Starting phenix.real_space_refine (version: dev) on Tue Dec 13 14:26:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3p_25667/12_2022/7t3p_25667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3p_25667/12_2022/7t3p_25667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3p_25667/12_2022/7t3p_25667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3p_25667/12_2022/7t3p_25667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3p_25667/12_2022/7t3p_25667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3p_25667/12_2022/7t3p_25667_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.058 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 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 66992 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2066, 16692 Classifications: {'peptide': 2066} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 2008} Chain breaks: 26 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 16692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2066, 16692 Classifications: {'peptide': 2066} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 2008} Chain breaks: 26 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 16692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2066, 16692 Classifications: {'peptide': 2066} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 2008} Chain breaks: 26 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 16692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2066, 16692 Classifications: {'peptide': 2066} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 2008} Chain breaks: 26 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'UNK:plan-1': 19} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15974 SG CYS A2538 100.622 128.105 100.327 1.00 35.00 S ATOM 15999 SG CYS A2541 101.879 125.743 97.648 1.00 26.08 S ATOM 32666 SG CYS B2538 110.264 100.556 100.394 1.00 35.00 S ATOM 32691 SG CYS B2541 112.629 101.802 97.713 1.00 26.08 S ATOM 49358 SG CYS C2538 137.835 110.352 100.326 1.00 35.00 S ATOM 49383 SG CYS C2541 136.578 112.713 97.646 1.00 26.08 S ATOM 66050 SG CYS D2538 128.108 137.838 100.324 1.00 35.00 S ATOM 66075 SG CYS D2541 125.746 136.581 97.645 1.00 26.08 S Time building chain proxies: 27.00, per 1000 atoms: 0.40 Number of scatterers: 66992 At special positions: 0 Unit cell: (239.292, 239.292, 181.332, 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 4 29.99 S 404 16.00 P 24 15.00 O 12340 8.00 N 11420 7.00 C 42800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2455 " - pdb=" SG CYS A2461 " distance=2.03 Simple disulfide: pdb=" SG CYS B2455 " - pdb=" SG CYS B2461 " distance=2.03 Simple disulfide: pdb=" SG CYS C2455 " - pdb=" SG CYS C2461 " distance=2.03 Simple disulfide: pdb=" SG CYS D2455 " - pdb=" SG CYS D2461 " distance=2.03 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: 21.15 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2701 " pdb="ZN ZN A2701 " - pdb=" NE2 HIS A2558 " pdb="ZN ZN A2701 " - pdb=" ND1 HIS A2563 " pdb="ZN ZN A2701 " - pdb=" SG CYS A2541 " pdb="ZN ZN A2701 " - pdb=" SG CYS A2538 " pdb=" ZN B2701 " pdb="ZN ZN B2701 " - pdb=" NE2 HIS B2558 " pdb="ZN ZN B2701 " - pdb=" ND1 HIS B2563 " pdb="ZN ZN B2701 " - pdb=" SG CYS B2541 " pdb="ZN ZN B2701 " - pdb=" SG CYS B2538 " pdb=" ZN C2701 " pdb="ZN ZN C2701 " - pdb=" NE2 HIS C2558 " pdb="ZN ZN C2701 " - pdb=" ND1 HIS C2563 " pdb="ZN ZN C2701 " - pdb=" SG CYS C2541 " pdb="ZN ZN C2701 " - pdb=" SG CYS C2538 " pdb=" ZN D2701 " pdb="ZN ZN D2701 " - pdb=" NE2 HIS D2558 " pdb="ZN ZN D2701 " - pdb=" ND1 HIS D2563 " pdb="ZN ZN D2701 " - pdb=" SG CYS D2541 " pdb="ZN ZN D2701 " - pdb=" SG CYS D2538 " Number of angles added : 4 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15872 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 384 helices and 60 sheets defined 60.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.17 Creating SS restraints... Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 87 through 111 Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 466 through 484 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.560A pdb=" N ARG A 510 " --> pdb=" O GLN A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 526 Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 547 through 563 Processing helix chain 'A' and resid 568 through 575 Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 591 through 601 removed outlier: 4.393A pdb=" N ASN A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 625 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 646 through 656 Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 723 through 739 Processing helix chain 'A' and resid 745 through 754 removed outlier: 4.306A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 764 Processing helix chain 'A' and resid 771 through 784 Processing helix chain 'A' and resid 812 through 819 Processing helix chain 'A' and resid 831 through 845 Processing helix chain 'A' and resid 854 through 873 removed outlier: 3.774A pdb=" N LYS A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 892 Processing helix chain 'A' and resid 962 through 997 Processing helix chain 'A' and resid 1027 through 1035 Processing helix chain 'A' and resid 1053 through 1064 Processing helix chain 'A' and resid 1068 through 1094 removed outlier: 3.856A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG A1085 " --> pdb=" O HIS A1081 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN A1094 " --> pdb=" O HIS A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1122 Processing helix chain 'A' and resid 1169 through 1182 Processing helix chain 'A' and resid 1189 through 1200 Processing helix chain 'A' and resid 1202 through 1211 Processing helix chain 'A' and resid 1220 through 1235 Processing helix chain 'A' and resid 1240 through 1249 removed outlier: 3.514A pdb=" N LYS A1248 " --> pdb=" O ALA A1244 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N HIS A1249 " --> pdb=" O LEU A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1267 Processing helix chain 'A' and resid 1272 through 1275 No H-bonds generated for 'chain 'A' and resid 1272 through 1275' Processing helix chain 'A' and resid 1280 through 1292 removed outlier: 3.822A pdb=" N PHE A1286 " --> pdb=" O VAL A1282 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A1287 " --> pdb=" O LEU A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1297 through 1307 Processing helix chain 'A' and resid 1315 through 1328 Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1361 through 1376 Processing helix chain 'A' and resid 1382 through 1390 Processing helix chain 'A' and resid 1393 through 1401 Processing helix chain 'A' and resid 1407 through 1420 Processing helix chain 'A' and resid 1430 through 1433 removed outlier: 3.600A pdb=" N THR A1433 " --> pdb=" O GLU A1430 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1430 through 1433' Processing helix chain 'A' and resid 1436 through 1450 Processing helix chain 'A' and resid 1463 through 1470 Processing helix chain 'A' and resid 1472 through 1481 Processing helix chain 'A' and resid 1492 through 1508 Processing helix chain 'A' and resid 1590 through 1605 Processing helix chain 'A' and resid 1607 through 1622 Processing helix chain 'A' and resid 1633 through 1639 Processing helix chain 'A' and resid 1642 through 1654 Processing helix chain 'A' and resid 1659 through 1673 removed outlier: 3.579A pdb=" N LEU A1673 " --> pdb=" O LEU A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1694 Processing helix chain 'A' and resid 1722 through 1731 Processing helix chain 'A' and resid 1733 through 1743 Processing helix chain 'A' and resid 1747 through 1761 Processing helix chain 'A' and resid 1766 through 1778 Processing helix chain 'A' and resid 1780 through 1802 removed outlier: 3.844A pdb=" N GLU A1783 " --> pdb=" O LYS A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1884 removed outlier: 3.567A pdb=" N MET A1870 " --> pdb=" O SER A1866 " (cutoff:3.500A) Proline residue: A1872 - end of helix removed outlier: 6.076A pdb=" N ASN A1883 " --> pdb=" O LEU A1879 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N HIS A1884 " --> pdb=" O LEU A1880 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1893 Processing helix chain 'A' and resid 1903 through 1915 Processing helix chain 'A' and resid 1934 through 1949 Processing helix chain 'A' and resid 1955 through 1961 Processing helix chain 'A' and resid 1967 through 1975 removed outlier: 3.578A pdb=" N THR A1971 " --> pdb=" O ILE A1967 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 2003 Processing helix chain 'A' and resid 2011 through 2019 removed outlier: 3.883A pdb=" N SER A2019 " --> pdb=" O ARG A2015 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2033 Processing helix chain 'A' and resid 2046 through 2063 removed outlier: 3.763A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N HIS A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2071 Processing helix chain 'A' and resid 2113 through 2120 Processing helix chain 'A' and resid 2142 through 2146 Processing helix chain 'A' and resid 2149 through 2158 Processing helix chain 'A' and resid 2168 through 2190 removed outlier: 4.402A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2199 Processing helix chain 'A' and resid 2202 through 2222 Processing helix chain 'A' and resid 2262 through 2275 Processing helix chain 'A' and resid 2280 through 2304 Processing helix chain 'A' and resid 2319 through 2335 Processing helix chain 'A' and resid 2338 through 2351 removed outlier: 3.528A pdb=" N ILE A2343 " --> pdb=" O PHE A2340 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2363 removed outlier: 3.771A pdb=" N VAL A2362 " --> pdb=" O VAL A2358 " (cutoff:3.500A) Processing helix chain 'A' and resid 2366 through 2390 Processing helix chain 'A' and resid 2392 through 2394 No H-bonds generated for 'chain 'A' and resid 2392 through 2394' Processing helix chain 'A' and resid 2458 through 2468 Processing helix chain 'A' and resid 2490 through 2504 Processing helix chain 'A' and resid 2508 through 2536 removed outlier: 3.575A pdb=" N ILE A2512 " --> pdb=" O VAL A2508 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) Processing helix chain 'A' and resid 2546 through 2548 No H-bonds generated for 'chain 'A' and resid 2546 through 2548' Processing helix chain 'A' and resid 2555 through 2560 Processing helix chain 'A' and resid 2565 through 2577 removed outlier: 3.710A pdb=" N LEU A2569 " --> pdb=" O MET A2565 " (cutoff:3.500A) Processing helix chain 'A' and resid 2580 through 2582 No H-bonds generated for 'chain 'A' and resid 2580 through 2582' Processing helix chain 'A' and resid 2585 through 2596 Processing helix chain 'A' and resid 2608 through 2610 No H-bonds generated for 'chain 'A' and resid 2608 through 2610' Processing helix chain 'A' and resid 2629 through 2645 removed outlier: 3.693A pdb=" N UNK A2633 " --> pdb=" O UNK A2629 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N UNK A2645 " --> pdb=" O UNK A2641 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 87 through 111 Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 466 through 484 Processing helix chain 'B' and resid 503 through 511 removed outlier: 3.560A pdb=" N ARG B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 526 Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 547 through 563 Processing helix chain 'B' and resid 568 through 575 Processing helix chain 'B' and resid 578 through 583 Processing helix chain 'B' and resid 591 through 601 removed outlier: 4.392A pdb=" N ASN B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 612 through 625 Processing helix chain 'B' and resid 628 through 638 Processing helix chain 'B' and resid 646 through 656 Processing helix chain 'B' and resid 659 through 661 No H-bonds generated for 'chain 'B' and resid 659 through 661' Processing helix chain 'B' and resid 708 through 717 Processing helix chain 'B' and resid 723 through 739 Processing helix chain 'B' and resid 745 through 754 removed outlier: 4.306A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 764 Processing helix chain 'B' and resid 771 through 784 Processing helix chain 'B' and resid 812 through 819 Processing helix chain 'B' and resid 831 through 845 Processing helix chain 'B' and resid 854 through 873 removed outlier: 3.774A pdb=" N LYS B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 892 Processing helix chain 'B' and resid 962 through 997 Processing helix chain 'B' and resid 1027 through 1035 Processing helix chain 'B' and resid 1053 through 1064 Processing helix chain 'B' and resid 1068 through 1094 removed outlier: 3.855A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG B1085 " --> pdb=" O HIS B1081 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN B1086 " --> pdb=" O PHE B1082 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B1094 " --> pdb=" O HIS B1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1122 Processing helix chain 'B' and resid 1169 through 1182 Processing helix chain 'B' and resid 1189 through 1200 Processing helix chain 'B' and resid 1202 through 1211 Processing helix chain 'B' and resid 1220 through 1235 Processing helix chain 'B' and resid 1240 through 1249 removed outlier: 3.514A pdb=" N LYS B1248 " --> pdb=" O ALA B1244 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1267 Processing helix chain 'B' and resid 1272 through 1275 No H-bonds generated for 'chain 'B' and resid 1272 through 1275' Processing helix chain 'B' and resid 1280 through 1292 removed outlier: 3.823A pdb=" N PHE B1286 " --> pdb=" O VAL B1282 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL B1287 " --> pdb=" O LEU B1283 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1307 Processing helix chain 'B' and resid 1315 through 1328 Processing helix chain 'B' and resid 1339 through 1351 Processing helix chain 'B' and resid 1361 through 1376 Processing helix chain 'B' and resid 1382 through 1390 Processing helix chain 'B' and resid 1393 through 1401 Processing helix chain 'B' and resid 1407 through 1420 Processing helix chain 'B' and resid 1430 through 1433 removed outlier: 3.600A pdb=" N THR B1433 " --> pdb=" O GLU B1430 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1430 through 1433' Processing helix chain 'B' and resid 1436 through 1450 Processing helix chain 'B' and resid 1463 through 1470 Processing helix chain 'B' and resid 1472 through 1481 Processing helix chain 'B' and resid 1492 through 1508 Processing helix chain 'B' and resid 1590 through 1605 Processing helix chain 'B' and resid 1607 through 1622 Processing helix chain 'B' and resid 1633 through 1639 Processing helix chain 'B' and resid 1642 through 1654 Processing helix chain 'B' and resid 1659 through 1673 removed outlier: 3.578A pdb=" N LEU B1673 " --> pdb=" O LEU B1669 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1694 Processing helix chain 'B' and resid 1722 through 1731 Processing helix chain 'B' and resid 1733 through 1743 Processing helix chain 'B' and resid 1747 through 1761 Processing helix chain 'B' and resid 1766 through 1778 Processing helix chain 'B' and resid 1780 through 1802 removed outlier: 3.844A pdb=" N GLU B1783 " --> pdb=" O LYS B1780 " (cutoff:3.500A) Processing helix chain 'B' and resid 1865 through 1884 removed outlier: 3.567A pdb=" N MET B1870 " --> pdb=" O SER B1866 " (cutoff:3.500A) Proline residue: B1872 - end of helix removed outlier: 6.076A pdb=" N ASN B1883 " --> pdb=" O LEU B1879 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N HIS B1884 " --> pdb=" O LEU B1880 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1893 Processing helix chain 'B' and resid 1903 through 1915 Processing helix chain 'B' and resid 1934 through 1949 Processing helix chain 'B' and resid 1955 through 1961 Processing helix chain 'B' and resid 1967 through 1975 removed outlier: 3.578A pdb=" N THR B1971 " --> pdb=" O ILE B1967 " (cutoff:3.500A) Processing helix chain 'B' and resid 1987 through 2003 Processing helix chain 'B' and resid 2011 through 2019 removed outlier: 3.883A pdb=" N SER B2019 " --> pdb=" O ARG B2015 " (cutoff:3.500A) Processing helix chain 'B' and resid 2022 through 2033 Processing helix chain 'B' and resid 2046 through 2063 removed outlier: 3.763A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N HIS B2063 " --> pdb=" O GLN B2059 " (cutoff:3.500A) Processing helix chain 'B' and resid 2065 through 2071 Processing helix chain 'B' and resid 2113 through 2120 Processing helix chain 'B' and resid 2142 through 2146 Processing helix chain 'B' and resid 2149 through 2158 Processing helix chain 'B' and resid 2168 through 2190 removed outlier: 4.401A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2192 through 2199 Processing helix chain 'B' and resid 2202 through 2222 Processing helix chain 'B' and resid 2262 through 2275 Processing helix chain 'B' and resid 2280 through 2304 Processing helix chain 'B' and resid 2319 through 2335 Processing helix chain 'B' and resid 2338 through 2351 removed outlier: 3.528A pdb=" N ILE B2343 " --> pdb=" O PHE B2340 " (cutoff:3.500A) Processing helix chain 'B' and resid 2353 through 2363 removed outlier: 3.771A pdb=" N VAL B2362 " --> pdb=" O VAL B2358 " (cutoff:3.500A) Processing helix chain 'B' and resid 2366 through 2390 Processing helix chain 'B' and resid 2392 through 2394 No H-bonds generated for 'chain 'B' and resid 2392 through 2394' Processing helix chain 'B' and resid 2458 through 2468 Processing helix chain 'B' and resid 2490 through 2504 Processing helix chain 'B' and resid 2508 through 2536 removed outlier: 3.575A pdb=" N ILE B2512 " --> pdb=" O VAL B2508 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2546 through 2548 No H-bonds generated for 'chain 'B' and resid 2546 through 2548' Processing helix chain 'B' and resid 2555 through 2560 Processing helix chain 'B' and resid 2565 through 2577 removed outlier: 3.710A pdb=" N LEU B2569 " --> pdb=" O MET B2565 " (cutoff:3.500A) Processing helix chain 'B' and resid 2580 through 2582 No H-bonds generated for 'chain 'B' and resid 2580 through 2582' Processing helix chain 'B' and resid 2585 through 2596 Processing helix chain 'B' and resid 2608 through 2610 No H-bonds generated for 'chain 'B' and resid 2608 through 2610' Processing helix chain 'B' and resid 2629 through 2645 removed outlier: 3.693A pdb=" N UNK B2633 " --> pdb=" O UNK B2629 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N UNK B2645 " --> pdb=" O UNK B2641 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 87 through 111 Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 466 through 484 Processing helix chain 'C' and resid 503 through 511 removed outlier: 3.560A pdb=" N ARG C 510 " --> pdb=" O GLN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 526 Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 547 through 563 Processing helix chain 'C' and resid 568 through 575 Processing helix chain 'C' and resid 578 through 583 Processing helix chain 'C' and resid 591 through 601 removed outlier: 4.393A pdb=" N ASN C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 609 Processing helix chain 'C' and resid 612 through 625 Processing helix chain 'C' and resid 628 through 638 Processing helix chain 'C' and resid 646 through 656 Processing helix chain 'C' and resid 659 through 661 No H-bonds generated for 'chain 'C' and resid 659 through 661' Processing helix chain 'C' and resid 708 through 717 Processing helix chain 'C' and resid 723 through 739 Processing helix chain 'C' and resid 745 through 754 removed outlier: 4.306A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 764 Processing helix chain 'C' and resid 771 through 784 Processing helix chain 'C' and resid 812 through 819 Processing helix chain 'C' and resid 831 through 845 Processing helix chain 'C' and resid 854 through 873 removed outlier: 3.774A pdb=" N LYS C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 892 Processing helix chain 'C' and resid 962 through 997 Processing helix chain 'C' and resid 1027 through 1035 Processing helix chain 'C' and resid 1053 through 1064 Processing helix chain 'C' and resid 1068 through 1094 removed outlier: 3.856A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG C1085 " --> pdb=" O HIS C1081 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLN C1086 " --> pdb=" O PHE C1082 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C1094 " --> pdb=" O HIS C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1122 Processing helix chain 'C' and resid 1169 through 1182 Processing helix chain 'C' and resid 1189 through 1200 Processing helix chain 'C' and resid 1202 through 1211 Processing helix chain 'C' and resid 1220 through 1235 Processing helix chain 'C' and resid 1240 through 1249 removed outlier: 3.514A pdb=" N LYS C1248 " --> pdb=" O ALA C1244 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 through 1267 Processing helix chain 'C' and resid 1272 through 1275 No H-bonds generated for 'chain 'C' and resid 1272 through 1275' Processing helix chain 'C' and resid 1280 through 1292 removed outlier: 3.822A pdb=" N PHE C1286 " --> pdb=" O VAL C1282 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C1287 " --> pdb=" O LEU C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1307 Processing helix chain 'C' and resid 1315 through 1328 Processing helix chain 'C' and resid 1339 through 1351 Processing helix chain 'C' and resid 1361 through 1376 Processing helix chain 'C' and resid 1382 through 1390 Processing helix chain 'C' and resid 1393 through 1401 Processing helix chain 'C' and resid 1407 through 1420 Processing helix chain 'C' and resid 1430 through 1433 removed outlier: 3.599A pdb=" N THR C1433 " --> pdb=" O GLU C1430 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1430 through 1433' Processing helix chain 'C' and resid 1436 through 1450 Processing helix chain 'C' and resid 1463 through 1470 Processing helix chain 'C' and resid 1472 through 1481 Processing helix chain 'C' and resid 1492 through 1508 Processing helix chain 'C' and resid 1590 through 1605 Processing helix chain 'C' and resid 1607 through 1622 Processing helix chain 'C' and resid 1633 through 1639 Processing helix chain 'C' and resid 1642 through 1654 Processing helix chain 'C' and resid 1659 through 1673 removed outlier: 3.579A pdb=" N LEU C1673 " --> pdb=" O LEU C1669 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1694 Processing helix chain 'C' and resid 1722 through 1731 Processing helix chain 'C' and resid 1733 through 1743 Processing helix chain 'C' and resid 1747 through 1761 Processing helix chain 'C' and resid 1766 through 1778 Processing helix chain 'C' and resid 1780 through 1802 removed outlier: 3.844A pdb=" N GLU C1783 " --> pdb=" O LYS C1780 " (cutoff:3.500A) Processing helix chain 'C' and resid 1865 through 1884 removed outlier: 3.567A pdb=" N MET C1870 " --> pdb=" O SER C1866 " (cutoff:3.500A) Proline residue: C1872 - end of helix removed outlier: 6.076A pdb=" N ASN C1883 " --> pdb=" O LEU C1879 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N HIS C1884 " --> pdb=" O LEU C1880 " (cutoff:3.500A) Processing helix chain 'C' and resid 1886 through 1893 Processing helix chain 'C' and resid 1903 through 1915 Processing helix chain 'C' and resid 1934 through 1949 Processing helix chain 'C' and resid 1955 through 1961 Processing helix chain 'C' and resid 1967 through 1975 removed outlier: 3.578A pdb=" N THR C1971 " --> pdb=" O ILE C1967 " (cutoff:3.500A) Processing helix chain 'C' and resid 1987 through 2003 Processing helix chain 'C' and resid 2011 through 2019 removed outlier: 3.883A pdb=" N SER C2019 " --> pdb=" O ARG C2015 " (cutoff:3.500A) Processing helix chain 'C' and resid 2022 through 2033 Processing helix chain 'C' and resid 2046 through 2063 removed outlier: 3.764A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS C2063 " --> pdb=" O GLN C2059 " (cutoff:3.500A) Processing helix chain 'C' and resid 2065 through 2071 Processing helix chain 'C' and resid 2113 through 2120 Processing helix chain 'C' and resid 2142 through 2146 Processing helix chain 'C' and resid 2149 through 2158 Processing helix chain 'C' and resid 2168 through 2190 removed outlier: 4.401A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) Processing helix chain 'C' and resid 2192 through 2199 Processing helix chain 'C' and resid 2202 through 2222 Processing helix chain 'C' and resid 2262 through 2275 Processing helix chain 'C' and resid 2280 through 2304 Processing helix chain 'C' and resid 2319 through 2335 Processing helix chain 'C' and resid 2338 through 2351 removed outlier: 3.528A pdb=" N ILE C2343 " --> pdb=" O PHE C2340 " (cutoff:3.500A) Processing helix chain 'C' and resid 2353 through 2363 removed outlier: 3.771A pdb=" N VAL C2362 " --> pdb=" O VAL C2358 " (cutoff:3.500A) Processing helix chain 'C' and resid 2366 through 2390 Processing helix chain 'C' and resid 2392 through 2394 No H-bonds generated for 'chain 'C' and resid 2392 through 2394' Processing helix chain 'C' and resid 2458 through 2468 Processing helix chain 'C' and resid 2490 through 2504 Processing helix chain 'C' and resid 2508 through 2536 removed outlier: 3.575A pdb=" N ILE C2512 " --> pdb=" O VAL C2508 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) Processing helix chain 'C' and resid 2546 through 2548 No H-bonds generated for 'chain 'C' and resid 2546 through 2548' Processing helix chain 'C' and resid 2555 through 2560 Processing helix chain 'C' and resid 2565 through 2577 removed outlier: 3.710A pdb=" N LEU C2569 " --> pdb=" O MET C2565 " (cutoff:3.500A) Processing helix chain 'C' and resid 2580 through 2582 No H-bonds generated for 'chain 'C' and resid 2580 through 2582' Processing helix chain 'C' and resid 2585 through 2596 Processing helix chain 'C' and resid 2608 through 2610 No H-bonds generated for 'chain 'C' and resid 2608 through 2610' Processing helix chain 'C' and resid 2629 through 2645 removed outlier: 3.693A pdb=" N UNK C2633 " --> pdb=" O UNK C2629 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N UNK C2645 " --> pdb=" O UNK C2641 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 87 through 111 Processing helix chain 'D' and resid 273 through 275 No H-bonds generated for 'chain 'D' and resid 273 through 275' Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 466 through 484 Processing helix chain 'D' and resid 503 through 511 removed outlier: 3.560A pdb=" N ARG D 510 " --> pdb=" O GLN D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 526 Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 547 through 563 Processing helix chain 'D' and resid 568 through 575 Processing helix chain 'D' and resid 578 through 583 Processing helix chain 'D' and resid 591 through 601 removed outlier: 4.393A pdb=" N ASN D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 609 Processing helix chain 'D' and resid 612 through 625 Processing helix chain 'D' and resid 628 through 638 Processing helix chain 'D' and resid 646 through 656 Processing helix chain 'D' and resid 659 through 661 No H-bonds generated for 'chain 'D' and resid 659 through 661' Processing helix chain 'D' and resid 708 through 717 Processing helix chain 'D' and resid 723 through 739 Processing helix chain 'D' and resid 745 through 754 removed outlier: 4.306A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 764 Processing helix chain 'D' and resid 771 through 784 Processing helix chain 'D' and resid 812 through 819 Processing helix chain 'D' and resid 831 through 845 Processing helix chain 'D' and resid 854 through 873 removed outlier: 3.773A pdb=" N LYS D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 878 through 892 Processing helix chain 'D' and resid 962 through 997 Processing helix chain 'D' and resid 1027 through 1035 Processing helix chain 'D' and resid 1053 through 1064 Processing helix chain 'D' and resid 1068 through 1094 removed outlier: 3.856A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG D1085 " --> pdb=" O HIS D1081 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN D1086 " --> pdb=" O PHE D1082 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN D1094 " --> pdb=" O HIS D1090 " (cutoff:3.500A) Processing helix chain 'D' and resid 1101 through 1122 Processing helix chain 'D' and resid 1169 through 1182 Processing helix chain 'D' and resid 1189 through 1200 Processing helix chain 'D' and resid 1202 through 1211 Processing helix chain 'D' and resid 1220 through 1235 Processing helix chain 'D' and resid 1240 through 1249 removed outlier: 3.514A pdb=" N LYS D1248 " --> pdb=" O ALA D1244 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) Processing helix chain 'D' and resid 1258 through 1267 Processing helix chain 'D' and resid 1272 through 1275 No H-bonds generated for 'chain 'D' and resid 1272 through 1275' Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.822A pdb=" N PHE D1286 " --> pdb=" O VAL D1282 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL D1287 " --> pdb=" O LEU D1283 " (cutoff:3.500A) Processing helix chain 'D' and resid 1297 through 1307 Processing helix chain 'D' and resid 1315 through 1328 Processing helix chain 'D' and resid 1339 through 1351 Processing helix chain 'D' and resid 1361 through 1376 Processing helix chain 'D' and resid 1382 through 1390 Processing helix chain 'D' and resid 1393 through 1401 Processing helix chain 'D' and resid 1407 through 1420 Processing helix chain 'D' and resid 1430 through 1433 removed outlier: 3.600A pdb=" N THR D1433 " --> pdb=" O GLU D1430 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1430 through 1433' Processing helix chain 'D' and resid 1436 through 1450 Processing helix chain 'D' and resid 1463 through 1470 Processing helix chain 'D' and resid 1472 through 1481 Processing helix chain 'D' and resid 1492 through 1508 Processing helix chain 'D' and resid 1590 through 1605 Processing helix chain 'D' and resid 1607 through 1622 Processing helix chain 'D' and resid 1633 through 1639 Processing helix chain 'D' and resid 1642 through 1654 Processing helix chain 'D' and resid 1659 through 1673 removed outlier: 3.579A pdb=" N LEU D1673 " --> pdb=" O LEU D1669 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1694 Processing helix chain 'D' and resid 1722 through 1731 Processing helix chain 'D' and resid 1733 through 1743 Processing helix chain 'D' and resid 1747 through 1761 Processing helix chain 'D' and resid 1766 through 1778 Processing helix chain 'D' and resid 1780 through 1802 removed outlier: 3.844A pdb=" N GLU D1783 " --> pdb=" O LYS D1780 " (cutoff:3.500A) Processing helix chain 'D' and resid 1865 through 1884 removed outlier: 3.567A pdb=" N MET D1870 " --> pdb=" O SER D1866 " (cutoff:3.500A) Proline residue: D1872 - end of helix removed outlier: 6.076A pdb=" N ASN D1883 " --> pdb=" O LEU D1879 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N HIS D1884 " --> pdb=" O LEU D1880 " (cutoff:3.500A) Processing helix chain 'D' and resid 1886 through 1893 Processing helix chain 'D' and resid 1903 through 1915 Processing helix chain 'D' and resid 1934 through 1949 Processing helix chain 'D' and resid 1955 through 1961 Processing helix chain 'D' and resid 1967 through 1975 removed outlier: 3.578A pdb=" N THR D1971 " --> pdb=" O ILE D1967 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 2003 Processing helix chain 'D' and resid 2011 through 2019 removed outlier: 3.883A pdb=" N SER D2019 " --> pdb=" O ARG D2015 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2033 Processing helix chain 'D' and resid 2046 through 2063 removed outlier: 3.763A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS D2063 " --> pdb=" O GLN D2059 " (cutoff:3.500A) Processing helix chain 'D' and resid 2065 through 2071 Processing helix chain 'D' and resid 2113 through 2120 Processing helix chain 'D' and resid 2142 through 2146 Processing helix chain 'D' and resid 2149 through 2158 Processing helix chain 'D' and resid 2168 through 2190 removed outlier: 4.401A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER D2190 " --> pdb=" O ARG D2186 " (cutoff:3.500A) Processing helix chain 'D' and resid 2192 through 2199 Processing helix chain 'D' and resid 2202 through 2222 Processing helix chain 'D' and resid 2262 through 2275 Processing helix chain 'D' and resid 2280 through 2304 Processing helix chain 'D' and resid 2319 through 2335 Processing helix chain 'D' and resid 2338 through 2351 removed outlier: 3.528A pdb=" N ILE D2343 " --> pdb=" O PHE D2340 " (cutoff:3.500A) Processing helix chain 'D' and resid 2353 through 2363 removed outlier: 3.771A pdb=" N VAL D2362 " --> pdb=" O VAL D2358 " (cutoff:3.500A) Processing helix chain 'D' and resid 2366 through 2390 Processing helix chain 'D' and resid 2392 through 2394 No H-bonds generated for 'chain 'D' and resid 2392 through 2394' Processing helix chain 'D' and resid 2458 through 2468 Processing helix chain 'D' and resid 2490 through 2504 Processing helix chain 'D' and resid 2508 through 2536 removed outlier: 3.574A pdb=" N ILE D2512 " --> pdb=" O VAL D2508 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) Processing helix chain 'D' and resid 2546 through 2548 No H-bonds generated for 'chain 'D' and resid 2546 through 2548' Processing helix chain 'D' and resid 2555 through 2560 Processing helix chain 'D' and resid 2565 through 2577 removed outlier: 3.710A pdb=" N LEU D2569 " --> pdb=" O MET D2565 " (cutoff:3.500A) Processing helix chain 'D' and resid 2580 through 2582 No H-bonds generated for 'chain 'D' and resid 2580 through 2582' Processing helix chain 'D' and resid 2585 through 2596 Processing helix chain 'D' and resid 2608 through 2610 No H-bonds generated for 'chain 'D' and resid 2608 through 2610' Processing helix chain 'D' and resid 2629 through 2645 removed outlier: 3.693A pdb=" N UNK D2633 " --> pdb=" O UNK D2629 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N UNK D2645 " --> pdb=" O UNK D2641 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 Processing sheet with id= B, first strand: chain 'A' and resid 57 through 61 removed outlier: 3.820A pdb=" N SER A 120 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 194 through 196 Processing sheet with id= D, first strand: chain 'A' and resid 241 through 245 Processing sheet with id= E, first strand: chain 'A' and resid 251 through 257 removed outlier: 4.428A pdb=" N PHE A 251 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 283 through 287 Processing sheet with id= G, first strand: chain 'A' and resid 314 through 318 Processing sheet with id= H, first strand: chain 'A' and resid 367 through 371 Processing sheet with id= I, first strand: chain 'A' and resid 397 through 400 Processing sheet with id= J, first strand: chain 'A' and resid 667 through 670 Processing sheet with id= K, first strand: chain 'A' and resid 800 through 802 removed outlier: 6.181A pdb=" N GLN A1096 " --> pdb=" O ARG A 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'A' and resid 2121 through 2127 Processing sheet with id= M, first strand: chain 'A' and resid 2396 through 2398 Processing sheet with id= N, first strand: chain 'A' and resid 13 through 18 removed outlier: 6.132A pdb=" N SER A 15 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU A 223 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A 17 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE A 221 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 132 through 140 removed outlier: 3.877A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 26 through 28 Processing sheet with id= Q, first strand: chain 'B' and resid 57 through 61 removed outlier: 3.819A pdb=" N SER B 120 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 194 through 196 Processing sheet with id= S, first strand: chain 'B' and resid 241 through 245 Processing sheet with id= T, first strand: chain 'B' and resid 251 through 257 removed outlier: 4.429A pdb=" N PHE B 251 " --> pdb=" O ARG B 266 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 283 through 287 Processing sheet with id= V, first strand: chain 'B' and resid 314 through 318 Processing sheet with id= W, first strand: chain 'B' and resid 367 through 371 Processing sheet with id= X, first strand: chain 'B' and resid 397 through 400 Processing sheet with id= Y, first strand: chain 'B' and resid 667 through 670 Processing sheet with id= Z, first strand: chain 'B' and resid 800 through 802 removed outlier: 6.181A pdb=" N GLN B1096 " --> pdb=" O ARG B 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'B' and resid 2121 through 2127 Processing sheet with id= AB, first strand: chain 'B' and resid 2396 through 2398 Processing sheet with id= AC, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.132A pdb=" N SER B 15 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LEU B 223 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR B 17 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE B 221 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 132 through 140 removed outlier: 3.877A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 26 through 28 Processing sheet with id= AF, first strand: chain 'C' and resid 57 through 61 removed outlier: 3.820A pdb=" N SER C 120 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 194 through 196 Processing sheet with id= AH, first strand: chain 'C' and resid 241 through 245 Processing sheet with id= AI, first strand: chain 'C' and resid 251 through 257 removed outlier: 4.428A pdb=" N PHE C 251 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 283 through 287 Processing sheet with id= AK, first strand: chain 'C' and resid 314 through 318 Processing sheet with id= AL, first strand: chain 'C' and resid 367 through 371 Processing sheet with id= AM, first strand: chain 'C' and resid 397 through 400 Processing sheet with id= AN, first strand: chain 'C' and resid 667 through 670 Processing sheet with id= AO, first strand: chain 'C' and resid 800 through 802 removed outlier: 6.181A pdb=" N GLN C1096 " --> pdb=" O ARG C 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'C' and resid 2121 through 2127 Processing sheet with id= AQ, first strand: chain 'C' and resid 2396 through 2398 Processing sheet with id= AR, first strand: chain 'C' and resid 13 through 18 removed outlier: 6.131A pdb=" N SER C 15 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU C 223 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR C 17 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE C 221 " --> pdb=" O TYR C 17 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'C' and resid 132 through 140 removed outlier: 3.877A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'D' and resid 26 through 28 Processing sheet with id= AU, first strand: chain 'D' and resid 57 through 61 removed outlier: 3.819A pdb=" N SER D 120 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'D' and resid 194 through 196 Processing sheet with id= AW, first strand: chain 'D' and resid 241 through 245 Processing sheet with id= AX, first strand: chain 'D' and resid 251 through 257 removed outlier: 4.428A pdb=" N PHE D 251 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'D' and resid 283 through 287 Processing sheet with id= AZ, first strand: chain 'D' and resid 314 through 318 Processing sheet with id= BA, first strand: chain 'D' and resid 367 through 371 Processing sheet with id= BB, first strand: chain 'D' and resid 397 through 400 Processing sheet with id= BC, first strand: chain 'D' and resid 667 through 670 Processing sheet with id= BD, first strand: chain 'D' and resid 800 through 802 removed outlier: 6.181A pdb=" N GLN D1096 " --> pdb=" O ARG D 801 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'D' and resid 2121 through 2127 Processing sheet with id= BF, first strand: chain 'D' and resid 2396 through 2398 Processing sheet with id= BG, first strand: chain 'D' and resid 13 through 18 removed outlier: 6.132A pdb=" N SER D 15 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LEU D 223 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR D 17 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE D 221 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'D' and resid 132 through 140 removed outlier: 3.877A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) 3548 hydrogen bonds defined for protein. 10176 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: 29.29 Time building geometry restraints manager: 23.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 21836 1.34 - 1.46: 13385 1.46 - 1.58: 32299 1.58 - 1.70: 32 1.70 - 1.81: 640 Bond restraints: 68192 Sorted by residual: bond pdb=" N ASN B1239 " pdb=" CA ASN B1239 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.21e-02 6.83e+03 7.63e+00 bond pdb=" N ASN A1239 " pdb=" CA ASN A1239 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.36e+00 bond pdb=" N ASN C1239 " pdb=" CA ASN C1239 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.36e+00 bond pdb=" N ASN D1239 " pdb=" CA ASN D1239 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.21e-02 6.83e+03 7.36e+00 bond pdb=" O4 I3P A2702 " pdb=" P4 I3P A2702 " ideal model delta sigma weight residual 1.697 1.644 0.053 2.00e-02 2.50e+03 6.89e+00 ... (remaining 68187 not shown) Histogram of bond angle deviations from ideal: 98.16 - 106.50: 1443 106.50 - 114.84: 41957 114.84 - 123.18: 46538 123.18 - 131.52: 2114 131.52 - 139.86: 84 Bond angle restraints: 92136 Sorted by residual: angle pdb=" CA PRO D1281 " pdb=" N PRO D1281 " pdb=" CD PRO D1281 " ideal model delta sigma weight residual 112.00 107.07 4.93 1.40e+00 5.10e-01 1.24e+01 angle pdb=" CA PRO C1281 " pdb=" N PRO C1281 " pdb=" CD PRO C1281 " ideal model delta sigma weight residual 112.00 107.07 4.93 1.40e+00 5.10e-01 1.24e+01 angle pdb=" CA PRO A1281 " pdb=" N PRO A1281 " pdb=" CD PRO A1281 " ideal model delta sigma weight residual 112.00 107.07 4.93 1.40e+00 5.10e-01 1.24e+01 angle pdb=" CA PRO B1281 " pdb=" N PRO B1281 " pdb=" CD PRO B1281 " ideal model delta sigma weight residual 112.00 107.08 4.92 1.40e+00 5.10e-01 1.23e+01 angle pdb=" C ASN D1239 " pdb=" N PRO D1240 " pdb=" CA PRO D1240 " ideal model delta sigma weight residual 119.28 122.69 -3.41 1.10e+00 8.26e-01 9.58e+00 ... (remaining 92131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 36924 17.92 - 35.84: 3617 35.84 - 53.76: 547 53.76 - 71.69: 92 71.69 - 89.61: 28 Dihedral angle restraints: 41208 sinusoidal: 16916 harmonic: 24292 Sorted by residual: dihedral pdb=" CB CYS D2455 " pdb=" SG CYS D2455 " pdb=" SG CYS D2461 " pdb=" CB CYS D2461 " ideal model delta sinusoidal sigma weight residual 93.00 149.84 -56.84 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CB CYS C2455 " pdb=" SG CYS C2455 " pdb=" SG CYS C2461 " pdb=" CB CYS C2461 " ideal model delta sinusoidal sigma weight residual 93.00 149.83 -56.83 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" CB CYS B2455 " pdb=" SG CYS B2455 " pdb=" SG CYS B2461 " pdb=" CB CYS B2461 " ideal model delta sinusoidal sigma weight residual 93.00 149.83 -56.83 1 1.00e+01 1.00e-02 4.35e+01 ... (remaining 41205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 9433 0.059 - 0.118: 1121 0.118 - 0.178: 58 0.178 - 0.237: 4 0.237 - 0.296: 12 Chirality restraints: 10628 Sorted by residual: chirality pdb=" C3' ATP D2703 " pdb=" C2' ATP D2703 " pdb=" C4' ATP D2703 " pdb=" O3' ATP D2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' ATP A2703 " pdb=" C2' ATP A2703 " pdb=" C4' ATP A2703 " pdb=" O3' ATP A2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C3' ATP C2703 " pdb=" C2' ATP C2703 " pdb=" C4' ATP C2703 " pdb=" O3' ATP C2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 10625 not shown) Planarity restraints: 11628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B1280 " -0.068 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO B1281 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO B1281 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B1281 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1280 " 0.068 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO C1281 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO C1281 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C1281 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1280 " -0.068 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO A1281 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO A1281 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO A1281 " -0.056 5.00e-02 4.00e+02 ... (remaining 11625 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 705 2.59 - 3.17: 60756 3.17 - 3.75: 105678 3.75 - 4.32: 148862 4.32 - 4.90: 249773 Nonbonded interactions: 565774 Sorted by model distance: nonbonded pdb=" OD1 ASP B1968 " pdb=" OG SER B2019 " model vdw 2.019 2.440 nonbonded pdb=" OD1 ASP D1968 " pdb=" OG SER D2019 " model vdw 2.019 2.440 nonbonded pdb=" OD1 ASP A1968 " pdb=" OG SER A2019 " model vdw 2.019 2.440 nonbonded pdb=" OD1 ASP C1968 " pdb=" OG SER C2019 " model vdw 2.020 2.440 nonbonded pdb=" OG1 THR B1255 " pdb=" OE1 GLU B1260 " model vdw 2.022 2.440 ... (remaining 565769 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 'B' selection = chain 'C' 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 Zn 4 6.06 5 P 24 5.49 5 S 404 5.16 5 C 42800 2.51 5 N 11420 2.21 5 O 12340 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 25.740 Check model and map are aligned: 0.740 Convert atoms to be neutral: 0.440 Process input model: 147.570 Find NCS groups from input model: 3.300 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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 : 0.004 0.053 68192 Z= 0.279 Angle : 0.536 7.728 92136 Z= 0.287 Chirality : 0.038 0.296 10628 Planarity : 0.004 0.100 11628 Dihedral : 13.898 89.608 25324 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 1.75 (0.10), residues: 7980 helix: 2.08 (0.07), residues: 5100 sheet: -0.80 (0.20), residues: 664 loop : -0.34 (0.13), residues: 2216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1749 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1749 time to evaluate : 5.747 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 outliers start: 0 outliers final: 0 residues processed: 1749 average time/residue: 0.6273 time to fit residues: 1837.2976 Evaluate side-chains 918 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 918 time to evaluate : 5.683 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 695 optimal weight: 0.3980 chunk 624 optimal weight: 2.9990 chunk 346 optimal weight: 0.5980 chunk 213 optimal weight: 3.9990 chunk 421 optimal weight: 6.9990 chunk 333 optimal weight: 9.9990 chunk 645 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 392 optimal weight: 0.5980 chunk 480 optimal weight: 1.9990 chunk 748 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 123 GLN A 384 ASN A 502 ASN A 600 HIS A 609 HIS A 744 GLN ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1773 HIS ** A1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1883 ASN ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2069 HIS B 47 ASN B 91 GLN B 98 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 502 ASN B 609 HIS B 783 HIS ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 GLN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1243 GLN B1288 HIS B1402 HIS B1773 HIS ** B1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1883 ASN B2069 HIS C 101 GLN C 108 ASN C 123 GLN C 384 ASN C 502 ASN C 600 HIS C 609 HIS C 744 GLN ** C 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1773 HIS ** C1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1883 ASN ** C1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2069 HIS D 108 ASN D 123 GLN D 384 ASN D 502 ASN D 600 HIS D 609 HIS D 744 GLN ** D 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1084 GLN ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1670 GLN D1773 HIS ** D1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1883 ASN ** D1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2069 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 68192 Z= 0.165 Angle : 0.538 12.314 92136 Z= 0.272 Chirality : 0.039 0.171 10628 Planarity : 0.003 0.047 11628 Dihedral : 4.061 48.134 8844 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 1.89 % 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: 1.90 (0.10), residues: 7980 helix: 2.13 (0.07), residues: 5064 sheet: -0.46 (0.20), residues: 620 loop : -0.15 (0.14), residues: 2296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1244 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1103 time to evaluate : 5.870 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: 141 outliers final: 66 residues processed: 1180 average time/residue: 0.6498 time to fit residues: 1318.0034 Evaluate side-chains 950 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 884 time to evaluate : 5.804 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.4975 time to fit residues: 71.0162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 415 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 chunk 622 optimal weight: 0.0370 chunk 509 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 749 optimal weight: 8.9990 chunk 809 optimal weight: 1.9990 chunk 667 optimal weight: 0.9980 chunk 743 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 601 optimal weight: 2.9990 overall best weight: 2.0064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1243 GLN A1443 ASN ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1670 GLN ** A1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1895 GLN ** A1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1239 ASN B1443 ASN ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 GLN ** B1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1243 GLN C1443 ASN ** C1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1670 GLN ** C1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1895 GLN ** C1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1243 GLN D1443 ASN ** D1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1670 GLN ** D1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1895 GLN ** D1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 68192 Z= 0.276 Angle : 0.566 12.321 92136 Z= 0.288 Chirality : 0.041 0.159 10628 Planarity : 0.004 0.033 11628 Dihedral : 4.219 59.764 8844 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 1.49 % 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: 1.55 (0.10), residues: 7980 helix: 1.88 (0.07), residues: 5064 sheet: -0.71 (0.19), residues: 656 loop : -0.31 (0.14), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1008 time to evaluate : 5.841 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 outliers start: 111 outliers final: 48 residues processed: 1068 average time/residue: 0.6063 time to fit residues: 1123.5436 Evaluate side-chains 900 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 852 time to evaluate : 5.784 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.5268 time to fit residues: 54.2928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 740 optimal weight: 10.0000 chunk 563 optimal weight: 6.9990 chunk 389 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 357 optimal weight: 4.9990 chunk 503 optimal weight: 0.9980 chunk 752 optimal weight: 0.9990 chunk 796 optimal weight: 5.9990 chunk 393 optimal weight: 2.9990 chunk 713 optimal weight: 30.0000 chunk 214 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1622 HIS ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1670 GLN ** A1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1939 GLN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 ASN B 460 ASN B 502 ASN ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1622 HIS ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 GLN ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2063 HIS ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1622 HIS ** C1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1670 GLN ** C1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1939 GLN ** D 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1622 HIS ** D1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1670 GLN ** D1798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1939 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 68192 Z= 0.202 Angle : 0.524 12.119 92136 Z= 0.265 Chirality : 0.039 0.141 10628 Planarity : 0.003 0.035 11628 Dihedral : 4.061 57.363 8844 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.35 % 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: 1.57 (0.10), residues: 7980 helix: 1.90 (0.07), residues: 5060 sheet: -0.70 (0.20), residues: 660 loop : -0.29 (0.14), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 931 time to evaluate : 5.814 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 outliers start: 101 outliers final: 38 residues processed: 1003 average time/residue: 0.6050 time to fit residues: 1053.6221 Evaluate side-chains 871 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 833 time to evaluate : 5.769 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4991 time to fit residues: 43.8376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 663 optimal weight: 0.0870 chunk 452 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 593 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 679 optimal weight: 0.6980 chunk 550 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 406 optimal weight: 2.9990 chunk 714 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1798 GLN A1933 ASN A2063 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN B 600 HIS ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1199 ASN B1318 GLN ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1797 GLN C1798 GLN C1933 ASN ** D 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1670 GLN D1798 GLN D1933 ASN D2063 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 68192 Z= 0.205 Angle : 0.527 11.632 92136 Z= 0.268 Chirality : 0.039 0.304 10628 Planarity : 0.003 0.044 11628 Dihedral : 4.024 57.685 8844 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 0.91 % 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: 1.54 (0.10), residues: 7980 helix: 1.90 (0.07), residues: 5040 sheet: -0.75 (0.20), residues: 656 loop : -0.34 (0.14), residues: 2284 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 913 time to evaluate : 5.897 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: 68 outliers final: 32 residues processed: 966 average time/residue: 0.6445 time to fit residues: 1087.2745 Evaluate side-chains 851 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 819 time to evaluate : 5.789 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4940 time to fit residues: 38.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 267 optimal weight: 8.9990 chunk 717 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 chunk 467 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 797 optimal weight: 5.9990 chunk 661 optimal weight: 1.9990 chunk 369 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 418 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1636 GLN ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1976 ASN A2063 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1199 ASN ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1933 ASN C 512 GLN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1636 GLN ** C1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1976 ASN C2063 HIS D 512 GLN ** D 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 785 HIS ** D1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1636 GLN ** D1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1976 ASN D2063 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.064 68192 Z= 0.369 Angle : 0.618 11.412 92136 Z= 0.317 Chirality : 0.043 0.292 10628 Planarity : 0.004 0.044 11628 Dihedral : 4.453 64.706 8844 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.25 % 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: 1.16 (0.10), residues: 7980 helix: 1.64 (0.07), residues: 5008 sheet: -1.08 (0.19), residues: 688 loop : -0.49 (0.14), residues: 2284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 872 time to evaluate : 7.215 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: 93 outliers final: 47 residues processed: 929 average time/residue: 0.6319 time to fit residues: 1018.1526 Evaluate side-chains 836 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 789 time to evaluate : 5.827 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.5070 time to fit residues: 52.7591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 768 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 454 optimal weight: 6.9990 chunk 582 optimal weight: 0.7980 chunk 451 optimal weight: 0.8980 chunk 671 optimal weight: 10.0000 chunk 445 optimal weight: 6.9990 chunk 794 optimal weight: 9.9990 chunk 497 optimal weight: 5.9990 chunk 484 optimal weight: 2.9990 chunk 366 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1273 GLN ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1773 HIS C 512 GLN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2063 HIS D 512 GLN ** D 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2063 HIS D2323 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 68192 Z= 0.278 Angle : 0.583 12.682 92136 Z= 0.296 Chirality : 0.041 0.255 10628 Planarity : 0.003 0.041 11628 Dihedral : 4.331 62.008 8844 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 0.67 % 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: 1.13 (0.10), residues: 7980 helix: 1.64 (0.07), residues: 5008 sheet: -0.93 (0.20), residues: 628 loop : -0.64 (0.13), residues: 2344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 871 time to evaluate : 5.818 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 outliers start: 50 outliers final: 23 residues processed: 908 average time/residue: 0.6233 time to fit residues: 978.5433 Evaluate side-chains 813 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 790 time to evaluate : 5.866 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5230 time to fit residues: 30.5536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 491 optimal weight: 4.9990 chunk 317 optimal weight: 0.9990 chunk 474 optimal weight: 6.9990 chunk 239 optimal weight: 0.0570 chunk 156 optimal weight: 0.9990 chunk 153 optimal weight: 0.0370 chunk 504 optimal weight: 5.9990 chunk 541 optimal weight: 9.9990 chunk 392 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 624 optimal weight: 10.0000 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 GLN ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1773 HIS A2323 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1199 ASN ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1895 GLN ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1773 HIS C2323 HIS D 222 ASN ** D 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 783 HIS D1304 HIS D1773 HIS ** D1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2063 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 68192 Z= 0.151 Angle : 0.532 14.464 92136 Z= 0.268 Chirality : 0.038 0.276 10628 Planarity : 0.003 0.038 11628 Dihedral : 4.030 56.421 8844 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.38 % 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: 1.37 (0.10), residues: 7980 helix: 1.83 (0.07), residues: 5020 sheet: -1.04 (0.19), residues: 676 loop : -0.49 (0.13), residues: 2284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 895 time to evaluate : 5.866 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: 28 outliers final: 10 residues processed: 915 average time/residue: 0.6370 time to fit residues: 1001.1842 Evaluate side-chains 819 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 809 time to evaluate : 5.853 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6573 time to fit residues: 19.2807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 722 optimal weight: 10.0000 chunk 760 optimal weight: 6.9990 chunk 694 optimal weight: 0.9980 chunk 740 optimal weight: 20.0000 chunk 445 optimal weight: 2.9990 chunk 322 optimal weight: 0.9990 chunk 581 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 668 optimal weight: 2.9990 chunk 699 optimal weight: 9.9990 chunk 737 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1199 ASN ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2063 HIS C 512 GLN ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 783 HIS ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2063 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 68192 Z= 0.268 Angle : 0.589 14.655 92136 Z= 0.297 Chirality : 0.041 0.471 10628 Planarity : 0.003 0.038 11628 Dihedral : 4.200 58.318 8844 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.25 % 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: 1.23 (0.10), residues: 7980 helix: 1.73 (0.07), residues: 4996 sheet: -0.88 (0.20), residues: 628 loop : -0.60 (0.13), residues: 2356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 812 time to evaluate : 5.844 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 outliers start: 19 outliers final: 13 residues processed: 822 average time/residue: 0.6490 time to fit residues: 929.7907 Evaluate side-chains 801 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 788 time to evaluate : 5.921 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.5044 time to fit residues: 20.7678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 485 optimal weight: 8.9990 chunk 782 optimal weight: 0.9990 chunk 477 optimal weight: 0.6980 chunk 371 optimal weight: 1.9990 chunk 544 optimal weight: 9.9990 chunk 820 optimal weight: 3.9990 chunk 755 optimal weight: 7.9990 chunk 653 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 504 optimal weight: 2.9990 chunk 400 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1649 GLN A1773 HIS ** A1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2063 HIS ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1649 GLN C1773 HIS D 600 HIS ** D 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1773 HIS D2063 HIS ** D2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 68192 Z= 0.227 Angle : 0.580 13.662 92136 Z= 0.292 Chirality : 0.041 0.639 10628 Planarity : 0.003 0.040 11628 Dihedral : 4.197 57.457 8844 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.21 % 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: 1.18 (0.10), residues: 7980 helix: 1.66 (0.07), residues: 5012 sheet: -0.86 (0.20), residues: 628 loop : -0.60 (0.13), residues: 2340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15960 Ramachandran restraints generated. 7980 Oldfield, 0 Emsley, 7980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 831 time to evaluate : 5.915 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: 16 outliers final: 10 residues processed: 842 average time/residue: 0.6504 time to fit residues: 951.6936 Evaluate side-chains 809 residues out of total 7460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 799 time to evaluate : 5.831 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5324 time to fit residues: 18.1173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 824 random chunks: chunk 519 optimal weight: 8.9990 chunk 696 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 602 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 chunk 654 optimal weight: 0.7980 chunk 274 optimal weight: 3.9990 chunk 672 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1273 GLN ** A1797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN ** B 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1061 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2063 HIS ** C 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 GLN ** D 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1273 GLN D1285 HIS ** D1909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.213569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.180889 restraints weight = 95493.790| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.29 r_work: 0.3995 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3956 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 68192 Z= 0.307 Angle : 0.621 15.229 92136 Z= 0.314 Chirality : 0.042 0.244 10628 Planarity : 0.004 0.040 11628 Dihedral : 4.367 59.429 8844 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.28 % 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: 0.95 (0.10), residues: 7980 helix: 1.50 (0.07), residues: 5028 sheet: -1.17 (0.20), residues: 668 loop : -0.64 (0.13), residues: 2284 =============================================================================== Job complete usr+sys time: 17408.13 seconds wall clock time: 305 minutes 54.45 seconds (18354.45 seconds total)