Starting phenix.real_space_refine (version: dev) on Fri Apr 8 00:53:13 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elb_31179/04_2022/7elb_31179_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elb_31179/04_2022/7elb_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elb_31179/04_2022/7elb_31179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elb_31179/04_2022/7elb_31179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elb_31179/04_2022/7elb_31179_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7elb_31179/04_2022/7elb_31179_neut.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 31012 Number of models: 1 Model: "" Number of chains: 8 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, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 9, 'GLU:plan': 15, 'ARG:plan': 11} 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: "C" 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, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 9, 'GLU:plan': 15, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 257 Chain: "D" 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} Chain: "C" 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: "D" 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 ATOM 17672 SG CYS C 284 35.957 32.919 73.759 1.00146.24 S ATOM 17696 SG CYS C 287 34.767 32.150 70.037 1.00147.61 S ATOM 18975 SG CYS C 470 33.991 29.703 73.108 1.00170.47 S ATOM 26913 SG CYS C1650 91.426 40.020 80.492 1.00117.47 S ATOM 26926 SG CYS C1652 92.298 41.435 83.529 1.00123.40 S ATOM 26945 SG CYS C1655 88.250 41.148 81.363 1.00104.90 S ATOM 27017 SG CYS C1664 91.698 43.447 80.846 1.00 94.43 S ATOM 30656 SG CYS D 39 30.657 64.446 98.896 1.00150.20 S ATOM 30677 SG CYS D 42 28.276 63.367 96.417 1.00142.25 S ATOM 30811 SG CYS D 58 28.190 63.445 100.987 1.00172.20 S ATOM 30836 SG CYS D 61 30.099 61.046 99.380 1.00160.32 S ATOM 30759 SG CYS D 52 38.194 66.180 105.742 1.00186.56 S ATOM 30926 SG CYS D 72 39.020 63.471 103.831 1.00172.93 S ATOM 30950 SG CYS D 75 41.059 66.181 103.848 1.00162.88 S Time building chain proxies: 17.31, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 13.00 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 2.47 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: 12.33 Time building geometry restraints manager: 13.64 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: 100.39 - 107.12: 689 107.12 - 113.84: 18088 113.84 - 120.57: 12449 120.57 - 127.29: 11167 127.29 - 134.02: 233 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 2.440 nonbonded pdb=" O SER A1553 " pdb=" OG SER A1553 " model vdw 2.169 2.440 nonbonded pdb=" OD1 ASP C 650 " pdb=" OG SER C 653 " model vdw 2.208 2.440 ... (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 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 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. 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: 0.680 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: 6.390 Check model and map are aligned: 0.410 Convert atoms to be neutral: 0.250 Process input model: 84.880 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.330 ------------------------------------------------------------------------------- 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 : 0.002 0.049 31536 Z= 0.148 Angle : 0.590 9.130 42626 Z= 0.320 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 : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (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 *********************** 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 fitting. rotamer outliers: 72 poor density : 690 time to evaluate : 3.683 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 outliers start: 72 outliers final: 21 residues processed: 745 average time/residue: 0.4439 time to fit residues: 516.9339 Evaluate side-chains 439 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 418 time to evaluate : 3.754 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2701 time to fit residues: 15.8524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 332 optimal weight: 2.9990 chunk 298 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 201 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 308 optimal weight: 30.0000 chunk 119 optimal weight: 8.9990 chunk 187 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 357 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN A 390 ASN ** A 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN A 629 GLN A 647 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 ASN A1414 GLN ** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1551 ASN A1611 GLN ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1791 HIS A1805 GLN ** A1829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1871 GLN A1888 ASN A1916 ASN B 38 ASN ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN C 430 HIS ** C 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN C 607 ASN ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 HIS ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 741 ASN ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1128 ASN C1296 HIS ** C1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 GLN ** C1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1551 ASN ** C1611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1783 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1861 ASN C1871 GLN C1888 ASN D 38 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.104 31536 Z= 0.368 Angle : 0.821 13.601 42626 Z= 0.421 Chirality : 0.046 0.218 4970 Planarity : 0.006 0.070 5398 Dihedral : 5.162 31.091 4194 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.02 % Favored : 88.90 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.13), residues: 3892 helix: -0.27 (0.12), residues: 1834 sheet: -0.95 (0.30), residues: 296 loop : -3.56 (0.12), residues: 1762 *********************** 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 470 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 454 time to evaluate : 3.772 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 outliers start: 16 outliers final: 6 residues processed: 466 average time/residue: 0.4253 time to fit residues: 318.5685 Evaluate side-chains 315 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 309 time to evaluate : 3.712 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2630 time to fit residues: 8.1541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 198 optimal weight: 0.0030 chunk 111 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 358 optimal weight: 4.9990 chunk 387 optimal weight: 0.9980 chunk 319 optimal weight: 0.9990 chunk 355 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 287 optimal weight: 9.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 390 ASN A 522 ASN ** A 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 704 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1271 HIS ** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN ** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1669 ASN ** A1829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** 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 522 ASN C 629 GLN C 704 HIS ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 HIS C1405 HIS C1414 GLN ** C1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1611 GLN C1669 ASN C1833 ASN C1837 GLN ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 31536 Z= 0.169 Angle : 0.634 14.853 42626 Z= 0.319 Chirality : 0.042 0.213 4970 Planarity : 0.004 0.076 5398 Dihedral : 4.596 27.890 4194 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 3892 helix: 0.30 (0.12), residues: 1848 sheet: -0.46 (0.31), residues: 284 loop : -3.33 (0.13), residues: 1760 *********************** 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 457 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 453 time to evaluate : 3.631 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 outliers start: 4 outliers final: 0 residues processed: 456 average time/residue: 0.4179 time to fit residues: 311.5591 Evaluate side-chains 332 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 3.800 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 354 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 39 optimal weight: 0.0570 chunk 171 optimal weight: 2.9990 chunk 240 optimal weight: 30.0000 chunk 359 optimal weight: 7.9990 chunk 380 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 340 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 546 GLN A 629 GLN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN ** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN ** C 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 GLN ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1271 HIS ** C1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 GLN C1517 ASN ** C1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1791 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** D 73 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 31536 Z= 0.271 Angle : 0.704 12.403 42626 Z= 0.358 Chirality : 0.044 0.220 4970 Planarity : 0.005 0.072 5398 Dihedral : 4.877 29.124 4194 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.41 % Favored : 88.54 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.13), residues: 3892 helix: 0.22 (0.12), residues: 1876 sheet: -0.41 (0.31), residues: 286 loop : -3.30 (0.13), residues: 1730 *********************** 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 417 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 4.055 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 outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.4165 time to fit residues: 284.5229 Evaluate side-chains 290 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 3.798 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 317 optimal weight: 0.5980 chunk 216 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 283 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 chunk 263 optimal weight: 0.0270 chunk 0 optimal weight: 20.0000 chunk 194 optimal weight: 0.2980 chunk 341 optimal weight: 0.2980 chunk 96 optimal weight: 10.0000 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 629 GLN A 704 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 ASN ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1861 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 15 HIS C 629 GLN ** C 644 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** C1517 ASN ** C1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1783 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** D 73 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 31536 Z= 0.162 Angle : 0.635 9.811 42626 Z= 0.313 Chirality : 0.042 0.218 4970 Planarity : 0.004 0.069 5398 Dihedral : 4.495 30.195 4194 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3892 helix: 0.57 (0.12), residues: 1864 sheet: -0.19 (0.34), residues: 250 loop : -3.07 (0.14), residues: 1778 *********************** 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 438 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 438 time to evaluate : 3.873 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 outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.4226 time to fit residues: 302.0803 Evaluate side-chains 315 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 3.713 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 128 optimal weight: 6.9990 chunk 342 optimal weight: 4.9990 chunk 75 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 381 optimal weight: 9.9990 chunk 316 optimal weight: 6.9990 chunk 176 optimal weight: 0.0970 chunk 31 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN ** A1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN A1496 ASN A1517 ASN ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2122 HIS B 53 ASN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN ** C 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1414 GLN C1463 GLN ** C1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1751 HIS D 53 ASN ** D 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 31536 Z= 0.304 Angle : 0.747 13.247 42626 Z= 0.379 Chirality : 0.045 0.252 4970 Planarity : 0.005 0.076 5398 Dihedral : 5.116 31.338 4194 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.08 % Favored : 87.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.13), residues: 3892 helix: 0.27 (0.12), residues: 1868 sheet: -0.63 (0.33), residues: 272 loop : -3.08 (0.14), residues: 1752 *********************** 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 380 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 3.732 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 outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.4349 time to fit residues: 273.8918 Evaluate side-chains 282 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 3.763 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 367 optimal weight: 0.0570 chunk 42 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 278 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 320 optimal weight: 0.0370 chunk 212 optimal weight: 20.0000 chunk 379 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 231 optimal weight: 0.5980 chunk 175 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 704 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1463 GLN ** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 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** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN C 629 GLN ** C 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1463 GLN ** C1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 31536 Z= 0.161 Angle : 0.650 10.892 42626 Z= 0.323 Chirality : 0.041 0.173 4970 Planarity : 0.004 0.067 5398 Dihedral : 4.626 28.368 4194 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3892 helix: 0.63 (0.12), residues: 1852 sheet: -0.20 (0.31), residues: 280 loop : -2.92 (0.14), residues: 1760 *********************** 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 fitting. rotamer outliers: 2 poor density : 421 time to evaluate : 3.783 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 outliers start: 2 outliers final: 0 residues processed: 421 average time/residue: 0.4128 time to fit residues: 284.8447 Evaluate side-chains 311 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 3.686 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 234 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 226 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 241 optimal weight: 0.8980 chunk 258 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 499 ASN A 629 GLN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1414 GLN ** A1517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1751 HIS ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2043 ASN ** 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 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN C 704 HIS ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1517 ASN ** C1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 31536 Z= 0.197 Angle : 0.675 17.006 42626 Z= 0.337 Chirality : 0.042 0.166 4970 Planarity : 0.004 0.066 5398 Dihedral : 4.658 30.575 4194 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.61 % Favored : 89.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3892 helix: 0.67 (0.12), residues: 1854 sheet: -0.15 (0.33), residues: 246 loop : -2.84 (0.14), residues: 1792 *********************** 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 403 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 3.755 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 outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.4108 time to fit residues: 273.3053 Evaluate side-chains 299 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 3.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 345 optimal weight: 5.9990 chunk 363 optimal weight: 0.8980 chunk 331 optimal weight: 4.9990 chunk 353 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 277 optimal weight: 40.0000 chunk 108 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 334 optimal weight: 0.9980 chunk 352 optimal weight: 0.0870 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 GLN A 704 HIS ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1463 GLN A1517 ASN ** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 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** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS C 629 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1496 ASN C1517 ASN ** C2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 31536 Z= 0.160 Angle : 0.654 14.339 42626 Z= 0.322 Chirality : 0.041 0.198 4970 Planarity : 0.004 0.066 5398 Dihedral : 4.487 27.999 4194 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3892 helix: 0.78 (0.12), residues: 1850 sheet: -0.09 (0.33), residues: 246 loop : -2.77 (0.14), residues: 1796 *********************** 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 419 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 418 time to evaluate : 3.724 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 outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.4169 time to fit residues: 290.3379 Evaluate side-chains 298 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.923 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 232 optimal weight: 1.9990 chunk 374 optimal weight: 50.0000 chunk 228 optimal weight: 9.9990 chunk 177 optimal weight: 50.0000 chunk 260 optimal weight: 6.9990 chunk 392 optimal weight: 8.9990 chunk 361 optimal weight: 6.9990 chunk 312 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 629 GLN ** A 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1463 GLN ** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** 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 629 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1517 ASN ** C2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.612 31536 Z= 0.340 Angle : 0.809 73.899 42626 Z= 0.385 Chirality : 0.043 0.211 4970 Planarity : 0.006 0.203 5398 Dihedral : 4.564 28.056 4194 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.87 % Favored : 89.11 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.14), residues: 3892 helix: 0.76 (0.12), residues: 1852 sheet: -0.19 (0.31), residues: 280 loop : -2.82 (0.14), residues: 1760 ********************** 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 406 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 405 time to evaluate : 4.270 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 outliers start: 1 outliers final: 0 residues processed: 405 average time/residue: 0.4123 time to fit residues: 277.3669 Evaluate side-chains 298 residues out of total 3632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.918 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 394 random chunks: chunk 248 optimal weight: 10.0000 chunk 332 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 313 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 321 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 chunk 57 optimal weight: 2.9990 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 629 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1734 ASN ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1837 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** ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 HIS ** C 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 887 GLN C1517 ASN ** C2043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.132868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.099654 restraints weight = 133835.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.100328 restraints weight = 96465.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.100445 restraints weight = 72789.936| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.6825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 31536 Z= 0.185 Angle : 0.665 15.351 42626 Z= 0.330 Chirality : 0.042 0.183 4970 Planarity : 0.004 0.102 5398 Dihedral : 4.579 27.776 4194 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3892 helix: 0.75 (0.12), residues: 1856 sheet: -0.08 (0.31), residues: 278 loop : -2.75 (0.14), residues: 1758 =============================================================================== Job complete usr+sys time: 6143.40 seconds wall clock time: 113 minutes 12.90 seconds (6792.90 seconds total)