C' and resid 586 through 598 Processing helix chain 'C' and resid 605 through 622 Proline residue: C 611 - end of helix Processing helix chain 'C' and resid 625 through 644 removed outlier: 3.735A pdb=" N GLN C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN C 644 " --> pdb=" O MET C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 680 removed outlier: 4.098A pdb=" N VAL C 667 " --> pdb=" O SER C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 701 Processing helix chain 'C' and resid 702 through 705 Processing helix chain 'C' and resid 712 through 732 Proline residue: C 727 - end of helix Processing helix chain 'C' and resid 745 through 760 Processing helix chain 'C' and resid 776 through 789 removed outlier: 3.669A pdb=" N ARG C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 852 Processing helix chain 'C' and resid 863 through 874 removed outlier: 3.752A pdb=" N TYR C 867 " --> pdb=" O ASP C 863 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR C 874 " --> pdb=" O LEU C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 896 removed outlier: 4.113A pdb=" N ALA C 896 " --> pdb=" O LEU C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 921 Processing helix chain 'C' and resid 963 through 968 removed outlier: 4.484A pdb=" N VAL C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 968 " --> pdb=" O LEU C 964 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 963 through 968' Processing helix chain 'C' and resid 971 through 975 removed outlier: 3.763A pdb=" N VAL C 974 " --> pdb=" O ASP C 971 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 975 " --> pdb=" O PRO C 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 971 through 975' Processing helix chain 'C' and resid 976 through 980 removed outlier: 3.863A pdb=" N VAL C 979 " --> pdb=" O PRO C 976 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 980 " --> pdb=" O PRO C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 980' Processing helix chain 'C' and resid 981 through 989 removed outlier: 3.820A pdb=" N ASP C 985 " --> pdb=" O LYS C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1021 removed outlier: 3.716A pdb=" N ASP C1021 " --> pdb=" O SER C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1024 through 1035 Processing helix chain 'C' and resid 1135 through 1156 Processing helix chain 'C' and resid 1163 through 1181 Processing helix chain 'C' and resid 1197 through 1208 removed outlier: 3.852A pdb=" N PHE C1201 " --> pdb=" O SER C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1221 through 1233 removed outlier: 3.635A pdb=" N HIS C1233 " --> pdb=" O LYS C1229 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1249 Processing helix chain 'C' and resid 1264 through 1273 Processing helix chain 'C' and resid 1295 through 1319 Processing helix chain 'C' and resid 1351 through 1365 Processing helix chain 'C' and resid 1395 through 1405 removed outlier: 3.712A pdb=" N PHE C1399 " --> pdb=" O LEU C1395 " (cutoff:3.500A) Processing helix chain 'C' and resid 1411 through 1428 Processing helix chain 'C' and resid 1435 through 1450 Processing helix chain 'C' and resid 1472 through 1485 removed outlier: 3.786A pdb=" N PHE C1485 " --> pdb=" O ILE C1481 " (cutoff:3.500A) Processing helix chain 'C' and resid 1489 through 1507 Processing helix chain 'C' and resid 1513 through 1520 removed outlier: 3.575A pdb=" N ASN C1517 " --> pdb=" O GLU C1513 " (cutoff:3.500A) Processing helix chain 'C' and resid 1523 through 1535 Processing helix chain 'C' and resid 1537 through 1545 removed outlier: 3.549A pdb=" N LEU C1545 " --> pdb=" O VAL C1541 " (cutoff:3.500A) Processing helix chain 'C' and resid 1579 through 1590 removed outlier: 3.929A pdb=" N LYS C1583 " --> pdb=" O PRO C1579 " (cutoff:3.500A) Processing helix chain 'C' and resid 1613 through 1625 Processing helix chain 'C' and resid 1639 through 1645 removed outlier: 3.611A pdb=" N VAL C1643 " --> pdb=" O TYR C1639 " (cutoff:3.500A) Processing helix chain 'C' and resid 1665 through 1669 removed outlier: 3.662A pdb=" N ASN C1669 " --> pdb=" O ASN C1666 " (cutoff:3.500A) Processing helix chain 'C' and resid 1678 through 1694 removed outlier: 3.596A pdb=" N GLY C1694 " --> pdb=" O ALA C1690 " (cutoff:3.500A) Processing helix chain 'C' and resid 1735 through 1744 Processing helix chain 'C' and resid 1744 through 1750 Processing helix chain 'C' and resid 1758 through 1764 removed outlier: 3.743A pdb=" N SER C1762 " --> pdb=" O ASP C1758 " (cutoff:3.500A) Processing helix chain 'C' and resid 1777 through 1783 removed outlier: 3.597A pdb=" N MET C1781 " --> pdb=" O ILE C1777 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C1782 " --> pdb=" O ALA C1778 " (cutoff:3.500A) Processing helix chain 'C' and resid 1788 through 1793 removed outlier: 3.728A pdb=" N LEU C1793 " --> pdb=" O ILE C1789 " (cutoff:3.500A) Processing helix chain 'C' and resid 1805 through 1809 Processing helix chain 'C' and resid 1826 through 1843 removed outlier: 3.606A pdb=" N ILE C1830 " --> pdb=" O SER C1826 " (cutoff:3.500A) Processing helix chain 'C' and resid 1860 through 1864 removed outlier: 4.307A pdb=" N VAL C1863 " --> pdb=" O PHE C1860 " (cutoff:3.500A) Processing helix chain 'C' and resid 1875 through 1884 removed outlier: 3.580A pdb=" N VAL C1884 " --> pdb=" O PHE C1880 " (cutoff:3.500A) Processing helix chain 'C' and resid 1919 through 1924 removed outlier: 4.604A pdb=" N LEU C1924 " --> pdb=" O ASP C1920 " (cutoff:3.500A) Processing helix chain 'C' and resid 1933 through 1941 Processing helix chain 'C' and resid 2003 through 2015 removed outlier: 3.501A pdb=" N ALA C2015 " --> pdb=" O VAL C2011 " (cutoff:3.500A) Processing helix chain 'C' and resid 2031 through 2037 Processing helix chain 'C' and resid 2101 through 2109 Processing helix chain 'C' and resid 2113 through 2129 removed outlier: 3.582A pdb=" N VAL C2117 " --> pdb=" O ASP C2113 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP C2125 " --> pdb=" O LEU C2121 " (cutoff:3.500A) Proline residue: C2126 - end of helix Processing helix chain 'C' and resid 2139 through 2146 Processing helix chain 'C' and resid 2150 through 2157 removed outlier: 4.280A pdb=" N ILE C2157 " --> pdb=" O LEU C2153 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 69 removed outlier: 3.604A pdb=" N HIS D 62 " --> pdb=" O CYS D 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 94 removed outlier: 6.959A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU A 100 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 387 Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 534 removed outlier: 6.040A pdb=" N LEU A 559 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLU A 567 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1129 through 1134 removed outlier: 3.854A pdb=" N LEU A1119 " --> pdb=" O GLU A1237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1379 through 1381 Processing sheet with id=AA7, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1630 through 1631 Processing sheet with id=AA9, first strand: chain 'A' and resid 1716 through 1719 Processing sheet with id=AB1, first strand: chain 'A' and resid 1847 through 1848 removed outlier: 6.652A pdb=" N PHE A2085 " --> pdb=" O LEU A2092 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1952 through 1961 removed outlier: 6.597A pdb=" N SER A1972 " --> pdb=" O GLY A2000 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY A2000 " --> pdb=" O SER A1972 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU A1974 " --> pdb=" O VAL A1998 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N VAL A1998 " --> pdb=" O GLU A1974 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A1976 " --> pdb=" O GLN A1996 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN A1996 " --> pdb=" O ILE A1976 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP A1978 " --> pdb=" O VAL A1994 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A1994 " --> pdb=" O ASP A1978 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY A1980 " --> pdb=" O VAL A1992 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 94 removed outlier: 6.961A pdb=" N LEU C 98 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE C 140 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU C 100 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP C 142 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU C 102 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ARG C 144 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 104 " --> pdb=" O ARG C 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 258 through 260 Processing sheet with id=AB5, first strand: chain 'C' and resid 385 through 387 Processing sheet with id=AB6, first strand: chain 'C' and resid 529 through 534 removed outlier: 6.040A pdb=" N LEU C 559 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N GLU C 567 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1129 through 1134 removed outlier: 3.852A pdb=" N LEU C1119 " --> pdb=" O GLU C1237 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1379 through 1381 Processing sheet with id=AB9, first strand: chain 'C' and resid 1548 through 1549 Processing sheet with id=AC1, first strand: chain 'C' and resid 1630 through 1631 Processing sheet with id=AC2, first strand: chain 'C' and resid 1716 through 1719 Processing sheet with id=AC3, first strand: chain 'C' and resid 1847 through 1848 removed outlier: 6.652A pdb=" N PHE C2085 " --> pdb=" O LEU C2092 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1952 through 1961 removed outlier: 6.598A pdb=" N SER C1972 " --> pdb=" O GLY C2000 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY C2000 " --> pdb=" O SER C1972 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU C1974 " --> pdb=" O VAL C1998 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL C1998 " --> pdb=" O GLU C1974 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C1976 " --> pdb=" O GLN C1996 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLN C1996 " --> pdb=" O ILE C1976 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP C1978 " --> pdb=" O VAL C1994 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL C1994 " --> pdb=" O ASP C1978 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY C1980 " --> pdb=" O VAL C1992 " (cutoff:3.500A) 1366 hydrogen bonds defined for protein. 3972 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: 5.99 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 10055 1.35 - 1.47: 7124 1.47 - 1.59: 14063 1.59 - 1.71: 0 1.71 - 1.83: 294 Bond restraints: 31536 Sorted by residual: bond pdb=" N GLY A1732 " pdb=" CA GLY A1732 " ideal model delta sigma weight residual 1.447 1.496 -0.049 1.23e-02 6.61e+03 1.56e+01 bond pdb=" C LEU A1731 " pdb=" N GLY A1732 " ideal model delta sigma weight residual 1.329 1.376 -0.047 1.62e-02 3.81e+03 8.45e+00 bond pdb=" N GLY C1732 " pdb=" CA GLY C1732 " ideal model delta sigma weight residual 1.447 1.476 -0.029 1.89e-02 2.80e+03 2.38e+00 bond pdb=" CB GLU C2072 " pdb=" CG GLU C2072 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 bond pdb=" C MET C1733 " pdb=" O MET C1733 " ideal model delta sigma weight residual 1.234 1.248 -0.014 1.16e-02 7.43e+03 1.41e+00 ... (remaining 31531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 41868 1.83 - 3.65: 610 3.65 - 5.48: 123 5.48 - 7.30: 16 7.30 - 9.13: 9 Bond angle restraints: 42626 Sorted by residual: angle pdb=" C LEU A1731 " pdb=" N GLY A1732 " pdb=" CA GLY A1732 " ideal model delta sigma weight residual 122.55 130.16 -7.61 1.10e+00 8.26e-01 4.79e+01 angle pdb=" CA GLY C1732 " pdb=" C GLY C1732 " pdb=" O GLY C1732 " ideal model delta sigma weight residual 121.53 117.62 3.91 1.06e+00 8.90e-01 1.36e+01 angle pdb=" CB GLU C2072 " pdb=" CG GLU C2072 " pdb=" CD GLU C2072 " ideal model delta sigma weight residual 112.60 117.50 -4.90 1.70e+00 3.46e-01 8.32e+00 angle pdb=" CB GLU A2072 " pdb=" CG GLU A2072 " pdb=" CD GLU A2072 " ideal model delta sigma weight residual 112.60 117.49 -4.89 1.70e+00 3.46e-01 8.28e+00 angle pdb=" C ASN C1798 " pdb=" N SER C1799 " pdb=" CA SER C1799 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.18e+00 ... (remaining 42621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 17408 16.51 - 33.02: 1294 33.02 - 49.52: 250 49.52 - 66.03: 124 66.03 - 82.54: 30 Dihedral angle restraints: 19106 sinusoidal: 7510 harmonic: 11596 Sorted by residual: dihedral pdb=" CA THR C1753 " pdb=" C THR C1753 " pdb=" N PRO C1754 " pdb=" CA PRO C1754 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR A1753 " pdb=" C THR A1753 " pdb=" N PRO A1754 " pdb=" CA PRO A1754 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CB CYS C1691 " pdb=" SG CYS C1691 " pdb=" SG CYS C1776 " pdb=" CB CYS C1776 " ideal model delta sinusoidal sigma weight residual 93.00 57.30 35.70 1 1.00e+01 1.00e-02 1.80e+01 ... (remaining 19103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3807 0.045 - 0.089: 961 0.089 - 0.134: 183 0.134 - 0.178: 17 0.178 - 0.223: 2 Chirality restraints: 4970 Sorted by residual: chirality pdb=" CB ILE C1510 " pdb=" CA ILE C1510 " pdb=" CG1 ILE C1510 " pdb=" CG2 ILE C1510 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB ILE A1510 " pdb=" CA ILE A1510 " pdb=" CG1 ILE A1510 " pdb=" CG2 ILE A1510 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL C1949 " pdb=" CA VAL C1949 " pdb=" CG1 VAL C1949 " pdb=" CG2 VAL C1949 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 4967 not shown) Planarity restraints: 5398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A2017 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.29e+00 pdb=" N PRO A2018 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A2018 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A2018 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C2017 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO C2018 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C2018 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C2018 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 354 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" CG ASP C 354 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP C 354 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP C 354 " -0.013 2.00e-02 2.50e+03 ... (remaining 5395 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 288 2.60 - 3.17: 27186 3.17 - 3.75: 46637 3.75 - 4.32: 61541 4.32 - 4.90: 100556 Nonbonded interactions: 236208 Sorted by model distance: nonbonded pdb=" OD2 ASP C1330 " pdb="MN MN C2301 " model vdw 2.021 2.320 nonbonded pdb=" OD2 ASP A1330 " pdb="MN MN A2301 " model vdw 2.022 2.320 nonbonded pdb=" O SER C1553 " pdb=" OG SER C1553 " model vdw 2.168 3.040 nonbonded pdb=" O SER A1553 " pdb=" OG SER A1553 " model vdw 2.169 3.040 nonbonded pdb=" OD1 ASP C 650 " pdb=" OG SER C 653 " model vdw 2.208 3.040 ... (remaining 236203 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 48.650 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 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 : 0.003 0.102 31572 Z= 0.143 Angle : 0.810 37.589 42670 Z= 0.339 Chirality : 0.039 0.223 4970 Planarity : 0.004 0.063 5398 Dihedral : 13.339 82.541 11542 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.07 % Allowed : 4.12 % Favored : 93.81 % 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: -3.36 (0.12), residues: 3892 helix: -0.90 (0.11), residues: 1790 sheet: -1.82 (0.27), residues: 320 loop : -3.86 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 67 TYR 0.009 0.001 TYR C1019 PHE 0.024 0.001 PHE C1511 TRP 0.007 0.001 TRP A 598 HIS 0.003 0.001 HIS C 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 (31536) covalent geometry : angle 0.58996 / 0.32 (42626) SS BOND : bond 0.01295 / 0.65 ( 4) SS BOND : angle 2.37247 / 1.50 ( 8) hydrogen bonds : bond 0.14769 / 9.85 ( 1366) hydrogen bonds : angle 5.45133 / 3.78 ( 3972) metal coordination : bond 0.06988 / 4.17 ( 32) metal coordination : angle 19.08637 / 11.08 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 690 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.9217 (pp) cc_final: 0.8866 (pp) REVERT: A 501 MET cc_start: 0.7652 (tpp) cc_final: 0.7174 (tpp) REVERT: A 593 GLU cc_start: 0.8943 (tt0) cc_final: 0.8662 (tm-30) REVERT: A 594 GLU cc_start: 0.7898 (tp30) cc_final: 0.7199 (tp30) REVERT: A 598 TRP cc_start: 0.7872 (m-10) cc_final: 0.7252 (m-10) REVERT: A 637 TYR cc_start: 0.7831 (m-80) cc_final: 0.7614 (m-10) REVERT: A 659 CYS cc_start: 0.6519 (OUTLIER) cc_final: 0.6043 (p) REVERT: A 696 LEU cc_start: 0.9004 (mt) cc_final: 0.8803 (mt) REVERT: A 838 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7022 (tp30) REVERT: A 910 HIS cc_start: 0.8777 (t-90) cc_final: 0.8504 (m170) REVERT: A 1137 ASN cc_start: 0.8943 (t0) cc_final: 0.8272 (p0) REVERT: A 1146 GLU cc_start: 0.8980 (pt0) cc_final: 0.8475 (mm-30) REVERT: A 1183 LEU cc_start: 0.9392 (tp) cc_final: 0.9112 (tt) REVERT: A 1310 LEU cc_start: 0.9410 (mm) cc_final: 0.9150 (mt) REVERT: A 1511 PHE cc_start: 0.6216 (m-80) cc_final: 0.5973 (m-80) REVERT: A 1717 TRP cc_start: 0.7125 (p-90) cc_final: 0.6856 (p-90) REVERT: A 1793 LEU cc_start: 0.7509 (mt) cc_final: 0.7146 (mt) REVERT: A 1883 MET cc_start: 0.7584 (mmp) cc_final: 0.7246 (ptp) REVERT: A 2124 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7448 (tp) REVERT: A 2142 PHE cc_start: 0.7801 (t80) cc_final: 0.7549 (m-10) REVERT: A 2156 SER cc_start: 0.1226 (OUTLIER) cc_final: 0.0664 (p) REVERT: B 59 LEU cc_start: 0.8885 (tp) cc_final: 0.8602 (mm) REVERT: C 52 LEU cc_start: 0.6445 (tt) cc_final: 0.6222 (tt) REVERT: C 270 LEU cc_start: 0.9225 (pp) cc_final: 0.8938 (pp) REVERT: C 347 ARG cc_start: 0.9308 (ttt-90) cc_final: 0.9094 (ttm110) REVERT: C 593 GLU cc_start: 0.8927 (tt0) cc_final: 0.8650 (tm-30) REVERT: C 594 GLU cc_start: 0.7874 (tp30) cc_final: 0.7323 (tp30) REVERT: C 598 TRP cc_start: 0.7826 (m-10) cc_final: 0.7318 (m-10) REVERT: C 659 CYS cc_start: 0.6765 (OUTLIER) cc_final: 0.6555 (p) REVERT: C 1137 ASN cc_start: 0.8955 (t0) cc_final: 0.8346 (p0) REVERT: C 1146 GLU cc_start: 0.8884 (pt0) cc_final: 0.8425 (mm-30) REVERT: C 1183 LEU cc_start: 0.9308 (tp) cc_final: 0.8936 (tt) REVERT: C 1310 LEU cc_start: 0.9295 (mm) cc_final: 0.9045 (mt) REVERT: C 1381 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7744 (tm-30) REVERT: C 1717 TRP cc_start: 0.7100 (p-90) cc_final: 0.6846 (p-90) REVERT: C 1793 LEU cc_start: 0.7915 (mt) cc_final: 0.7534 (mm) REVERT: C 1883 MET cc_start: 0.7707 (mmp) cc_final: 0.7360 (ptp) REVERT: C 2052 ASP cc_start: 0.4076 (OUTLIER) cc_final: 0.3823 (p0) REVERT: C 2142 PHE cc_start: 0.7695 (t80) cc_final: 0.7401 (m-10) REVERT: D 59 LEU cc_start: 0.8931 (tp) cc_final: 0.8654 (mm) outliers start: 72 outliers final: 21 residues processed: 745 average time/residue: 0.2149 time to fit residues: 252.0113 Evaluate side-chains 465 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 438 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 197 optimal weight: 30.0000 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 335 ASN A 390 ASN A 522 ASN A 647 HIS A 741 ASN A1414 GLN A1496 ASN ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS A1805 GLN ** A1829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1871 GLN A1888 ASN A1916 ASN ** A2146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN C 430 HIS C 522 ASN C 607 ASN C 647 HIS C 741 ASN C 748 GLN C1128 ASN C1405 HIS C1414 GLN C1517 ASN ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1805 GLN ** C1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1861 ASN C1871 GLN C1888 ASN ** C2146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.134425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.099188 restraints weight = 127774.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.099076 restraints weight = 96863.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099927 restraints weight = 71723.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.100077 restraints weight = 64451.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.099931 restraints weight = 58143.345| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 31572 Z= 0.320 Angle : 0.928 17.766 42670 Z= 0.463 Chirality : 0.048 0.303 4970 Planarity : 0.006 0.067 5398 Dihedral : 5.413 33.218 4194 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.23 % Favored : 88.72 % Rotamer: Outliers : 0.35 % Allowed : 8.87 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.05 % 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: -2.74 (0.12), residues: 3892 helix: -0.45 (0.11), residues: 1848 sheet: -1.02 (0.32), residues: 262 loop : -3.58 (0.12), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 376 TYR 0.032 0.003 TYR A1318 PHE 0.027 0.003 PHE C1511 TRP 0.022 0.003 TRP A2125 HIS 0.008 0.002 HIS C2122 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.32 (31536) covalent geometry : angle 0.89155 / 0.46 (42626) SS BOND : bond 0.01300 / 0.64 ( 4) SS BOND : angle 3.88965 / 2.60 ( 8) hydrogen bonds : bond 0.04913 / 3.31 ( 1366) hydrogen bonds : angle 5.07835 / 3.54 ( 3972) metal coordination : bond 0.01900 / 1.16 ( 32) metal coordination : angle 8.70190 / 5.31 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 450 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.3999 (p90) cc_final: 0.3642 (p90) REVERT: A 292 MET cc_start: 0.8516 (mmt) cc_final: 0.8028 (tpp) REVERT: A 352 PHE cc_start: 0.9041 (t80) cc_final: 0.8693 (t80) REVERT: A 380 LEU cc_start: 0.8302 (pt) cc_final: 0.7479 (pp) REVERT: A 385 MET cc_start: 0.7354 (mmp) cc_final: 0.7057 (mmm) REVERT: A 565 MET cc_start: 0.7388 (ppp) cc_final: 0.7106 (ppp) REVERT: A 593 GLU cc_start: 0.9145 (tt0) cc_final: 0.8627 (tm-30) REVERT: A 594 GLU cc_start: 0.8311 (tp30) cc_final: 0.7696 (tp30) REVERT: A 827 GLU cc_start: 0.5163 (pt0) cc_final: 0.4795 (pm20) REVERT: A 910 HIS cc_start: 0.8962 (t-90) cc_final: 0.8470 (m90) REVERT: A 1137 ASN cc_start: 0.8979 (t0) cc_final: 0.8569 (p0) REVERT: A 1183 LEU cc_start: 0.9463 (tp) cc_final: 0.8980 (tt) REVERT: A 1184 SER cc_start: 0.8942 (p) cc_final: 0.8741 (p) REVERT: A 1290 MET cc_start: 0.7531 (tmm) cc_final: 0.7233 (tmm) REVERT: A 1310 LEU cc_start: 0.9436 (mm) cc_final: 0.9083 (mt) REVERT: A 1425 GLN cc_start: 0.9198 (pp30) cc_final: 0.8939 (pp30) REVERT: A 1511 PHE cc_start: 0.6373 (m-80) cc_final: 0.4817 (m-80) REVERT: A 1893 MET cc_start: 0.1830 (ppp) cc_final: 0.1533 (ppp) REVERT: A 2142 PHE cc_start: 0.7810 (t80) cc_final: 0.7334 (m-10) REVERT: C 104 PHE cc_start: 0.4999 (p90) cc_final: 0.4220 (p90) REVERT: C 352 PHE cc_start: 0.9027 (t80) cc_final: 0.8447 (t80) REVERT: C 380 LEU cc_start: 0.7969 (pt) cc_final: 0.7560 (pt) REVERT: C 385 MET cc_start: 0.7627 (mmp) cc_final: 0.7146 (mmm) REVERT: C 498 ILE cc_start: 0.9313 (pt) cc_final: 0.8303 (pt) REVERT: C 565 MET cc_start: 0.7378 (ppp) cc_final: 0.6549 (ppp) REVERT: C 593 GLU cc_start: 0.9082 (tt0) cc_final: 0.8600 (tm-30) REVERT: C 594 GLU cc_start: 0.8380 (tp30) cc_final: 0.7766 (tp30) REVERT: C 1137 ASN cc_start: 0.9004 (t0) cc_final: 0.8548 (p0) REVERT: C 1183 LEU cc_start: 0.9548 (tp) cc_final: 0.9095 (tt) REVERT: C 1290 MET cc_start: 0.7416 (tmm) cc_final: 0.7080 (tmm) REVERT: C 1310 LEU cc_start: 0.9371 (mm) cc_final: 0.9036 (mt) REVERT: C 1382 PHE cc_start: 0.8681 (t80) cc_final: 0.8371 (t80) REVERT: C 1387 PHE cc_start: 0.8096 (m-80) cc_final: 0.7813 (m-80) REVERT: C 1511 PHE cc_start: 0.6333 (m-80) cc_final: 0.4507 (m-80) REVERT: C 1731 LEU cc_start: 0.9137 (tp) cc_final: 0.8922 (tt) REVERT: C 1830 ILE cc_start: 0.6574 (mt) cc_final: 0.6113 (mt) outliers start: 12 outliers final: 6 residues processed: 460 average time/residue: 0.1928 time to fit residues: 142.8414 Evaluate side-chains 326 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 320 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 213 optimal weight: 6.9990 chunk 292 optimal weight: 1.9990 chunk 243 optimal weight: 0.7980 chunk 331 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 92 optimal weight: 40.0000 chunk 392 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 182 optimal weight: 30.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN A1271 HIS A1414 GLN ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1829 GLN ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1871 GLN ** A2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1271 HIS C1414 GLN ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1669 ASN C1833 ASN C1837 GLN ** C2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2146 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.135335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.099436 restraints weight = 127067.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.100695 restraints weight = 93522.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.100288 restraints weight = 66563.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.100408 restraints weight = 62433.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.100596 restraints weight = 58695.300| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31572 Z= 0.187 Angle : 0.714 10.201 42670 Z= 0.358 Chirality : 0.044 0.216 4970 Planarity : 0.005 0.153 5398 Dihedral : 4.997 31.020 4194 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.17 % Favored : 89.77 % Rotamer: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.03 % 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: -2.18 (0.13), residues: 3892 helix: 0.07 (0.12), residues: 1862 sheet: -0.79 (0.33), residues: 256 loop : -3.37 (0.13), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 485 TYR 0.022 0.002 TYR A1533 PHE 0.025 0.002 PHE C2142 TRP 0.030 0.002 TRP A1717 HIS 0.013 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (31536) covalent geometry : angle 0.69390 / 0.36 (42626) SS BOND : bond 0.01085 / 0.54 ( 4) SS BOND : angle 2.57346 / 1.74 ( 8) hydrogen bonds : bond 0.03907 / 2.61 ( 1366) hydrogen bonds : angle 4.56341 / 3.19 ( 3972) metal coordination : bond 0.01377 / 0.85 ( 32) metal coordination : angle 5.69652 / 3.37 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 444 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.3564 (p90) cc_final: 0.3212 (p90) REVERT: A 258 PHE cc_start: 0.8160 (m-80) cc_final: 0.7943 (m-80) REVERT: A 352 PHE cc_start: 0.8936 (t80) cc_final: 0.8600 (t80) REVERT: A 498 ILE cc_start: 0.9234 (pt) cc_final: 0.8332 (pt) REVERT: A 499 ASN cc_start: 0.9297 (m-40) cc_final: 0.9091 (m-40) REVERT: A 565 MET cc_start: 0.7372 (ppp) cc_final: 0.7067 (ppp) REVERT: A 593 GLU cc_start: 0.9026 (tt0) cc_final: 0.8651 (tm-30) REVERT: A 594 GLU cc_start: 0.8389 (tp30) cc_final: 0.7870 (tp30) REVERT: A 827 GLU cc_start: 0.4927 (pt0) cc_final: 0.4544 (pm20) REVERT: A 910 HIS cc_start: 0.8956 (t-90) cc_final: 0.8492 (m170) REVERT: A 1174 MET cc_start: 0.9021 (ptp) cc_final: 0.8761 (ptm) REVERT: A 1290 MET cc_start: 0.7394 (tmm) cc_final: 0.7073 (tmm) REVERT: A 1509 ARG cc_start: 0.6801 (tpm170) cc_final: 0.6063 (tpt-90) REVERT: A 1511 PHE cc_start: 0.6667 (m-80) cc_final: 0.6404 (m-80) REVERT: A 1540 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7636 (mp0) REVERT: A 1695 GLU cc_start: 0.7530 (pp20) cc_final: 0.7294 (tm-30) REVERT: A 1733 MET cc_start: 0.8557 (tpp) cc_final: 0.8274 (tpp) REVERT: A 1734 ASN cc_start: 0.7640 (m-40) cc_final: 0.7122 (p0) REVERT: A 1765 MET cc_start: 0.6675 (mmm) cc_final: 0.6290 (mmp) REVERT: A 1782 MET cc_start: 0.8555 (mmp) cc_final: 0.8295 (ppp) REVERT: A 1825 LEU cc_start: 0.6427 (mm) cc_final: 0.6201 (mt) REVERT: A 1829 GLN cc_start: 0.8854 (tp40) cc_final: 0.8484 (tp40) REVERT: A 1830 ILE cc_start: 0.6943 (mt) cc_final: 0.6624 (mt) REVERT: A 1833 ASN cc_start: 0.8839 (m-40) cc_final: 0.8395 (m110) REVERT: A 1835 LYS cc_start: 0.7491 (mmmm) cc_final: 0.7150 (tttt) REVERT: C 104 PHE cc_start: 0.4419 (p90) cc_final: 0.3657 (p90) REVERT: C 270 LEU cc_start: 0.9335 (pp) cc_final: 0.9114 (pp) REVERT: C 352 PHE cc_start: 0.8924 (t80) cc_final: 0.8434 (t80) REVERT: C 385 MET cc_start: 0.7246 (mmp) cc_final: 0.6863 (mmm) REVERT: C 593 GLU cc_start: 0.8962 (tt0) cc_final: 0.8684 (tm-30) REVERT: C 594 GLU cc_start: 0.8269 (tp30) cc_final: 0.7803 (tp30) REVERT: C 1137 ASN cc_start: 0.9021 (t0) cc_final: 0.8588 (p0) REVERT: C 1174 MET cc_start: 0.9034 (ptp) cc_final: 0.8658 (ptm) REVERT: C 1290 MET cc_start: 0.7287 (tmm) cc_final: 0.7041 (tmm) REVERT: C 1310 LEU cc_start: 0.9274 (mm) cc_final: 0.8919 (mt) REVERT: C 1355 ILE cc_start: 0.9459 (pt) cc_final: 0.8830 (pt) REVERT: C 1387 PHE cc_start: 0.8205 (m-80) cc_final: 0.7864 (m-80) REVERT: C 1509 ARG cc_start: 0.6939 (tpm170) cc_final: 0.4816 (tpm170) REVERT: C 1510 ILE cc_start: 0.9134 (pt) cc_final: 0.8860 (pt) REVERT: C 1619 ILE cc_start: 0.8695 (mm) cc_final: 0.8450 (tt) REVERT: C 1695 GLU cc_start: 0.7707 (pp20) cc_final: 0.7479 (tm-30) REVERT: C 1734 ASN cc_start: 0.7737 (m-40) cc_final: 0.7229 (p0) REVERT: C 1782 MET cc_start: 0.8687 (mmm) cc_final: 0.8338 (ppp) REVERT: C 1830 ILE cc_start: 0.6885 (mt) cc_final: 0.6402 (mt) REVERT: D 57 LEU cc_start: 0.8899 (tp) cc_final: 0.8544 (tp) outliers start: 2 outliers final: 0 residues processed: 446 average time/residue: 0.1818 time to fit residues: 131.3731 Evaluate side-chains 329 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 192 optimal weight: 8.9990 chunk 195 optimal weight: 0.9980 chunk 307 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 305 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS A 189 HIS A1405 HIS ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1669 ASN A1783 ASN ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2146 HIS ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1405 HIS C1496 ASN C1517 ASN ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1783 ASN C2043 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.134286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.099541 restraints weight = 127688.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.100383 restraints weight = 95655.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.100034 restraints weight = 67819.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.100294 restraints weight = 71188.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.100710 restraints weight = 59984.875| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31572 Z= 0.153 Angle : 0.682 12.843 42670 Z= 0.338 Chirality : 0.043 0.227 4970 Planarity : 0.004 0.071 5398 Dihedral : 4.834 30.178 4194 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.23 % Favored : 89.75 % Rotamer: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.13), residues: 3892 helix: 0.34 (0.12), residues: 1856 sheet: -0.48 (0.34), residues: 250 loop : -3.24 (0.13), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 485 TYR 0.023 0.002 TYR C1318 PHE 0.027 0.002 PHE A2142 TRP 0.036 0.002 TRP C1717 HIS 0.010 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (31536) covalent geometry : angle 0.66290 / 0.34 (42626) SS BOND : bond 0.00813 / 0.40 ( 4) SS BOND : angle 2.80423 / 1.84 ( 8) hydrogen bonds : bond 0.03648 / 2.47 ( 1366) hydrogen bonds : angle 4.41385 / 3.08 ( 3972) metal coordination : bond 0.01396 / 0.94 ( 32) metal coordination : angle 5.45349 / 3.23 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 433 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.9254 (pp) cc_final: 0.9033 (pp) REVERT: A 352 PHE cc_start: 0.8933 (t80) cc_final: 0.8543 (t80) REVERT: A 498 ILE cc_start: 0.9280 (pt) cc_final: 0.8895 (pt) REVERT: A 565 MET cc_start: 0.7309 (ppp) cc_final: 0.6940 (ppp) REVERT: A 593 GLU cc_start: 0.9069 (tt0) cc_final: 0.8707 (tm-30) REVERT: A 594 GLU cc_start: 0.8484 (tp30) cc_final: 0.8005 (tp30) REVERT: A 910 HIS cc_start: 0.8975 (t-90) cc_final: 0.8483 (m170) REVERT: A 1174 MET cc_start: 0.9054 (ptp) cc_final: 0.8763 (ptm) REVERT: A 1509 ARG cc_start: 0.6858 (tpm170) cc_final: 0.6322 (tpt-90) REVERT: A 1511 PHE cc_start: 0.6851 (m-80) cc_final: 0.6517 (m-80) REVERT: A 1540 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7679 (mp0) REVERT: A 1695 GLU cc_start: 0.7580 (pp20) cc_final: 0.7236 (tm-30) REVERT: A 1734 ASN cc_start: 0.7562 (m-40) cc_final: 0.6977 (p0) REVERT: A 1825 LEU cc_start: 0.6432 (mm) cc_final: 0.6151 (mt) REVERT: A 1829 GLN cc_start: 0.8741 (tp40) cc_final: 0.8376 (tp40) REVERT: A 1830 ILE cc_start: 0.7151 (mt) cc_final: 0.6755 (mt) REVERT: A 1833 ASN cc_start: 0.8919 (m-40) cc_final: 0.8340 (m110) REVERT: C 104 PHE cc_start: 0.4677 (p90) cc_final: 0.4073 (p90) REVERT: C 270 LEU cc_start: 0.9269 (pp) cc_final: 0.9054 (pp) REVERT: C 352 PHE cc_start: 0.8824 (t80) cc_final: 0.8407 (t80) REVERT: C 499 ASN cc_start: 0.9425 (m-40) cc_final: 0.9176 (m110) REVERT: C 565 MET cc_start: 0.7252 (ppp) cc_final: 0.6913 (ppp) REVERT: C 593 GLU cc_start: 0.9064 (tt0) cc_final: 0.8727 (tm-30) REVERT: C 594 GLU cc_start: 0.8405 (tp30) cc_final: 0.7939 (tp30) REVERT: C 1137 ASN cc_start: 0.9064 (t0) cc_final: 0.8852 (p0) REVERT: C 1146 GLU cc_start: 0.9063 (pt0) cc_final: 0.8824 (mm-30) REVERT: C 1156 MET cc_start: 0.8807 (tpp) cc_final: 0.8517 (tpp) REVERT: C 1174 MET cc_start: 0.9075 (ptp) cc_final: 0.8684 (ptm) REVERT: C 1355 ILE cc_start: 0.9307 (pt) cc_final: 0.8974 (pt) REVERT: C 1387 PHE cc_start: 0.8268 (m-80) cc_final: 0.7855 (m-80) REVERT: C 1695 GLU cc_start: 0.7741 (pp20) cc_final: 0.7361 (tm-30) REVERT: C 1734 ASN cc_start: 0.7989 (m-40) cc_final: 0.7024 (p0) REVERT: C 1830 ILE cc_start: 0.7069 (mt) cc_final: 0.6606 (mt) outliers start: 3 outliers final: 1 residues processed: 436 average time/residue: 0.1868 time to fit residues: 134.0032 Evaluate side-chains 319 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 266 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.0655 > 50:) chunk 368 optimal weight: 30.0000 chunk 223 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 390 optimal weight: 7.9990 chunk 89 optimal weight: 40.0000 chunk 197 optimal weight: 30.0000 chunk 283 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 343 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS A1414 GLN A1463 GLN ** A1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1861 ASN ** A2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS C 15 HIS ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 GLN C1463 GLN ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.130165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095530 restraints weight = 129774.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095994 restraints weight = 97121.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.095508 restraints weight = 70682.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.095868 restraints weight = 72316.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096394 restraints weight = 62137.573| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 31572 Z= 0.216 Angle : 0.773 14.957 42670 Z= 0.385 Chirality : 0.046 0.300 4970 Planarity : 0.005 0.068 5398 Dihedral : 5.204 33.841 4194 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.13), residues: 3892 helix: 0.16 (0.12), residues: 1864 sheet: -0.55 (0.33), residues: 250 loop : -3.16 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 614 TYR 0.025 0.002 TYR C1318 PHE 0.037 0.002 PHE C1511 TRP 0.022 0.002 TRP C1717 HIS 0.008 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (31536) covalent geometry : angle 0.74990 / 0.38 (42626) SS BOND : bond 0.00776 / 0.38 ( 4) SS BOND : angle 3.90109 / 2.62 ( 8) hydrogen bonds : bond 0.04138 / 2.81 ( 1366) hydrogen bonds : angle 4.72464 / 3.29 ( 3972) metal coordination : bond 0.01536 / 0.97 ( 32) metal coordination : angle 6.17589 / 3.55 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 390 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.4357 (p90) cc_final: 0.4083 (p90) REVERT: A 289 ASN cc_start: 0.8619 (t0) cc_final: 0.8241 (t0) REVERT: A 292 MET cc_start: 0.8800 (mmm) cc_final: 0.8481 (mmm) REVERT: A 352 PHE cc_start: 0.8747 (t80) cc_final: 0.8376 (t80) REVERT: A 498 ILE cc_start: 0.9190 (pt) cc_final: 0.8882 (pt) REVERT: A 593 GLU cc_start: 0.9032 (tt0) cc_final: 0.8643 (tm-30) REVERT: A 594 GLU cc_start: 0.8508 (tp30) cc_final: 0.7947 (tp30) REVERT: A 910 HIS cc_start: 0.8980 (t-90) cc_final: 0.8499 (m170) REVERT: A 1174 MET cc_start: 0.9058 (ptp) cc_final: 0.8793 (ptm) REVERT: A 1290 MET cc_start: 0.7861 (tmm) cc_final: 0.7611 (tmm) REVERT: A 1695 GLU cc_start: 0.7673 (pp20) cc_final: 0.7321 (tm-30) REVERT: A 1734 ASN cc_start: 0.8130 (m-40) cc_final: 0.7417 (p0) REVERT: A 1825 LEU cc_start: 0.6999 (mm) cc_final: 0.6718 (mt) REVERT: C 104 PHE cc_start: 0.4549 (p90) cc_final: 0.3024 (p90) REVERT: C 289 ASN cc_start: 0.8754 (t0) cc_final: 0.8540 (t0) REVERT: C 498 ILE cc_start: 0.9307 (pt) cc_final: 0.8563 (pt) REVERT: C 499 ASN cc_start: 0.9472 (m-40) cc_final: 0.9232 (m110) REVERT: C 565 MET cc_start: 0.7416 (ppp) cc_final: 0.6969 (ppp) REVERT: C 593 GLU cc_start: 0.9037 (tt0) cc_final: 0.8635 (tm-30) REVERT: C 594 GLU cc_start: 0.8421 (tp30) cc_final: 0.7887 (tp30) REVERT: C 1137 ASN cc_start: 0.9153 (t0) cc_final: 0.8918 (p0) REVERT: C 1156 MET cc_start: 0.8933 (tpp) cc_final: 0.8717 (tpp) REVERT: C 1174 MET cc_start: 0.9107 (ptp) cc_final: 0.8780 (ptm) REVERT: C 1290 MET cc_start: 0.7457 (tmm) cc_final: 0.7204 (tmm) REVERT: C 1355 ILE cc_start: 0.9302 (pt) cc_final: 0.8760 (pt) REVERT: C 1509 ARG cc_start: 0.7028 (tpm170) cc_final: 0.4339 (tpm170) REVERT: C 1619 ILE cc_start: 0.8633 (mm) cc_final: 0.8364 (tt) REVERT: C 1695 GLU cc_start: 0.7691 (pp20) cc_final: 0.7306 (tm-30) REVERT: C 1734 ASN cc_start: 0.8079 (m-40) cc_final: 0.7373 (p0) REVERT: C 1830 ILE cc_start: 0.7576 (mt) cc_final: 0.7218 (mt) outliers start: 3 outliers final: 0 residues processed: 393 average time/residue: 0.1954 time to fit residues: 128.1987 Evaluate side-chains 288 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 9 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 340 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 275 optimal weight: 8.9990 chunk 225 optimal weight: 3.9990 chunk 316 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS A1414 GLN A1463 GLN ** A1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1829 GLN ** A2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2122 HIS B 53 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 GLN C1463 GLN ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.130481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.095417 restraints weight = 128509.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096071 restraints weight = 95910.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.096039 restraints weight = 67389.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.096224 restraints weight = 61452.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.096405 restraints weight = 58882.483| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 31572 Z= 0.174 Angle : 0.714 12.500 42670 Z= 0.356 Chirality : 0.044 0.212 4970 Planarity : 0.004 0.068 5398 Dihedral : 5.097 31.423 4194 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 0.14 % Allowed : 3.25 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.13), residues: 3892 helix: 0.27 (0.12), residues: 1880 sheet: -0.40 (0.34), residues: 250 loop : -3.09 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 614 TYR 0.020 0.002 TYR C1318 PHE 0.025 0.002 PHE A 638 TRP 0.025 0.002 TRP A 413 HIS 0.007 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (31536) covalent geometry : angle 0.69791 / 0.35 (42626) SS BOND : bond 0.00713 / 0.35 ( 4) SS BOND : angle 2.93746 / 1.98 ( 8) hydrogen bonds : bond 0.03853 / 2.61 ( 1366) hydrogen bonds : angle 4.55532 / 3.18 ( 3972) metal coordination : bond 0.01620 / 0.83 ( 32) metal coordination : angle 5.11858 / 2.94 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 408 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.4100 (p90) cc_final: 0.3876 (p90) REVERT: A 289 ASN cc_start: 0.8610 (t0) cc_final: 0.8273 (t0) REVERT: A 292 MET cc_start: 0.8769 (mmm) cc_final: 0.8555 (mmm) REVERT: A 352 PHE cc_start: 0.8690 (t80) cc_final: 0.8430 (t80) REVERT: A 499 ASN cc_start: 0.9269 (m110) cc_final: 0.9050 (m110) REVERT: A 593 GLU cc_start: 0.8954 (tt0) cc_final: 0.8638 (tm-30) REVERT: A 594 GLU cc_start: 0.8349 (tp30) cc_final: 0.8069 (tp30) REVERT: A 646 ILE cc_start: 0.9320 (tt) cc_final: 0.9065 (mp) REVERT: A 910 HIS cc_start: 0.8962 (t-90) cc_final: 0.8487 (m90) REVERT: A 1174 MET cc_start: 0.9032 (ptp) cc_final: 0.8712 (ptm) REVERT: A 1285 MET cc_start: 0.6029 (mtp) cc_final: 0.5770 (mtp) REVERT: A 1290 MET cc_start: 0.7763 (tmm) cc_final: 0.7469 (tmm) REVERT: A 1695 GLU cc_start: 0.7632 (pp20) cc_final: 0.7333 (tm-30) REVERT: A 1833 ASN cc_start: 0.9082 (m-40) cc_final: 0.8726 (m-40) REVERT: A 2120 MET cc_start: 0.7510 (tpt) cc_final: 0.7276 (tpt) REVERT: C 104 PHE cc_start: 0.4689 (p90) cc_final: 0.3630 (p90) REVERT: C 261 THR cc_start: 0.7460 (p) cc_final: 0.7232 (p) REVERT: C 289 ASN cc_start: 0.8772 (t0) cc_final: 0.8569 (t0) REVERT: C 352 PHE cc_start: 0.8926 (t80) cc_final: 0.8598 (t80) REVERT: C 565 MET cc_start: 0.7282 (ppp) cc_final: 0.6788 (ppp) REVERT: C 593 GLU cc_start: 0.8971 (tt0) cc_final: 0.8653 (tm-30) REVERT: C 594 GLU cc_start: 0.8295 (tp30) cc_final: 0.7986 (tp30) REVERT: C 1137 ASN cc_start: 0.9122 (t0) cc_final: 0.8894 (p0) REVERT: C 1156 MET cc_start: 0.8789 (tpp) cc_final: 0.8526 (tpp) REVERT: C 1174 MET cc_start: 0.8994 (ptp) cc_final: 0.8678 (ptm) REVERT: C 1290 MET cc_start: 0.7483 (tmm) cc_final: 0.7243 (tmm) REVERT: C 1355 ILE cc_start: 0.9264 (pt) cc_final: 0.8830 (pt) REVERT: C 1463 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: C 1619 ILE cc_start: 0.8640 (mm) cc_final: 0.8382 (tt) REVERT: C 2103 LEU cc_start: 0.8009 (tp) cc_final: 0.7791 (tp) REVERT: D 57 LEU cc_start: 0.8931 (tp) cc_final: 0.8509 (tp) outliers start: 5 outliers final: 0 residues processed: 411 average time/residue: 0.1929 time to fit residues: 132.7477 Evaluate side-chains 300 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 285 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 346 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 381 optimal weight: 0.0870 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1331 GLN A1405 HIS A1414 GLN A1463 GLN ** A1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 GLN ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1751 HIS ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.132138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.099704 restraints weight = 130268.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.098941 restraints weight = 105320.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.099311 restraints weight = 83054.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.099842 restraints weight = 74659.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.099883 restraints weight = 64501.421| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.6710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31572 Z= 0.124 Angle : 0.674 11.155 42670 Z= 0.336 Chirality : 0.043 0.181 4970 Planarity : 0.004 0.069 5398 Dihedral : 4.828 32.116 4194 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3892 helix: 0.47 (0.12), residues: 1874 sheet: -0.02 (0.34), residues: 240 loop : -2.94 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 614 TYR 0.018 0.001 TYR C1318 PHE 0.049 0.001 PHE A1511 TRP 0.024 0.002 TRP A 413 HIS 0.006 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (31536) covalent geometry : angle 0.66345 / 0.33 (42626) SS BOND : bond 0.00552 / 0.27 ( 4) SS BOND : angle 2.26526 / 1.50 ( 8) hydrogen bonds : bond 0.03467 / 2.34 ( 1366) hydrogen bonds : angle 4.33726 / 3.03 ( 3972) metal coordination : bond 0.01503 / 1.11 ( 32) metal coordination : angle 4.10276 / 2.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 419 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 THR cc_start: 0.7480 (p) cc_final: 0.7248 (p) REVERT: A 289 ASN cc_start: 0.8520 (t0) cc_final: 0.8183 (t0) REVERT: A 292 MET cc_start: 0.8843 (mmm) cc_final: 0.8561 (mmm) REVERT: A 593 GLU cc_start: 0.8990 (tt0) cc_final: 0.8690 (tm-30) REVERT: A 594 GLU cc_start: 0.8398 (tp30) cc_final: 0.8132 (tp30) REVERT: A 614 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7998 (ptp-110) REVERT: A 646 ILE cc_start: 0.9249 (tt) cc_final: 0.9041 (mp) REVERT: A 827 GLU cc_start: 0.4548 (pt0) cc_final: 0.3899 (pm20) REVERT: A 910 HIS cc_start: 0.8947 (t-90) cc_final: 0.8481 (m90) REVERT: A 1174 MET cc_start: 0.9035 (ptp) cc_final: 0.8681 (ptm) REVERT: A 1290 MET cc_start: 0.7735 (tmm) cc_final: 0.7407 (tmm) REVERT: A 1512 GLU cc_start: 0.7834 (tp30) cc_final: 0.7542 (tp30) REVERT: A 1695 GLU cc_start: 0.7574 (pp20) cc_final: 0.7233 (tm-30) REVERT: A 1782 MET cc_start: 0.8530 (mmp) cc_final: 0.8290 (ppp) REVERT: A 1822 GLU cc_start: 0.7955 (pp20) cc_final: 0.7752 (pp20) REVERT: A 1833 ASN cc_start: 0.8921 (m-40) cc_final: 0.8556 (m-40) REVERT: A 2095 TYR cc_start: 0.7417 (p90) cc_final: 0.6993 (p90) REVERT: A 2103 LEU cc_start: 0.7800 (tp) cc_final: 0.7555 (tp) REVERT: B 65 MET cc_start: 0.8823 (tpp) cc_final: 0.8567 (tpp) REVERT: C 104 PHE cc_start: 0.4635 (p90) cc_final: 0.3686 (p90) REVERT: C 261 THR cc_start: 0.7617 (p) cc_final: 0.7416 (p) REVERT: C 289 ASN cc_start: 0.8663 (t0) cc_final: 0.8452 (t0) REVERT: C 352 PHE cc_start: 0.8947 (t80) cc_final: 0.8558 (t80) REVERT: C 478 MET cc_start: 0.6644 (mtp) cc_final: 0.6216 (mtp) REVERT: C 495 LEU cc_start: 0.9530 (tp) cc_final: 0.9323 (tp) REVERT: C 498 ILE cc_start: 0.9201 (pt) cc_final: 0.8926 (pt) REVERT: C 593 GLU cc_start: 0.8999 (tt0) cc_final: 0.8695 (tm-30) REVERT: C 594 GLU cc_start: 0.8322 (tp30) cc_final: 0.8047 (tp30) REVERT: C 1137 ASN cc_start: 0.9110 (t0) cc_final: 0.8884 (p0) REVERT: C 1156 MET cc_start: 0.8833 (tpp) cc_final: 0.8632 (tpp) REVERT: C 1174 MET cc_start: 0.9055 (ptp) cc_final: 0.8665 (ptm) REVERT: C 1290 MET cc_start: 0.7374 (tmm) cc_final: 0.7173 (tmm) REVERT: C 1355 ILE cc_start: 0.9262 (pt) cc_final: 0.8893 (pt) REVERT: C 1387 PHE cc_start: 0.8221 (m-80) cc_final: 0.7766 (m-80) REVERT: C 1619 ILE cc_start: 0.8593 (mm) cc_final: 0.8382 (tt) REVERT: C 1695 GLU cc_start: 0.7665 (pp20) cc_final: 0.7349 (tm-30) REVERT: C 2103 LEU cc_start: 0.7871 (tp) cc_final: 0.7621 (tp) REVERT: D 65 MET cc_start: 0.8662 (tpp) cc_final: 0.8346 (tpp) outliers start: 4 outliers final: 0 residues processed: 422 average time/residue: 0.1864 time to fit residues: 131.3317 Evaluate side-chains 308 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 87 optimal weight: 40.0000 chunk 315 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 308 optimal weight: 8.9990 chunk 384 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 27 optimal weight: 0.8980 chunk 338 optimal weight: 7.9990 chunk 373 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS A1414 GLN A1425 GLN A1463 GLN ** A1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1331 GLN C1414 GLN ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.131254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.096403 restraints weight = 127972.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.097506 restraints weight = 94593.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.097464 restraints weight = 64080.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.097597 restraints weight = 63845.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.097863 restraints weight = 56535.368| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 31572 Z= 0.130 Angle : 0.681 10.413 42670 Z= 0.336 Chirality : 0.043 0.188 4970 Planarity : 0.004 0.072 5398 Dihedral : 4.741 30.606 4194 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.14 % Allowed : 1.01 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.14), residues: 3892 helix: 0.48 (0.12), residues: 1884 sheet: -0.09 (0.34), residues: 244 loop : -2.92 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 614 TYR 0.018 0.001 TYR C1318 PHE 0.024 0.001 PHE A 352 TRP 0.026 0.002 TRP A 413 HIS 0.006 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (31536) covalent geometry : angle 0.66967 / 0.34 (42626) SS BOND : bond 0.00524 / 0.26 ( 4) SS BOND : angle 2.34311 / 1.54 ( 8) hydrogen bonds : bond 0.03501 / 2.36 ( 1366) hydrogen bonds : angle 4.31670 / 3.02 ( 3972) metal coordination : bond 0.01355 / 0.91 ( 32) metal coordination : angle 4.14601 / 2.33 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 410 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.3845 (p90) cc_final: 0.3538 (p90) REVERT: A 289 ASN cc_start: 0.8560 (t0) cc_final: 0.8334 (t0) REVERT: A 292 MET cc_start: 0.8710 (mmm) cc_final: 0.8453 (mmm) REVERT: A 352 PHE cc_start: 0.8898 (t80) cc_final: 0.8521 (t80) REVERT: A 385 MET cc_start: 0.7052 (mmm) cc_final: 0.6821 (mmm) REVERT: A 499 ASN cc_start: 0.9176 (m110) cc_final: 0.8970 (m110) REVERT: A 502 LYS cc_start: 0.8884 (ptpp) cc_final: 0.8680 (pttt) REVERT: A 593 GLU cc_start: 0.8893 (tt0) cc_final: 0.8652 (tm-30) REVERT: A 646 ILE cc_start: 0.9231 (tt) cc_final: 0.8982 (mp) REVERT: A 827 GLU cc_start: 0.4619 (pt0) cc_final: 0.3953 (pm20) REVERT: A 910 HIS cc_start: 0.8924 (t-90) cc_final: 0.8455 (m90) REVERT: A 1174 MET cc_start: 0.8956 (ptp) cc_final: 0.8602 (ptm) REVERT: A 1290 MET cc_start: 0.7626 (tmm) cc_final: 0.7299 (tmm) REVERT: A 1692 GLU cc_start: 0.8484 (tp30) cc_final: 0.8274 (tp30) REVERT: A 1695 GLU cc_start: 0.7572 (pp20) cc_final: 0.7243 (tm-30) REVERT: A 1833 ASN cc_start: 0.8953 (m-40) cc_final: 0.8569 (m-40) REVERT: A 1838 LEU cc_start: 0.8609 (tt) cc_final: 0.8186 (mt) REVERT: A 2120 MET cc_start: 0.7558 (tpt) cc_final: 0.7323 (tpt) REVERT: B 65 MET cc_start: 0.8793 (tpp) cc_final: 0.8514 (tpp) REVERT: C 104 PHE cc_start: 0.4627 (p90) cc_final: 0.3625 (p90) REVERT: C 289 ASN cc_start: 0.8668 (t0) cc_final: 0.8456 (t0) REVERT: C 352 PHE cc_start: 0.9000 (t80) cc_final: 0.8534 (t80) REVERT: C 478 MET cc_start: 0.6418 (mtp) cc_final: 0.6170 (mtp) REVERT: C 498 ILE cc_start: 0.9118 (pt) cc_final: 0.8918 (pt) REVERT: C 593 GLU cc_start: 0.8902 (tt0) cc_final: 0.8664 (tm-30) REVERT: C 1130 GLU cc_start: 0.6947 (tp30) cc_final: 0.6518 (tp30) REVERT: C 1174 MET cc_start: 0.8888 (ptp) cc_final: 0.8552 (ptm) REVERT: C 1310 LEU cc_start: 0.9336 (mm) cc_final: 0.9117 (mm) REVERT: C 1355 ILE cc_start: 0.9195 (pt) cc_final: 0.8830 (pt) REVERT: C 1387 PHE cc_start: 0.8174 (m-80) cc_final: 0.7784 (m-80) REVERT: C 1619 ILE cc_start: 0.8652 (mm) cc_final: 0.8422 (tt) REVERT: C 1695 GLU cc_start: 0.7685 (pp20) cc_final: 0.7366 (tm-30) REVERT: C 2095 TYR cc_start: 0.7401 (p90) cc_final: 0.7180 (p90) REVERT: C 2103 LEU cc_start: 0.7903 (tp) cc_final: 0.7654 (tp) REVERT: C 2120 MET cc_start: 0.7659 (tpt) cc_final: 0.7374 (tpt) REVERT: C 2127 TYR cc_start: 0.6957 (t80) cc_final: 0.6720 (t80) outliers start: 5 outliers final: 0 residues processed: 413 average time/residue: 0.1775 time to fit residues: 123.3128 Evaluate side-chains 311 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 137 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 365 optimal weight: 20.0000 chunk 286 optimal weight: 40.0000 chunk 353 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 382 optimal weight: 0.2980 chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A1405 HIS A1414 GLN A1463 GLN ** A1478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1829 GLN A1954 HIS ** A2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 GLN ** C1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.130874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.095769 restraints weight = 129661.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.097171 restraints weight = 95028.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.097287 restraints weight = 63219.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.097529 restraints weight = 62267.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.097415 restraints weight = 58255.060| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.7188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31572 Z= 0.140 Angle : 0.695 15.549 42670 Z= 0.343 Chirality : 0.043 0.190 4970 Planarity : 0.004 0.072 5398 Dihedral : 4.743 28.258 4194 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.17 % 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: -1.46 (0.14), residues: 3892 helix: 0.51 (0.12), residues: 1886 sheet: 0.01 (0.34), residues: 240 loop : -2.91 (0.14), residues: 1766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 614 TYR 0.019 0.001 TYR C1318 PHE 0.020 0.001 PHE C1357 TRP 0.026 0.002 TRP C 413 HIS 0.014 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (31536) covalent geometry : angle 0.68174 / 0.34 (42626) SS BOND : bond 0.00547 / 0.27 ( 4) SS BOND : angle 2.49360 / 1.62 ( 8) hydrogen bonds : bond 0.03499 / 2.36 ( 1366) hydrogen bonds : angle 4.31784 / 3.02 ( 3972) metal coordination : bond 0.01225 / 0.83 ( 32) metal coordination : angle 4.56927 / 2.67 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 392 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.3872 (p90) cc_final: 0.3472 (p90) REVERT: A 292 MET cc_start: 0.8718 (mmm) cc_final: 0.8456 (mmm) REVERT: A 352 PHE cc_start: 0.8962 (t80) cc_final: 0.8584 (t80) REVERT: A 593 GLU cc_start: 0.8983 (tt0) cc_final: 0.8693 (tm-30) REVERT: A 646 ILE cc_start: 0.9285 (tt) cc_final: 0.9010 (mp) REVERT: A 827 GLU cc_start: 0.4657 (pt0) cc_final: 0.3950 (pm20) REVERT: A 901 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8904 (pp30) REVERT: A 910 HIS cc_start: 0.8950 (t-90) cc_final: 0.8472 (m90) REVERT: A 1174 MET cc_start: 0.8994 (ptp) cc_final: 0.8692 (ptm) REVERT: A 1290 MET cc_start: 0.7685 (tmm) cc_final: 0.7330 (tmm) REVERT: A 1692 GLU cc_start: 0.8509 (tp30) cc_final: 0.8239 (tp30) REVERT: A 1695 GLU cc_start: 0.7595 (pp20) cc_final: 0.7204 (tm-30) REVERT: A 1833 ASN cc_start: 0.9036 (m-40) cc_final: 0.8669 (m-40) REVERT: A 2095 TYR cc_start: 0.7176 (p90) cc_final: 0.6901 (p90) REVERT: A 2120 MET cc_start: 0.7535 (tpt) cc_final: 0.7304 (tpt) REVERT: C 104 PHE cc_start: 0.4540 (p90) cc_final: 0.3571 (p90) REVERT: C 289 ASN cc_start: 0.8713 (t0) cc_final: 0.8479 (t0) REVERT: C 352 PHE cc_start: 0.9018 (t80) cc_final: 0.8570 (t80) REVERT: C 478 MET cc_start: 0.6392 (mtp) cc_final: 0.6092 (mtp) REVERT: C 593 GLU cc_start: 0.8980 (tt0) cc_final: 0.8720 (tm-30) REVERT: C 1174 MET cc_start: 0.9006 (ptp) cc_final: 0.8640 (ptm) REVERT: C 1290 MET cc_start: 0.7459 (tmm) cc_final: 0.7171 (tmm) REVERT: C 1310 LEU cc_start: 0.9325 (mm) cc_final: 0.9097 (mm) REVERT: C 1355 ILE cc_start: 0.9235 (pt) cc_final: 0.8898 (pt) REVERT: C 1387 PHE cc_start: 0.8231 (m-80) cc_final: 0.7755 (m-80) REVERT: C 1619 ILE cc_start: 0.8547 (mm) cc_final: 0.8332 (tt) REVERT: C 1695 GLU cc_start: 0.7746 (pp20) cc_final: 0.7386 (tm-30) REVERT: C 2095 TYR cc_start: 0.7491 (p90) cc_final: 0.7168 (p90) REVERT: C 2103 LEU cc_start: 0.7912 (tp) cc_final: 0.7667 (tp) REVERT: D 65 MET cc_start: 0.8776 (tpp) cc_final: 0.8509 (tpp) outliers start: 4 outliers final: 0 residues processed: 395 average time/residue: 0.1836 time to fit residues: 122.7351 Evaluate side-chains 305 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 92 optimal weight: 0.0020 chunk 308 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 152 optimal weight: 0.2980 chunk 151 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 345 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 289 optimal weight: 30.0000 overall best weight: 2.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1405 HIS A1414 GLN A1463 GLN ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 GLN ** C1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.130609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.097226 restraints weight = 128129.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.097230 restraints weight = 100321.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.097598 restraints weight = 71742.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.097744 restraints weight = 66504.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.097903 restraints weight = 60155.943| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.7372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 31572 Z= 0.131 Angle : 0.696 14.434 42670 Z= 0.341 Chirality : 0.043 0.183 4970 Planarity : 0.004 0.073 5398 Dihedral : 4.700 28.348 4194 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer: Outliers : 0.12 % Allowed : 0.40 % Favored : 99.48 % 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: -1.42 (0.14), residues: 3892 helix: 0.53 (0.12), residues: 1884 sheet: 0.05 (0.34), residues: 240 loop : -2.87 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 614 TYR 0.025 0.001 TYR A 835 PHE 0.022 0.001 PHE C 300 TRP 0.027 0.002 TRP C 413 HIS 0.013 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (31536) covalent geometry : angle 0.68467 / 0.34 (42626) SS BOND : bond 0.00538 / 0.27 ( 4) SS BOND : angle 2.23818 / 1.46 ( 8) hydrogen bonds : bond 0.03432 / 2.31 ( 1366) hydrogen bonds : angle 4.30694 / 3.01 ( 3972) metal coordination : bond 0.00994 / 0.64 ( 32) metal coordination : angle 4.18425 / 2.48 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7784 Ramachandran restraints generated. 3892 Oldfield, 0 Emsley, 3892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 391 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.3868 (p90) cc_final: 0.3449 (p90) REVERT: A 289 ASN cc_start: 0.8501 (t0) cc_final: 0.8290 (t0) REVERT: A 292 MET cc_start: 0.8774 (mmm) cc_final: 0.8515 (mmm) REVERT: A 352 PHE cc_start: 0.8988 (t80) cc_final: 0.8590 (t80) REVERT: A 499 ASN cc_start: 0.9202 (m110) cc_final: 0.8793 (m110) REVERT: A 593 GLU cc_start: 0.8994 (tt0) cc_final: 0.8731 (tm-30) REVERT: A 646 ILE cc_start: 0.9285 (tt) cc_final: 0.9008 (mp) REVERT: A 798 LEU cc_start: 0.8421 (pp) cc_final: 0.8207 (pt) REVERT: A 827 GLU cc_start: 0.4705 (pt0) cc_final: 0.3839 (pm20) REVERT: A 901 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8887 (pp30) REVERT: A 910 HIS cc_start: 0.8964 (t-90) cc_final: 0.8460 (m90) REVERT: A 1174 MET cc_start: 0.9017 (ptp) cc_final: 0.8665 (ptm) REVERT: A 1290 MET cc_start: 0.7637 (tmm) cc_final: 0.7269 (tmm) REVERT: A 1692 GLU cc_start: 0.8481 (tp30) cc_final: 0.8188 (tp30) REVERT: A 1695 GLU cc_start: 0.7603 (pp20) cc_final: 0.7183 (tm-30) REVERT: A 2095 TYR cc_start: 0.7367 (p90) cc_final: 0.7067 (p90) REVERT: A 2103 LEU cc_start: 0.7720 (tp) cc_final: 0.7488 (tp) REVERT: A 2120 MET cc_start: 0.7576 (tpt) cc_final: 0.7298 (tpt) REVERT: C 104 PHE cc_start: 0.4621 (p90) cc_final: 0.3977 (p90) REVERT: C 289 ASN cc_start: 0.8669 (t0) cc_final: 0.8405 (t0) REVERT: C 478 MET cc_start: 0.6496 (mtp) cc_final: 0.6239 (mtp) REVERT: C 499 ASN cc_start: 0.9216 (m110) cc_final: 0.8757 (m110) REVERT: C 593 GLU cc_start: 0.9017 (tt0) cc_final: 0.8715 (tm-30) REVERT: C 1174 MET cc_start: 0.8928 (ptp) cc_final: 0.8604 (ptm) REVERT: C 1183 LEU cc_start: 0.9203 (tt) cc_final: 0.9001 (mm) REVERT: C 1290 MET cc_start: 0.7426 (tmm) cc_final: 0.7169 (tmm) REVERT: C 1310 LEU cc_start: 0.9358 (mm) cc_final: 0.9096 (mm) REVERT: C 1355 ILE cc_start: 0.9270 (pt) cc_final: 0.8836 (pt) REVERT: C 1387 PHE cc_start: 0.8253 (m-80) cc_final: 0.7796 (m-80) REVERT: C 1511 PHE cc_start: 0.6722 (m-80) cc_final: 0.5966 (m-80) REVERT: C 1619 ILE cc_start: 0.8666 (mm) cc_final: 0.8339 (tt) REVERT: C 1695 GLU cc_start: 0.7663 (pp20) cc_final: 0.7292 (tm-30) REVERT: C 2095 TYR cc_start: 0.7439 (p90) cc_final: 0.7100 (p90) REVERT: C 2103 LEU cc_start: 0.7952 (tp) cc_final: 0.7695 (tp) REVERT: D 65 MET cc_start: 0.8734 (tpp) cc_final: 0.8484 (tpp) outliers start: 4 outliers final: 0 residues processed: 394 average time/residue: 0.1800 time to fit residues: 120.2163 Evaluate side-chains 308 residues out of total 3632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 84 optimal weight: 3.9990 chunk 352 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 225 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 351 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A1405 HIS A1414 GLN A1445 GLN A1463 GLN ** A1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1180 ASN C1414 GLN ** C1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.126762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.091646 restraints weight = 130121.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.093395 restraints weight = 92704.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.092518 restraints weight = 62464.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.092646 restraints weight = 68055.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.092910 restraints weight = 59263.152| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.7979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 31572 Z= 0.215 Angle : 0.796 15.547 42670 Z= 0.396 Chirality : 0.046 0.281 4970 Planarity : 0.005 0.073 5398 Dihedral : 5.276 31.731 4194 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 0.12 % Allowed : 0.63 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.72 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.13), residues: 3892 helix: 0.18 (0.12), residues: 1890 sheet: 0.28 (0.36), residues: 212 loop : -2.92 (0.14), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 614 TYR 0.037 0.002 TYR A 835 PHE 0.021 0.002 PHE C 300 TRP 0.030 0.003 TRP C 116 HIS 0.013 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (31536) covalent geometry : angle 0.77706 / 0.39 (42626) SS BOND : bond 0.00810 / 0.39 ( 4) SS BOND : angle 3.18370 / 2.19 ( 8) hydrogen bonds : bond 0.04222 / 2.86 ( 1366) hydrogen bonds : angle 4.72204 / 3.28 ( 3972) metal coordination : bond 0.01760 / 1.06 ( 32) metal coordination : angle 5.81127 / 3.38 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5829.69 seconds wall clock time: 101 minutes 53.52 seconds (6113.52 seconds total)