Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 12:38:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3q_25668/04_2023/7t3q_25668_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3q_25668/04_2023/7t3q_25668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3q_25668/04_2023/7t3q_25668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3q_25668/04_2023/7t3q_25668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3q_25668/04_2023/7t3q_25668_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3q_25668/04_2023/7t3q_25668_updated.pdb" } resolution = 3.3 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 416 5.16 5 C 43464 2.51 5 N 11648 2.21 5 O 12568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 2054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2350": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 68124 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2103, 16975 Classifications: {'peptide': 2103} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 2045} Chain breaks: 24 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: 16975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2103, 16975 Classifications: {'peptide': 2103} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 2045} Chain breaks: 24 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: 16975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2103, 16975 Classifications: {'peptide': 2103} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 2045} Chain breaks: 24 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: 16975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2103, 16975 Classifications: {'peptide': 2103} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 2045} Chain breaks: 24 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 16257 SG CYS A2538 100.338 127.468 99.496 1.00 36.58 S ATOM 16282 SG CYS A2541 101.471 124.975 96.819 1.00 37.81 S ATOM 33232 SG CYS B2538 111.064 100.324 99.494 1.00 40.75 S ATOM 33257 SG CYS B2541 113.529 101.488 96.804 1.00 41.44 S ATOM 50207 SG CYS C2538 138.214 111.089 99.502 1.00 37.02 S ATOM 50232 SG CYS C2541 137.026 113.542 96.798 1.00 38.20 S ATOM 67182 SG CYS D2538 127.452 138.183 99.508 1.00 36.33 S ATOM 67207 SG CYS D2541 124.955 137.024 96.822 1.00 37.40 S Time building chain proxies: 25.44, per 1000 atoms: 0.37 Number of scatterers: 68124 At special positions: 0 Unit cell: (239.292, 239.292, 180.504, 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 416 16.00 P 24 15.00 O 12568 8.00 N 11648 7.00 C 43464 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: 22.18 Conformation dependent library (CDL) restraints added in 7.5 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 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 391 helices and 56 sheets defined 60.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.44 Creating SS restraints... Processing helix chain 'A' and resid 52 through 55 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 88 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 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 436 through 461 Processing helix chain 'A' and resid 466 through 484 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 514 through 524 Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 568 through 575 Processing helix chain 'A' and resid 579 through 583 Processing helix chain 'A' and resid 591 through 600 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.579A pdb=" N GLU A 607 " --> pdb=" O ARG A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 625 Processing helix chain 'A' and resid 628 through 638 removed outlier: 4.038A pdb=" N TYR A 633 " --> pdb=" O PHE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 657 Processing helix chain 'A' and resid 708 through 717 Processing helix chain 'A' and resid 720 through 739 removed outlier: 4.015A pdb=" N VAL A 725 " --> pdb=" O HIS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 754 removed outlier: 4.267A pdb=" N GLU A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 764 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 812 through 819 removed outlier: 3.529A pdb=" N LEU A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 845 Processing helix chain 'A' and resid 854 through 873 removed outlier: 3.819A pdb=" N LYS A 858 " --> pdb=" O GLU A 854 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 859 " --> pdb=" O GLU A 855 " (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 1036 Processing helix chain 'A' and resid 1053 through 1064 Processing helix chain 'A' and resid 1068 through 1094 removed outlier: 3.910A pdb=" N PHE A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A1084 " --> pdb=" O LYS A1080 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG A1085 " --> pdb=" O HIS A1081 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN A1086 " --> pdb=" O PHE A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1121 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 1219 through 1235 Processing helix chain 'A' and resid 1240 through 1247 Processing helix chain 'A' and resid 1258 through 1267 Processing helix chain 'A' and resid 1272 through 1276 Processing helix chain 'A' and resid 1280 through 1292 removed outlier: 3.874A pdb=" N PHE A1286 " --> pdb=" O VAL A1282 " (cutoff:3.500A) removed outlier: 3.956A 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 1381 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 Processing helix chain 'A' and resid 1436 through 1454 Processing helix chain 'A' and resid 1462 through 1481 removed outlier: 3.680A pdb=" N VAL A1472 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU A1473 " --> pdb=" O LEU A1469 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1509 removed outlier: 3.575A pdb=" N ILE A1497 " --> pdb=" O THR A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1531 Processing helix chain 'A' and resid 1590 through 1622 Proline residue: A1608 - end of helix removed outlier: 4.057A pdb=" N GLN A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1633 through 1639 Processing helix chain 'A' and resid 1642 through 1653 removed outlier: 3.968A pdb=" N ASP A1653 " --> pdb=" O GLN A1649 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1673 removed outlier: 4.003A pdb=" N LEU A1673 " --> pdb=" O LEU A1669 " (cutoff:3.500A) Processing helix chain 'A' and resid 1682 through 1694 Processing helix chain 'A' and resid 1720 through 1731 Processing helix chain 'A' and resid 1733 through 1743 Processing helix chain 'A' and resid 1747 through 1761 removed outlier: 3.631A pdb=" N GLN A1751 " --> pdb=" O GLU A1747 " (cutoff:3.500A) Processing helix chain 'A' and resid 1766 through 1778 Processing helix chain 'A' and resid 1780 through 1802 removed outlier: 3.537A pdb=" N GLU A1783 " --> pdb=" O LYS A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1866 through 1880 Proline residue: A1872 - end of helix Processing helix chain 'A' and resid 1886 through 1893 Processing helix chain 'A' and resid 1903 through 1915 Processing helix chain 'A' and resid 1933 through 1949 Processing helix chain 'A' and resid 1955 through 1960 Processing helix chain 'A' and resid 1966 through 1975 removed outlier: 3.788A pdb=" N ILE A1970 " --> pdb=" O ILE A1967 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR A1971 " --> pdb=" O ASP A1968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1987 through 2003 Processing helix chain 'A' and resid 2011 through 2019 removed outlier: 3.792A 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: 3.788A pdb=" N ARG A2062 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 5.176A 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 2119 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: 4.280A pdb=" N SER A2176 " --> pdb=" O PHE A2172 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE A2177 " --> pdb=" O ASP A2173 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A2190 " --> pdb=" O ARG A2186 " (cutoff:3.500A) Processing helix chain 'A' and resid 2192 through 2198 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 2340 through 2351 Processing helix chain 'A' and resid 2353 through 2363 removed outlier: 3.768A 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 2476 through 2478 No H-bonds generated for 'chain 'A' and resid 2476 through 2478' Processing helix chain 'A' and resid 2490 through 2503 Processing helix chain 'A' and resid 2508 through 2536 removed outlier: 3.619A pdb=" N PHE A2513 " --> pdb=" O LEU A2509 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2548 Processing helix chain 'A' and resid 2555 through 2560 Processing helix chain 'A' and resid 2565 through 2577 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 2595 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 Processing helix chain 'B' and resid 52 through 55 Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 88 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 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 436 through 461 Processing helix chain 'B' and resid 466 through 484 Processing helix chain 'B' and resid 493 through 495 No H-bonds generated for 'chain 'B' and resid 493 through 495' Processing helix chain 'B' and resid 503 through 511 Processing helix chain 'B' and resid 514 through 524 Processing helix chain 'B' and resid 547 through 563 Processing helix chain 'B' and resid 568 through 575 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 591 through 600 Processing helix chain 'B' and resid 603 through 609 removed outlier: 3.589A pdb=" N GLU B 607 " --> pdb=" O ARG B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 625 Processing helix chain 'B' and resid 628 through 638 removed outlier: 4.060A pdb=" N TYR B 633 " --> pdb=" O PHE B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 657 Processing helix chain 'B' and resid 708 through 717 Processing helix chain 'B' and resid 720 through 739 removed outlier: 4.002A pdb=" N VAL B 725 " --> pdb=" O HIS B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 754 removed outlier: 4.296A pdb=" N GLU B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 764 Processing helix chain 'B' and resid 773 through 784 Processing helix chain 'B' and resid 812 through 819 removed outlier: 3.533A pdb=" N LEU B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 845 Processing helix chain 'B' and resid 854 through 873 removed outlier: 3.865A pdb=" N LYS B 858 " --> pdb=" O GLU B 854 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 859 " --> pdb=" O GLU B 855 " (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: 3.911A pdb=" N PHE B1082 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER B1083 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN B1084 " --> pdb=" O LYS B1080 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ARG B1085 " --> pdb=" O HIS B1081 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN B1086 " --> pdb=" O PHE B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1101 through 1121 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 1219 through 1235 Processing helix chain 'B' and resid 1240 through 1253 removed outlier: 3.570A pdb=" N LYS B1248 " --> pdb=" O ALA B1244 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N HIS B1249 " --> pdb=" O LEU B1245 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B1250 " --> pdb=" O LEU B1246 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N HIS B1251 " --> pdb=" O HIS B1247 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B1252 " --> pdb=" O LYS B1248 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE B1253 " --> pdb=" O HIS B1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 1258 through 1267 Processing helix chain 'B' and resid 1272 through 1276 Processing helix chain 'B' and resid 1280 through 1292 removed outlier: 3.874A pdb=" N PHE B1286 " --> pdb=" O VAL B1282 " (cutoff:3.500A) removed outlier: 3.923A 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 1381 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 Processing helix chain 'B' and resid 1436 through 1454 Processing helix chain 'B' and resid 1462 through 1470 Processing helix chain 'B' and resid 1472 through 1481 Processing helix chain 'B' and resid 1493 through 1509 removed outlier: 3.595A pdb=" N ILE B1497 " --> pdb=" O THR B1493 " (cutoff:3.500A) Processing helix chain 'B' and resid 1521 through 1531 Processing helix chain 'B' and resid 1590 through 1622 Proline residue: B1608 - end of helix removed outlier: 4.064A pdb=" N GLN B1611 " --> pdb=" O LYS B1607 " (cutoff:3.500A) Processing helix chain 'B' and resid 1633 through 1639 Processing helix chain 'B' and resid 1642 through 1653 removed outlier: 3.978A pdb=" N ASP B1653 " --> pdb=" O GLN B1649 " (cutoff:3.500A) Processing helix chain 'B' and resid 1659 through 1673 removed outlier: 3.999A pdb=" N LEU B1673 " --> pdb=" O LEU B1669 " (cutoff:3.500A) Processing helix chain 'B' and resid 1682 through 1694 Processing helix chain 'B' and resid 1720 through 1731 Processing helix chain 'B' and resid 1733 through 1743 Processing helix chain 'B' and resid 1747 through 1761 removed outlier: 3.618A pdb=" N GLN B1751 " --> pdb=" O GLU B1747 " (cutoff:3.500A) Processing helix chain 'B' and resid 1766 through 1778 Processing helix chain 'B' and resid 1780 through 1802 removed outlier: 3.585A pdb=" N GLU B1783 " --> pdb=" O LYS B1780 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1880 Proline residue: B1872 - end of helix 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 1960 Processing helix chain 'B' and resid 1966 through 1975 removed outlier: 3.802A pdb=" N ILE B1970 " --> pdb=" O ILE B1967 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR B1971 " --> pdb=" O ASP B1968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1987 through 2003 Processing helix chain 'B' and resid 2011 through 2019 removed outlier: 3.819A 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: 3.806A pdb=" N ARG B2062 " --> pdb=" O LEU B2058 " (cutoff:3.500A) removed outlier: 5.145A 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 2119 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: 4.304A pdb=" N SER B2176 " --> pdb=" O PHE B2172 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE B2177 " --> pdb=" O ASP B2173 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER B2190 " --> pdb=" O ARG B2186 " (cutoff:3.500A) Processing helix chain 'B' and resid 2192 through 2198 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 2340 through 2351 Processing helix chain 'B' and resid 2353 through 2363 removed outlier: 3.799A 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 2476 through 2478 No H-bonds generated for 'chain 'B' and resid 2476 through 2478' Processing helix chain 'B' and resid 2490 through 2503 Processing helix chain 'B' and resid 2508 through 2536 removed outlier: 3.614A pdb=" N PHE B2513 " --> pdb=" O LEU B2509 " (cutoff:3.500A) Processing helix chain 'B' and resid 2545 through 2548 Processing helix chain 'B' and resid 2555 through 2560 Processing helix chain 'B' and resid 2565 through 2577 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 2595 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 Processing helix chain 'C' and resid 52 through 55 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 88 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 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 436 through 461 Processing helix chain 'C' and resid 466 through 484 Processing helix chain 'C' and resid 493 through 495 No H-bonds generated for 'chain 'C' and resid 493 through 495' Processing helix chain 'C' and resid 503 through 511 Processing helix chain 'C' and resid 514 through 524 Processing helix chain 'C' and resid 547 through 564 removed outlier: 3.697A pdb=" N GLN C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 575 Processing helix chain 'C' and resid 579 through 583 Processing helix chain 'C' and resid 591 through 600 Processing helix chain 'C' and resid 603 through 609 removed outlier: 3.563A pdb=" N GLU C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 625 Processing helix chain 'C' and resid 628 through 638 removed outlier: 4.051A pdb=" N TYR C 633 " --> pdb=" O PHE C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 657 Processing helix chain 'C' and resid 708 through 717 Processing helix chain 'C' and resid 720 through 739 removed outlier: 4.020A pdb=" N VAL C 725 " --> pdb=" O HIS C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 754 removed outlier: 4.302A pdb=" N GLU C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLN C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 764 Processing helix chain 'C' and resid 773 through 784 Processing helix chain 'C' and resid 812 through 819 removed outlier: 3.527A pdb=" N LEU C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 845 Processing helix chain 'C' and resid 854 through 873 removed outlier: 3.815A pdb=" N LYS C 858 " --> pdb=" O GLU C 854 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU C 859 " --> pdb=" O GLU C 855 " (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: 3.912A pdb=" N PHE C1082 " --> pdb=" O LEU C1078 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER C1083 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN C1084 " --> pdb=" O LYS C1080 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG C1085 " --> pdb=" O HIS C1081 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN C1086 " --> pdb=" O PHE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1121 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 1219 through 1235 Processing helix chain 'C' and resid 1240 through 1253 removed outlier: 3.540A pdb=" N LYS C1248 " --> pdb=" O ALA C1244 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N HIS C1249 " --> pdb=" O LEU C1245 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU C1250 " --> pdb=" O LEU C1246 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N HIS C1251 " --> pdb=" O HIS C1247 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C1252 " --> pdb=" O LYS C1248 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE C1253 " --> pdb=" O HIS C1249 " (cutoff:3.500A) Processing helix chain 'C' and resid 1258 through 1267 Processing helix chain 'C' and resid 1272 through 1276 Processing helix chain 'C' and resid 1280 through 1292 removed outlier: 3.902A pdb=" N PHE C1286 " --> pdb=" O VAL C1282 " (cutoff:3.500A) removed outlier: 3.896A 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 1381 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 Processing helix chain 'C' and resid 1436 through 1454 Processing helix chain 'C' and resid 1462 through 1470 Processing helix chain 'C' and resid 1472 through 1481 Processing helix chain 'C' and resid 1493 through 1509 removed outlier: 3.590A pdb=" N ILE C1497 " --> pdb=" O THR C1493 " (cutoff:3.500A) Processing helix chain 'C' and resid 1521 through 1531 Processing helix chain 'C' and resid 1590 through 1622 Proline residue: C1608 - end of helix removed outlier: 4.080A pdb=" N GLN C1611 " --> pdb=" O LYS C1607 " (cutoff:3.500A) Processing helix chain 'C' and resid 1633 through 1639 Processing helix chain 'C' and resid 1642 through 1653 removed outlier: 3.936A pdb=" N ASP C1653 " --> pdb=" O GLN C1649 " (cutoff:3.500A) Processing helix chain 'C' and resid 1659 through 1673 removed outlier: 3.997A pdb=" N LEU C1673 " --> pdb=" O LEU C1669 " (cutoff:3.500A) Processing helix chain 'C' and resid 1682 through 1694 Processing helix chain 'C' and resid 1720 through 1731 Processing helix chain 'C' and resid 1733 through 1743 Processing helix chain 'C' and resid 1747 through 1761 removed outlier: 3.611A pdb=" N GLN C1751 " --> pdb=" O GLU C1747 " (cutoff:3.500A) Processing helix chain 'C' and resid 1766 through 1778 Processing helix chain 'C' and resid 1780 through 1802 removed outlier: 3.652A pdb=" N GLU C1783 " --> pdb=" O LYS C1780 " (cutoff:3.500A) Processing helix chain 'C' and resid 1866 through 1880 Proline residue: C1872 - end of helix 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 1960 Processing helix chain 'C' and resid 1966 through 1975 removed outlier: 3.786A pdb=" N ILE C1970 " --> pdb=" O ILE C1967 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR C1971 " --> pdb=" O ASP C1968 " (cutoff:3.500A) Processing helix chain 'C' and resid 1987 through 2003 Processing helix chain 'C' and resid 2011 through 2019 removed outlier: 3.663A 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: 3.809A pdb=" N ARG C2062 " --> pdb=" O LEU C2058 " (cutoff:3.500A) removed outlier: 5.140A 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 2119 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: 4.290A pdb=" N SER C2176 " --> pdb=" O PHE C2172 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE C2177 " --> pdb=" O ASP C2173 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C2190 " --> pdb=" O ARG C2186 " (cutoff:3.500A) Processing helix chain 'C' and resid 2192 through 2198 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 2340 through 2351 Processing helix chain 'C' and resid 2353 through 2363 removed outlier: 3.788A 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 2476 through 2478 No H-bonds generated for 'chain 'C' and resid 2476 through 2478' Processing helix chain 'C' and resid 2490 through 2503 Processing helix chain 'C' and resid 2508 through 2536 removed outlier: 3.589A pdb=" N PHE C2513 " --> pdb=" O LEU C2509 " (cutoff:3.500A) Processing helix chain 'C' and resid 2545 through 2548 Processing helix chain 'C' and resid 2555 through 2560 Processing helix chain 'C' and resid 2565 through 2577 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 2595 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 Processing helix chain 'D' and resid 52 through 55 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 88 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 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 436 through 461 Processing helix chain 'D' and resid 466 through 484 Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 503 through 511 Processing helix chain 'D' and resid 514 through 524 Processing helix chain 'D' and resid 547 through 564 removed outlier: 3.687A pdb=" N GLN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 575 Processing helix chain 'D' and resid 579 through 583 Processing helix chain 'D' and resid 591 through 600 Processing helix chain 'D' and resid 603 through 609 removed outlier: 3.591A pdb=" N GLU D 607 " --> pdb=" O ARG D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 625 Processing helix chain 'D' and resid 628 through 638 removed outlier: 4.094A pdb=" N TYR D 633 " --> pdb=" O PHE D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 657 Processing helix chain 'D' and resid 708 through 717 Processing helix chain 'D' and resid 720 through 739 removed outlier: 4.008A pdb=" N VAL D 725 " --> pdb=" O HIS D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 754 removed outlier: 4.298A pdb=" N GLU D 750 " --> pdb=" O LEU D 746 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 764 Processing helix chain 'D' and resid 773 through 784 Processing helix chain 'D' and resid 812 through 819 removed outlier: 3.523A pdb=" N LEU D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 845 Processing helix chain 'D' and resid 854 through 873 removed outlier: 3.808A pdb=" N LYS D 858 " --> pdb=" O GLU D 854 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 859 " --> pdb=" O GLU D 855 " (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 1036 Processing helix chain 'D' and resid 1053 through 1064 Processing helix chain 'D' and resid 1068 through 1094 removed outlier: 3.908A pdb=" N PHE D1082 " --> pdb=" O LEU D1078 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER D1083 " --> pdb=" O PHE D1079 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN D1084 " --> pdb=" O LYS D1080 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG D1085 " --> pdb=" O HIS D1081 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN D1086 " --> pdb=" O PHE D1082 " (cutoff:3.500A) Processing helix chain 'D' and resid 1101 through 1121 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 1219 through 1235 Processing helix chain 'D' and resid 1240 through 1253 removed outlier: 3.584A pdb=" N LYS D1248 " --> pdb=" O ALA D1244 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS D1249 " --> pdb=" O LEU D1245 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU D1250 " --> pdb=" O LEU D1246 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N HIS D1251 " --> pdb=" O HIS D1247 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D1252 " --> pdb=" O LYS D1248 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE D1253 " --> pdb=" O HIS D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1258 through 1267 Processing helix chain 'D' and resid 1272 through 1276 Processing helix chain 'D' and resid 1280 through 1292 removed outlier: 3.904A pdb=" N PHE D1286 " --> pdb=" O VAL D1282 " (cutoff:3.500A) removed outlier: 3.905A 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 1381 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 Processing helix chain 'D' and resid 1436 through 1454 Processing helix chain 'D' and resid 1462 through 1470 Processing helix chain 'D' and resid 1472 through 1481 Processing helix chain 'D' and resid 1493 through 1509 removed outlier: 3.598A pdb=" N ILE D1497 " --> pdb=" O THR D1493 " (cutoff:3.500A) Processing helix chain 'D' and resid 1521 through 1531 Processing helix chain 'D' and resid 1590 through 1622 Proline residue: D1608 - end of helix removed outlier: 4.064A pdb=" N GLN D1611 " --> pdb=" O LYS D1607 " (cutoff:3.500A) Processing helix chain 'D' and resid 1633 through 1639 Processing helix chain 'D' and resid 1642 through 1653 removed outlier: 3.962A pdb=" N ASP D1653 " --> pdb=" O GLN D1649 " (cutoff:3.500A) Processing helix chain 'D' and resid 1659 through 1673 removed outlier: 3.998A pdb=" N LEU D1673 " --> pdb=" O LEU D1669 " (cutoff:3.500A) Processing helix chain 'D' and resid 1682 through 1694 Processing helix chain 'D' and resid 1720 through 1731 Processing helix chain 'D' and resid 1733 through 1743 Processing helix chain 'D' and resid 1747 through 1761 removed outlier: 3.613A pdb=" N GLN D1751 " --> pdb=" O GLU D1747 " (cutoff:3.500A) Processing helix chain 'D' and resid 1766 through 1778 Processing helix chain 'D' and resid 1780 through 1802 removed outlier: 3.643A pdb=" N GLU D1783 " --> pdb=" O LYS D1780 " (cutoff:3.500A) Processing helix chain 'D' and resid 1866 through 1880 Proline residue: D1872 - end of helix Processing helix chain 'D' and resid 1886 through 1893 Processing helix chain 'D' and resid 1903 through 1915 Processing helix chain 'D' and resid 1933 through 1949 Processing helix chain 'D' and resid 1955 through 1960 Processing helix chain 'D' and resid 1966 through 1975 removed outlier: 3.791A pdb=" N ILE D1970 " --> pdb=" O ILE D1967 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR D1971 " --> pdb=" O ASP D1968 " (cutoff:3.500A) Processing helix chain 'D' and resid 1987 through 2003 Processing helix chain 'D' and resid 2011 through 2019 removed outlier: 3.658A 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: 3.801A pdb=" N ARG D2062 " --> pdb=" O LEU D2058 " (cutoff:3.500A) removed outlier: 5.132A 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 2119 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: 4.263A pdb=" N SER D2176 " --> pdb=" O PHE D2172 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N PHE D2177 " --> pdb=" O ASP D2173 " (cutoff:3.500A) removed outlier: 3.612A 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 2340 through 2351 Processing helix chain 'D' and resid 2353 through 2363 removed outlier: 3.757A 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 2476 through 2478 No H-bonds generated for 'chain 'D' and resid 2476 through 2478' Processing helix chain 'D' and resid 2490 through 2503 Processing helix chain 'D' and resid 2508 through 2536 removed outlier: 3.612A pdb=" N PHE D2513 " --> pdb=" O LEU D2509 " (cutoff:3.500A) Processing helix chain 'D' and resid 2545 through 2548 Processing helix chain 'D' and resid 2555 through 2560 Processing helix chain 'D' and resid 2565 through 2577 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 2595 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 Processing sheet with id= A, first strand: chain 'A' and resid 183 through 187 removed outlier: 3.814A pdb=" N SER A 120 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N SER A 15 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU A 223 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N TYR A 17 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE A 221 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= C, first strand: chain 'A' and resid 26 through 28 Processing sheet with id= D, first strand: chain 'A' and resid 194 through 196 Processing sheet with id= E, first strand: chain 'A' and resid 241 through 245 Processing sheet with id= F, first strand: chain 'A' and resid 251 through 257 removed outlier: 4.410A pdb=" N PHE A 251 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 283 through 287 Processing sheet with id= H, first strand: chain 'A' and resid 314 through 317 Processing sheet with id= I, first strand: chain 'A' and resid 367 through 371 Processing sheet with id= J, first strand: chain 'A' and resid 397 through 400 Processing sheet with id= K, first strand: chain 'A' and resid 667 through 670 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 132 through 140 removed outlier: 3.609A pdb=" N ARG A 149 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 183 through 187 removed outlier: 3.817A pdb=" N SER B 120 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER B 15 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU B 223 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B 17 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE B 221 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= Q, first strand: chain 'B' and resid 26 through 28 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: 4.448A 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 317 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 2121 through 2127 Processing sheet with id= AA, first strand: chain 'B' and resid 2396 through 2398 Processing sheet with id= AB, first strand: chain 'B' and resid 132 through 140 removed outlier: 3.607A pdb=" N ARG B 149 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 183 through 187 removed outlier: 3.844A pdb=" N SER C 120 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER C 15 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU C 223 " --> pdb=" O SER C 15 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N TYR C 17 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE C 221 " --> pdb=" O TYR C 17 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 17 through 19 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 194 through 196 Processing sheet with id= AG, first strand: chain 'C' and resid 241 through 245 Processing sheet with id= AH, first strand: chain 'C' and resid 251 through 257 removed outlier: 4.451A pdb=" N PHE C 251 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 283 through 287 Processing sheet with id= AJ, first strand: chain 'C' and resid 314 through 317 Processing sheet with id= AK, first strand: chain 'C' and resid 367 through 371 Processing sheet with id= AL, first strand: chain 'C' and resid 397 through 400 Processing sheet with id= AM, first strand: chain 'C' and resid 667 through 670 Processing sheet with id= AN, first strand: chain 'C' and resid 2121 through 2127 Processing sheet with id= AO, first strand: chain 'C' and resid 2396 through 2398 Processing sheet with id= AP, first strand: chain 'C' and resid 132 through 140 removed outlier: 3.645A pdb=" N ARG C 149 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'D' and resid 183 through 187 removed outlier: 3.857A pdb=" N SER D 120 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER D 15 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU D 223 " --> pdb=" O SER D 15 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR D 17 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE D 221 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'D' and resid 17 through 19 Processing sheet with id= AS, first strand: chain 'D' and resid 26 through 28 Processing sheet with id= AT, first strand: chain 'D' and resid 194 through 196 Processing sheet with id= AU, first strand: chain 'D' and resid 241 through 245 Processing sheet with id= AV, first strand: chain 'D' and resid 251 through 257 removed outlier: 4.456A pdb=" N PHE D 251 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'D' and resid 283 through 287 Processing sheet with id= AX, first strand: chain 'D' and resid 314 through 317 Processing sheet with id= AY, first strand: chain 'D' and resid 367 through 371 Processing sheet with id= AZ, first strand: chain 'D' and resid 397 through 400 Processing sheet with id= BA, first strand: chain 'D' and resid 667 through 670 Processing sheet with id= BB, first strand: chain 'D' and resid 2121 through 2127 Processing sheet with id= BC, first strand: chain 'D' and resid 2396 through 2398 Processing sheet with id= BD, first strand: chain 'D' and resid 132 through 140 removed outlier: 3.629A pdb=" N ARG D 149 " --> pdb=" O ASN D 136 " (cutoff:3.500A) 3612 hydrogen bonds defined for protein. 10212 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: 30.69 Time building geometry restraints manager: 24.17 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: 22269 1.34 - 1.46: 11432 1.46 - 1.58: 34947 1.58 - 1.69: 32 1.69 - 1.81: 656 Bond restraints: 69336 Sorted by residual: bond pdb=" N ASN A1239 " pdb=" CA ASN A1239 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.13e-02 7.83e+03 8.02e+00 bond pdb=" N ASN B1239 " pdb=" CA ASN B1239 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.13e-02 7.83e+03 7.79e+00 bond pdb=" N ASN C1239 " pdb=" CA ASN C1239 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.21e-02 6.83e+03 7.60e+00 bond pdb=" N ASN D1239 " pdb=" CA ASN D1239 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.21e-02 6.83e+03 7.19e+00 bond pdb=" O4 I3P C2702 " pdb=" P4 I3P C2702 " ideal model delta sigma weight residual 1.697 1.644 0.053 2.00e-02 2.50e+03 6.96e+00 ... (remaining 69331 not shown) Histogram of bond angle deviations from ideal: 97.87 - 106.26: 1351 106.26 - 114.65: 42512 114.65 - 123.05: 46942 123.05 - 131.44: 2781 131.44 - 139.83: 86 Bond angle restraints: 93672 Sorted by residual: angle pdb=" CA CYS B1236 " pdb=" C CYS B1236 " pdb=" O CYS B1236 " ideal model delta sigma weight residual 122.38 117.61 4.77 1.49e+00 4.50e-01 1.03e+01 angle pdb=" CA CYS A1236 " pdb=" C CYS A1236 " pdb=" O CYS A1236 " ideal model delta sigma weight residual 122.20 117.56 4.64 1.57e+00 4.06e-01 8.72e+00 angle pdb=" CA CYS D1236 " pdb=" C CYS D1236 " pdb=" O CYS D1236 " ideal model delta sigma weight residual 122.20 117.61 4.59 1.57e+00 4.06e-01 8.56e+00 angle pdb=" N LYS C1181 " pdb=" CA LYS C1181 " pdb=" CB LYS C1181 " ideal model delta sigma weight residual 110.28 114.58 -4.30 1.55e+00 4.16e-01 7.70e+00 angle pdb=" CA ALA B1237 " pdb=" C ALA B1237 " pdb=" O ALA B1237 " ideal model delta sigma weight residual 121.11 117.71 3.40 1.23e+00 6.61e-01 7.65e+00 ... (remaining 93667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 37510 17.77 - 35.53: 3741 35.53 - 53.30: 597 53.30 - 71.07: 72 71.07 - 88.84: 28 Dihedral angle restraints: 41948 sinusoidal: 17228 harmonic: 24720 Sorted by residual: dihedral pdb=" CB CYS C2455 " pdb=" SG CYS C2455 " pdb=" SG CYS C2461 " pdb=" CB CYS C2461 " ideal model delta sinusoidal sigma weight residual 93.00 142.48 -49.48 1 1.00e+01 1.00e-02 3.36e+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 93.00 141.93 -48.93 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS D2455 " pdb=" SG CYS D2455 " pdb=" SG CYS D2461 " pdb=" CB CYS D2461 " ideal model delta sinusoidal sigma weight residual 93.00 141.82 -48.82 1 1.00e+01 1.00e-02 3.28e+01 ... (remaining 41945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 9543 0.058 - 0.116: 1156 0.116 - 0.175: 81 0.175 - 0.233: 0 0.233 - 0.291: 12 Chirality restraints: 10792 Sorted by residual: 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 2.12e+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 -2.92 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP B2703 " pdb=" C2' ATP B2703 " pdb=" C4' ATP B2703 " pdb=" O3' ATP B2703 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 10789 not shown) Planarity restraints: 11844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D1280 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO D1281 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D1281 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D1281 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1280 " 0.053 5.00e-02 4.00e+02 7.85e-02 9.87e+00 pdb=" N PRO C1281 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO C1281 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C1281 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C2279 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO C2280 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C2280 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C2280 " -0.040 5.00e-02 4.00e+02 ... (remaining 11841 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 912 2.62 - 3.19: 64401 3.19 - 3.76: 108110 3.76 - 4.33: 152209 4.33 - 4.90: 250573 Nonbonded interactions: 576205 Sorted by model distance: nonbonded pdb=" O VAL A2553 " pdb=" OG SER A2554 " model vdw 2.049 2.440 nonbonded pdb=" O VAL B2553 " pdb=" OG SER B2554 " model vdw 2.050 2.440 nonbonded pdb=" O VAL D2553 " pdb=" OG SER D2554 " model vdw 2.059 2.440 nonbonded pdb=" O VAL C2553 " pdb=" OG SER C2554 " model vdw 2.063 2.440 nonbonded pdb=" O LEU B 882 " pdb=" OG1 THR B 885 " model vdw 2.086 2.440 ... (remaining 576200 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 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: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 25.460 Check model and map are aligned: 0.740 Set scattering table: 0.450 Process input model: 148.130 Find NCS groups from input model: 3.540 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 186.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 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 69336 Z= 0.245 Angle : 0.541 7.834 93672 Z= 0.290 Chirality : 0.038 0.291 10792 Planarity : 0.003 0.079 11844 Dihedral : 13.868 88.837 25792 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % 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: 1.74 (0.10), residues: 8144 helix: 2.19 (0.07), residues: 5136 sheet: -0.75 (0.21), residues: 616 loop : -0.59 (0.13), residues: 2392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1960 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1960 time to evaluate : 6.028 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 outliers start: 0 outliers final: 0 residues processed: 1960 average time/residue: 0.7183 time to fit residues: 2343.2864 Evaluate side-chains 987 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 987 time to evaluate : 6.090 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.4320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 709 optimal weight: 10.0000 chunk 636 optimal weight: 4.9990 chunk 353 optimal weight: 0.9980 chunk 217 optimal weight: 9.9990 chunk 429 optimal weight: 10.0000 chunk 340 optimal weight: 20.0000 chunk 658 optimal weight: 5.9990 chunk 254 optimal weight: 5.9990 chunk 400 optimal weight: 1.9990 chunk 490 optimal weight: 0.7980 chunk 762 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 248 GLN A 301 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A1168 ASN ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 GLN ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 HIS A1318 GLN ** A1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1773 HIS A1871 GLN A1991 GLN A2069 HIS A2210 ASN ** A2357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN B 301 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN B 980 ASN ** B1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1194 GLN B1203 HIS ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1251 HIS B1318 GLN ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1611 GLN B1871 GLN B2066 GLN B2069 HIS B2210 ASN ** B2357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN C 301 ASN C 602 ASN C1168 ASN ** C1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1193 GLN C1194 GLN C1203 HIS ** C1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1251 HIS C1318 GLN ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1419 HIS C1500 GLN C1871 GLN C1902 ASN C2069 HIS C2210 ASN ** C2357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN D 301 ASN D 602 ASN ** D1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1194 GLN D1203 HIS ** D1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1251 HIS D1318 GLN ** D1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1419 HIS ** D1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1871 GLN D1902 ASN D2068 GLN D2069 HIS D2210 ASN ** D2357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 69336 Z= 0.318 Angle : 0.632 12.097 93672 Z= 0.327 Chirality : 0.042 0.217 10792 Planarity : 0.004 0.061 11844 Dihedral : 4.568 59.544 9012 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 1.93 % 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: 1.26 (0.10), residues: 8144 helix: 1.79 (0.07), residues: 5132 sheet: -1.07 (0.19), residues: 736 loop : -0.63 (0.14), residues: 2276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1114 time to evaluate : 6.146 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 outliers start: 146 outliers final: 81 residues processed: 1208 average time/residue: 0.6709 time to fit residues: 1381.1086 Evaluate side-chains 955 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 874 time to evaluate : 6.024 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 0.5584 time to fit residues: 94.6816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 423 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 634 optimal weight: 0.0770 chunk 519 optimal weight: 9.9990 chunk 210 optimal weight: 4.9990 chunk 764 optimal weight: 9.9990 chunk 825 optimal weight: 4.9990 chunk 680 optimal weight: 5.9990 chunk 757 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 613 optimal weight: 0.5980 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 301 ASN A 564 GLN A 602 ASN ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 HIS ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN A1168 ASN ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 HIS ** A1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1419 HIS A2066 GLN A2323 HIS ** A2357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 301 ASN B 602 ASN ** B 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 HIS ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1419 HIS B1500 GLN B1611 GLN B1773 HIS ** B1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2323 HIS C 301 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** C 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1168 ASN ** C1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 HIS ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1650 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1991 GLN C2066 GLN C2323 HIS D 192 GLN D 301 ASN ** D 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** D 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1061 HIS ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1193 GLN ** D1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1288 HIS ** D1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1500 GLN D1773 HIS D2066 GLN D2323 HIS ** D2357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 69336 Z= 0.258 Angle : 0.569 12.629 93672 Z= 0.295 Chirality : 0.040 0.207 10792 Planarity : 0.004 0.052 11844 Dihedral : 4.504 62.936 9012 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.21 % 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: 1.13 (0.10), residues: 8144 helix: 1.71 (0.07), residues: 5076 sheet: -1.04 (0.19), residues: 688 loop : -0.73 (0.13), residues: 2380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 980 time to evaluate : 6.108 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 outliers start: 92 outliers final: 26 residues processed: 1046 average time/residue: 0.6727 time to fit residues: 1206.9318 Evaluate side-chains 879 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 853 time to evaluate : 6.200 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5380 time to fit residues: 35.5743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 755 optimal weight: 20.0000 chunk 574 optimal weight: 0.0470 chunk 396 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 364 optimal weight: 9.9990 chunk 513 optimal weight: 0.9980 chunk 766 optimal weight: 0.9990 chunk 811 optimal weight: 4.9990 chunk 400 optimal weight: 0.9980 chunk 726 optimal weight: 20.0000 chunk 218 optimal weight: 0.7980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 564 GLN A 602 ASN A 853 ASN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1242 ASN ** A1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1871 GLN A2069 HIS ** A2357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN B 853 ASN ** B 980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1649 GLN ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1902 ASN B2069 HIS ** B2357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 564 GLN C 602 ASN C 853 ASN C1081 HIS ** C1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1649 GLN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1902 ASN C2069 HIS D 192 GLN D 602 ASN D 853 ASN D1081 HIS ** D1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1242 ASN ** D1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2069 HIS D2135 GLN ** D2357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 69336 Z= 0.174 Angle : 0.526 14.271 93672 Z= 0.272 Chirality : 0.039 0.251 10792 Planarity : 0.003 0.047 11844 Dihedral : 4.351 63.362 9012 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.50 % 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: 8144 helix: 1.76 (0.07), residues: 5072 sheet: -1.02 (0.20), residues: 684 loop : -0.79 (0.13), residues: 2388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 968 time to evaluate : 6.160 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 outliers start: 114 outliers final: 50 residues processed: 1048 average time/residue: 0.6663 time to fit residues: 1207.6114 Evaluate side-chains 880 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 830 time to evaluate : 6.009 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.5134 time to fit residues: 57.2873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 676 optimal weight: 4.9990 chunk 460 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 604 optimal weight: 4.9990 chunk 335 optimal weight: 5.9990 chunk 692 optimal weight: 9.9990 chunk 561 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 414 optimal weight: 2.9990 chunk 728 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 HIS A 602 ASN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 GLN ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1933 ASN A2066 GLN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 HIS B 602 ASN B 980 ASN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1242 ASN ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1909 GLN B1991 GLN B2066 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN C 546 ASN C 551 HIS ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C1081 HIS ** C1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1242 ASN ** C1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1419 HIS C1649 GLN ** C1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1902 ASN ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN D 551 HIS D1081 HIS ** D1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1649 GLN ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1902 ASN D1991 GLN D2135 GLN D2596 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.066 69336 Z= 0.511 Angle : 0.702 11.923 93672 Z= 0.362 Chirality : 0.046 0.268 10792 Planarity : 0.005 0.060 11844 Dihedral : 4.908 80.631 9012 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 1.58 % 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: 0.51 (0.09), residues: 8144 helix: 1.33 (0.07), residues: 5052 sheet: -1.22 (0.20), residues: 692 loop : -1.25 (0.13), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 924 time to evaluate : 6.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 55 residues processed: 1001 average time/residue: 0.6731 time to fit residues: 1155.8973 Evaluate side-chains 882 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 827 time to evaluate : 6.025 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.4976 time to fit residues: 61.2260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 273 optimal weight: 10.0000 chunk 731 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 476 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 812 optimal weight: 0.9980 chunk 674 optimal weight: 4.9990 chunk 376 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 268 optimal weight: 9.9990 chunk 426 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 602 ASN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 ASN ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1871 GLN ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2069 HIS A2303 ASN ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 ASN B 602 ASN ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 ASN ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1494 HIS ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1902 ASN B2069 HIS ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** C1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 ASN ** C1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1765 ASN C1902 ASN C2066 GLN ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 HIS D1106 ASN ** D1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1419 HIS ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1902 ASN D1991 GLN D2066 GLN D2303 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 69336 Z= 0.302 Angle : 0.597 14.683 93672 Z= 0.308 Chirality : 0.041 0.247 10792 Planarity : 0.004 0.047 11844 Dihedral : 4.747 81.188 9012 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 1.29 % 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: 0.58 (0.09), residues: 8144 helix: 1.41 (0.07), residues: 5052 sheet: -1.26 (0.20), residues: 692 loop : -1.27 (0.13), residues: 2400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 898 time to evaluate : 7.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 44 residues processed: 961 average time/residue: 0.6808 time to fit residues: 1132.1774 Evaluate side-chains 852 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 808 time to evaluate : 6.182 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5154 time to fit residues: 51.6629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 783 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 463 optimal weight: 3.9990 chunk 593 optimal weight: 2.9990 chunk 459 optimal weight: 0.9980 chunk 684 optimal weight: 2.9990 chunk 453 optimal weight: 4.9990 chunk 809 optimal weight: 7.9990 chunk 506 optimal weight: 20.0000 chunk 493 optimal weight: 8.9990 chunk 373 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A1081 HIS ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 HIS ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2066 GLN A2303 ASN B 95 HIS ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1419 HIS ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1902 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN ** C 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 HIS C1902 ASN C2069 HIS ** D 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1902 ASN D2069 HIS D2303 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 69336 Z= 0.356 Angle : 0.622 12.696 93672 Z= 0.320 Chirality : 0.042 0.266 10792 Planarity : 0.004 0.073 11844 Dihedral : 4.816 86.184 9012 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.84 % 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: 0.47 (0.09), residues: 8144 helix: 1.37 (0.07), residues: 5040 sheet: -1.44 (0.19), residues: 692 loop : -1.36 (0.12), residues: 2412 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 894 time to evaluate : 6.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 40 residues processed: 940 average time/residue: 0.6714 time to fit residues: 1085.7971 Evaluate side-chains 857 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 817 time to evaluate : 5.998 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5105 time to fit residues: 47.9313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 500 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 chunk 483 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 514 optimal weight: 3.9990 chunk 551 optimal weight: 2.9990 chunk 400 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 636 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 602 ASN A1081 HIS ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1798 GLN ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1061 HIS B1081 HIS ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1902 ASN B2068 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C1081 HIS C1494 HIS ** C1649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1902 ASN C2023 GLN C2066 GLN C2069 HIS D 192 GLN D1081 HIS ** D1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1188 GLN D1494 HIS ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1902 ASN D2303 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 69336 Z= 0.200 Angle : 0.573 12.640 93672 Z= 0.293 Chirality : 0.040 0.270 10792 Planarity : 0.003 0.047 11844 Dihedral : 4.621 85.455 9012 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.57 % 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: 0.69 (0.10), residues: 8144 helix: 1.52 (0.07), residues: 5044 sheet: -1.32 (0.20), residues: 672 loop : -1.25 (0.13), residues: 2428 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 897 time to evaluate : 6.028 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 21 residues processed: 921 average time/residue: 0.6851 time to fit residues: 1083.8607 Evaluate side-chains 857 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 836 time to evaluate : 6.000 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5244 time to fit residues: 29.5312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 736 optimal weight: 1.9990 chunk 775 optimal weight: 6.9990 chunk 707 optimal weight: 6.9990 chunk 754 optimal weight: 0.9990 chunk 454 optimal weight: 2.9990 chunk 328 optimal weight: 8.9990 chunk 592 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 681 optimal weight: 5.9990 chunk 713 optimal weight: 2.9990 chunk 751 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2068 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1902 ASN C 95 HIS ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C1081 HIS C1188 GLN ** C1649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1902 ASN D 551 HIS ** D1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1902 ASN D2069 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.091 69336 Z= 0.339 Angle : 0.638 14.569 93672 Z= 0.326 Chirality : 0.042 0.297 10792 Planarity : 0.004 0.067 11844 Dihedral : 4.768 89.260 9012 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.57 % 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: 0.51 (0.09), residues: 8144 helix: 1.39 (0.07), residues: 5044 sheet: -1.43 (0.19), residues: 692 loop : -1.31 (0.13), residues: 2408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 871 time to evaluate : 6.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 895 average time/residue: 0.6911 time to fit residues: 1059.8351 Evaluate side-chains 843 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 820 time to evaluate : 6.196 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5419 time to fit residues: 32.0911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 495 optimal weight: 0.9990 chunk 797 optimal weight: 7.9990 chunk 486 optimal weight: 0.9990 chunk 378 optimal weight: 0.5980 chunk 554 optimal weight: 9.9990 chunk 836 optimal weight: 0.9990 chunk 770 optimal weight: 5.9990 chunk 666 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 514 optimal weight: 5.9990 chunk 408 optimal weight: 0.5980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1798 GLN ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1902 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 ASN C1081 HIS ** C1649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1902 ASN C2069 HIS D 551 HIS D1081 HIS ** D1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1902 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 69336 Z= 0.190 Angle : 0.600 13.473 93672 Z= 0.306 Chirality : 0.041 0.296 10792 Planarity : 0.004 0.050 11844 Dihedral : 4.617 88.154 9012 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer Outliers : 0.36 % 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: 0.67 (0.10), residues: 8144 helix: 1.50 (0.07), residues: 5028 sheet: -1.34 (0.20), residues: 672 loop : -1.23 (0.13), residues: 2444 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16288 Ramachandran restraints generated. 8144 Oldfield, 0 Emsley, 8144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 876 time to evaluate : 6.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 886 average time/residue: 0.7277 time to fit residues: 1122.2907 Evaluate side-chains 840 residues out of total 7584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 828 time to evaluate : 6.030 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5728 time to fit residues: 21.6217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 840 random chunks: chunk 529 optimal weight: 7.9990 chunk 709 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 614 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 667 optimal weight: 0.6980 chunk 279 optimal weight: 3.9990 chunk 685 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1081 HIS ** B1402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1902 ASN B1976 ASN ** B1991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1081 HIS C1902 ASN D1081 HIS D1649 GLN ** D1765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1902 ASN D2069 HIS D2303 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.193857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.161235 restraints weight = 95612.384| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.16 r_work: 0.3805 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 69336 Z= 0.332 Angle : 0.648 14.718 93672 Z= 0.331 Chirality : 0.043 0.297 10792 Planarity : 0.004 0.051 11844 Dihedral : 4.745 89.055 9012 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.33 % 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: 0.52 (0.09), residues: 8144 helix: 1.39 (0.07), residues: 5040 sheet: -1.45 (0.19), residues: 692 loop : -1.28 (0.13), residues: 2412 =============================================================================== Job complete usr+sys time: 18996.89 seconds wall clock time: 334 minutes 8.92 seconds (20048.92 seconds total)