Starting phenix.real_space_refine (version: dev) on Wed Dec 14 00:31:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/12_2022/6v93_21115_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/12_2022/6v93_21115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/12_2022/6v93_21115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/12_2022/6v93_21115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/12_2022/6v93_21115_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/12_2022/6v93_21115_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 1.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A PHE 598": not complete - not flipped Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "A PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 806": "OD1" <-> "OD2" Residue "A TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1052": "OD1" <-> "OD2" Residue "A ASP 1055": "OD1" <-> "OD2" Residue "A PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1131": "OD1" <-> "OD2" Residue "A GLU 1132": "OE1" <-> "OE2" Residue "A ASP 1142": "OD1" <-> "OD2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A TYR 1201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1212": "OD1" <-> "OD2" Residue "A GLU 1217": "OE1" <-> "OE2" Residue "A ASP 1222": "OD1" <-> "OD2" Residue "A PHE 1270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1282": "OE1" <-> "OE2" Residue "A GLU 1325": "OE1" <-> "OE2" Residue "A ASP 1462": "OD1" <-> "OD2" Residue "A ASP 1472": "OD1" <-> "OD2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 115": "OD1" <-> "OD2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ASP 206": "OD1" <-> "OD2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F GLU 234": "OE1" <-> "OE2" Residue "F ASP 265": "OD1" <-> "OD2" Residue "F PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 430": "OD1" <-> "OD2" Residue "G PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 18105 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 9897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1259, 9882 Classifications: {'peptide': 1259} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 74} Link IDs: {'PTRANS': 60, 'TRANS': 1198} Chain breaks: 8 Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 18, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 35, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 258 Conformer: "B" Number of residues, atoms: 1259, 9882 Classifications: {'peptide': 1259} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 74} Link IDs: {'PTRANS': 60, 'TRANS': 1198} Chain breaks: 8 Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 18, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 35, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 258 bond proxies already assigned to first conformer: 10100 Chain: "D" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1286 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1660 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3541 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 26, 'TRANS': 434} Chain breaks: 4 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 13, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 116 Chain: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 929 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 23 Chain: "P" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 212 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 322 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 175 Unusual residues: {' CA': 2, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 4, 'water': 137} Link IDs: {None: 140} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9684 SG CYS A1473 60.219 72.205 67.257 1.00 42.97 S ATOM 9499 SG CYS A1449 54.514 69.839 65.125 1.00 44.24 S ATOM 9644 SG CYS A1468 57.621 66.825 70.044 1.00 41.77 S ATOM 9475 SG CYS A1446 55.075 72.427 71.345 1.00 45.69 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN A1259 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A1259 " occ=0.50 Time building chain proxies: 15.72, per 1000 atoms: 0.87 Number of scatterers: 18105 At special positions: 0 Unit cell: (134.156, 154.548, 115.911, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 82 16.00 P 29 15.00 O 3473 8.00 N 2981 7.00 C 11534 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.73 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1601 " pdb=" FE3 SF4 A1601 " - pdb=" SG CYS A1468 " pdb=" FE1 SF4 A1601 " - pdb=" SG CYS A1473 " pdb=" FE2 SF4 A1601 " - pdb=" SG CYS A1449 " pdb=" FE4 SF4 A1601 " - pdb=" SG CYS A1446 " Number of angles added : 12 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 17 sheets defined 33.3% alpha, 10.3% beta 10 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 6.35 Creating SS restraints... Processing helix chain 'A' and resid 96 through 115 Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.710A pdb=" N ASP A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 229 through 232 No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 236 through 245 Processing helix chain 'A' and resid 307 through 321 removed outlier: 4.299A pdb=" N ASP A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 386 through 389 No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 613 through 621 Processing helix chain 'A' and resid 726 through 734 Processing helix chain 'A' and resid 745 through 759 Processing helix chain 'A' and resid 773 through 783 Processing helix chain 'A' and resid 790 through 793 No H-bonds generated for 'chain 'A' and resid 790 through 793' Processing helix chain 'A' and resid 807 through 812 removed outlier: 3.578A pdb=" N ALA A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 812' Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 841 through 848 Processing helix chain 'A' and resid 858 through 865 Processing helix chain 'A' and resid 871 through 894 removed outlier: 3.671A pdb=" N ASN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 921 through 933 removed outlier: 3.773A pdb=" N ARG A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'A' and resid 979 through 986 Processing helix chain 'A' and resid 1020 through 1023 No H-bonds generated for 'chain 'A' and resid 1020 through 1023' Processing helix chain 'A' and resid 1045 through 1066 removed outlier: 3.557A pdb=" N MET A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A1066 " --> pdb=" O LYS A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1094 removed outlier: 4.419A pdb=" N LEU A1077 " --> pdb=" O THR A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1130 Processing helix chain 'A' and resid 1158 through 1172 removed outlier: 3.879A pdb=" N ASN A1172 " --> pdb=" O ARG A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1244 through 1260 Processing helix chain 'A' and resid 1287 through 1298 removed outlier: 3.717A pdb=" N VAL A1291 " --> pdb=" O ALA A1287 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1326 No H-bonds generated for 'chain 'A' and resid 1323 through 1326' Processing helix chain 'A' and resid 1330 through 1335 Processing helix chain 'A' and resid 1343 through 1360 Proline residue: A1353 - end of helix Processing helix chain 'A' and resid 1367 through 1371 removed outlier: 3.601A pdb=" N GLN A1371 " --> pdb=" O GLY A1367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1367 through 1371' Processing helix chain 'A' and resid 1424 through 1454 removed outlier: 3.571A pdb=" N TYR A1451 " --> pdb=" O ARG A1447 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N TYR A1453 " --> pdb=" O CYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1467 removed outlier: 3.916A pdb=" N LYS A1467 " --> pdb=" O HIS A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1486 Processing helix chain 'D' and resid 4 through 23 Processing helix chain 'D' and resid 52 through 67 Processing helix chain 'D' and resid 110 through 130 removed outlier: 4.174A pdb=" N LYS D 130 " --> pdb=" O MET D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 23 removed outlier: 3.521A pdb=" N ARG E 10 " --> pdb=" O GLU E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 52 through 70 removed outlier: 3.555A pdb=" N ASP E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 130 removed outlier: 4.052A pdb=" N LYS E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 174 Processing helix chain 'F' and resid 1 through 9 Processing helix chain 'F' and resid 53 through 75 Processing helix chain 'F' and resid 116 through 124 Processing helix chain 'F' and resid 132 through 137 removed outlier: 4.029A pdb=" N TYR F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 240 removed outlier: 3.707A pdb=" N LEU F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 253 removed outlier: 5.122A pdb=" N LEU F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 291 Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 392 through 404 Processing helix chain 'F' and resid 412 through 415 No H-bonds generated for 'chain 'F' and resid 412 through 415' Processing helix chain 'G' and resid 4 through 14 Processing helix chain 'G' and resid 22 through 29 Processing helix chain 'G' and resid 33 through 44 Processing sheet with id= A, first strand: chain 'A' and resid 23 through 26 Processing sheet with id= B, first strand: chain 'A' and resid 29 through 35 Processing sheet with id= C, first strand: chain 'A' and resid 696 through 698 removed outlier: 6.331A pdb=" N ILE A 763 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU A 672 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N SER A 765 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N HIS A 822 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLY A 766 " --> pdb=" O HIS A 822 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE A 824 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 714 through 717 Processing sheet with id= E, first strand: chain 'A' and resid 971 through 975 removed outlier: 3.838A pdb=" N TYR A1140 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A1149 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A1138 " --> pdb=" O TYR A1149 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1027 through 1029 removed outlier: 3.567A pdb=" N TYR A1036 " --> pdb=" O THR A1028 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 996 " --> pdb=" O VAL A1035 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA A1037 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET A 994 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1210 through 1214 removed outlier: 7.399A pdb=" N VAL A1197 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU A1190 " --> pdb=" O VAL A1197 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE A1199 " --> pdb=" O SER A1188 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER A1188 " --> pdb=" O PHE A1199 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1270 through 1274 removed outlier: 3.707A pdb=" N TYR A1312 " --> pdb=" O PHE A1270 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS A1272 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A1310 " --> pdb=" O LYS A1272 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU A1308 " --> pdb=" O VAL A1274 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 137 through 145 removed outlier: 6.821A pdb=" N SER A 162 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 140 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LYS A 160 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL A 142 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE A 158 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS A 144 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN A 156 " --> pdb=" O LYS A 144 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 139 through 146 removed outlier: 3.630A pdb=" N ARG D 74 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN D 81 " --> pdb=" O CYS D 87 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N CYS D 87 " --> pdb=" O ASN D 81 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 32 through 35 Processing sheet with id= L, first strand: chain 'E' and resid 139 through 141 removed outlier: 6.741A pdb=" N ASN E 81 " --> pdb=" O CYS E 87 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS E 87 " --> pdb=" O ASN E 81 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 72 through 76 removed outlier: 6.689A pdb=" N ASN E 146 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE E 75 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 144 " --> pdb=" O PHE E 75 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 107 through 109 removed outlier: 3.502A pdb=" N VAL F 155 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 480 through 484 removed outlier: 7.387A pdb=" N ALA F 215 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU F 257 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL F 217 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE F 259 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER F 295 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE F 259 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP F 297 " --> pdb=" O ILE F 259 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 343 through 347 removed outlier: 6.279A pdb=" N VAL F 435 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL F 355 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE F 437 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N TYR F 436 " --> pdb=" O ASN F 455 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS F 457 " --> pdb=" O TYR F 436 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL F 438 " --> pdb=" O LYS F 457 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE F 459 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY F 445 " --> pdb=" O SER F 460 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 64 through 67 removed outlier: 3.852A pdb=" N THR G 64 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE G 57 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE G 85 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N CYS G 59 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N CYS G 83 " --> pdb=" O CYS G 59 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 6.47 Time building geometry restraints manager: 8.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 6836 1.38 - 1.57: 11338 1.57 - 1.76: 57 1.76 - 1.95: 108 1.95 - 2.14: 12 Bond restraints: 18351 Sorted by residual: bond pdb=" C4' DCP A1604 " pdb=" O4' DCP A1604 " ideal model delta sigma weight residual 1.444 1.615 -0.171 1.00e-02 1.00e+04 2.91e+02 bond pdb=" C3' DCP A1604 " pdb=" C4' DCP A1604 " ideal model delta sigma weight residual 1.527 1.347 0.180 1.10e-02 8.26e+03 2.68e+02 bond pdb=" C4 DCP A1604 " pdb=" N4 DCP A1604 " ideal model delta sigma weight residual 1.334 1.473 -0.139 1.20e-02 6.94e+03 1.34e+02 bond pdb=" C1' DCP A1604 " pdb=" O4' DCP A1604 " ideal model delta sigma weight residual 1.418 1.305 0.113 1.20e-02 6.94e+03 8.86e+01 bond pdb=" C5 DCP A1604 " pdb=" C6 DCP A1604 " ideal model delta sigma weight residual 1.345 1.503 -0.158 1.80e-02 3.09e+03 7.69e+01 ... (remaining 18346 not shown) Histogram of bond angle deviations from ideal: 88.93 - 98.12: 24 98.12 - 107.32: 804 107.32 - 116.52: 12102 116.52 - 125.72: 11723 125.72 - 134.91: 363 Bond angle restraints: 25016 Sorted by residual: angle pdb=" PB DCP A1604 " pdb=" O3B DCP A1604 " pdb=" PG DCP A1604 " ideal model delta sigma weight residual 139.87 124.01 15.86 1.00e+00 1.00e+00 2.52e+02 angle pdb=" PA DCP A1604 " pdb=" O3A DCP A1604 " pdb=" PB DCP A1604 " ideal model delta sigma weight residual 136.83 124.92 11.91 1.00e+00 1.00e+00 1.42e+02 angle pdb=" FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb=" FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 91.07 -17.37 1.50e+00 4.44e-01 1.34e+02 angle pdb=" FE1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb=" FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.62 -16.92 1.50e+00 4.44e-01 1.27e+02 angle pdb=" FE1 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb=" FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.59 -16.89 1.50e+00 4.44e-01 1.27e+02 ... (remaining 25011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 10026 16.93 - 33.86: 673 33.86 - 50.79: 165 50.79 - 67.72: 38 67.72 - 84.65: 10 Dihedral angle restraints: 10912 sinusoidal: 4405 harmonic: 6507 Sorted by residual: dihedral pdb=" CA SER A 220 " pdb=" C SER A 220 " pdb=" N PRO A 221 " pdb=" CA PRO A 221 " ideal model delta harmonic sigma weight residual 180.00 -146.10 -33.90 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA PHE A 772 " pdb=" C PHE A 772 " pdb=" N SER A 773 " pdb=" CA SER A 773 " ideal model delta harmonic sigma weight residual 180.00 -147.97 -32.03 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA LYS F 36 " pdb=" C LYS F 36 " pdb=" N SER F 37 " pdb=" CA SER F 37 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 10909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.047: 2854 4.047 - 8.095: 0 8.095 - 12.142: 0 12.142 - 16.189: 0 16.189 - 20.237: 4 Chirality restraints: 2858 Sorted by residual: chirality pdb=" FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False -10.55 9.68 -20.24 2.00e-01 2.50e+01 1.02e+04 chirality pdb=" FE1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False -10.55 9.60 -20.15 2.00e-01 2.50e+01 1.02e+04 chirality pdb=" FE2 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb=" S3 SF4 A1601 " pdb=" S4 SF4 A1601 " both_signs ideal model delta sigma weight residual False 10.55 -9.59 20.14 2.00e-01 2.50e+01 1.01e+04 ... (remaining 2855 not shown) Planarity restraints: 3046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 341 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO F 342 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 342 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 342 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 683 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO A 684 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 684 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 684 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1352 " 0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO A1353 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1353 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1353 " 0.026 5.00e-02 4.00e+02 ... (remaining 3043 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 382 2.67 - 3.23: 16922 3.23 - 3.79: 27147 3.79 - 4.34: 38750 4.34 - 4.90: 63921 Nonbonded interactions: 147122 Sorted by model distance: nonbonded pdb=" O GLY A1162 " pdb=" O HOH A1701 " model vdw 2.117 2.440 nonbonded pdb=" O VAL F 122 " pdb=" OG1 THR F 126 " model vdw 2.131 2.440 nonbonded pdb=" OD1 ASP A 685 " pdb=" O HOH A1702 " model vdw 2.221 2.440 nonbonded pdb=" O SER A 170 " pdb=" OG SER A 173 " model vdw 2.245 2.440 nonbonded pdb=" O PHE D 114 " pdb=" O HOH D 301 " model vdw 2.258 2.440 ... (remaining 147117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 P 29 5.49 5 S 82 5.16 5 C 11534 2.51 5 N 2981 2.21 5 O 3473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.190 Check model and map are aligned: 0.290 Convert atoms to be neutral: 0.160 Process input model: 62.040 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.006 0.180 18351 Z= 0.283 Angle : 0.738 17.368 25016 Z= 0.461 Chirality : 0.755 20.237 2858 Planarity : 0.004 0.058 3046 Dihedral : 12.612 84.650 6688 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 93.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.16), residues: 2160 helix: -0.36 (0.17), residues: 757 sheet: -2.31 (0.27), residues: 280 loop : -2.96 (0.15), residues: 1123 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 2.284 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3058 time to fit residues: 136.0128 Evaluate side-chains 219 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 2.285 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 111 optimal weight: 0.0170 chunk 88 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 127 optimal weight: 0.0060 chunk 198 optimal weight: 4.9990 overall best weight: 1.2040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 239 GLN A 251 ASN A 288 HIS A 319 GLN A 342 GLN A 866 ASN A1002 ASN A1115 GLN A1206 GLN A1228 GLN D 2 ASN D 122 ASN D 214 GLN E 214 GLN F 221 ASN F 245 ASN F 246 ASN F 341 ASN G 77 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.249 18351 Z= 0.347 Angle : 1.269 50.422 25016 Z= 0.814 Chirality : 0.241 6.389 2858 Planarity : 0.004 0.057 3046 Dihedral : 10.546 66.973 2627 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.90 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % 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: -1.71 (0.17), residues: 2160 helix: 0.80 (0.19), residues: 755 sheet: -1.79 (0.27), residues: 297 loop : -2.43 (0.17), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 210 time to evaluate : 2.168 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 216 average time/residue: 0.2835 time to fit residues: 96.6995 Evaluate side-chains 202 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 2.130 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1635 time to fit residues: 5.9169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 54 optimal weight: 0.0570 chunk 199 optimal weight: 6.9990 chunk 215 optimal weight: 0.7980 chunk 177 optimal weight: 0.0870 chunk 197 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN F 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.245 18351 Z= 0.384 Angle : 1.280 50.500 25016 Z= 0.819 Chirality : 0.242 6.389 2858 Planarity : 0.004 0.054 3046 Dihedral : 10.636 68.696 2627 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.14 % Favored : 92.76 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 2160 helix: 1.15 (0.19), residues: 761 sheet: -1.54 (0.27), residues: 298 loop : -2.13 (0.18), residues: 1101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 2.101 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 204 average time/residue: 0.2644 time to fit residues: 87.8738 Evaluate side-chains 191 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 2.182 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1830 time to fit residues: 4.8810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 104 optimal weight: 0.1980 chunk 189 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 2 ASN F 221 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.242 18351 Z= 0.456 Angle : 1.305 50.511 25016 Z= 0.830 Chirality : 0.242 6.388 2858 Planarity : 0.005 0.087 3046 Dihedral : 10.833 68.931 2627 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.93 % Favored : 91.98 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.14 % 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 (0.18), residues: 2160 helix: 1.13 (0.19), residues: 761 sheet: -1.47 (0.27), residues: 303 loop : -2.01 (0.18), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 2.172 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 197 average time/residue: 0.2702 time to fit residues: 87.2412 Evaluate side-chains 192 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1683 time to fit residues: 7.3288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1032 ASN ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.244 18351 Z= 0.342 Angle : 1.271 50.502 25016 Z= 0.816 Chirality : 0.240 6.358 2858 Planarity : 0.004 0.085 3046 Dihedral : 10.567 68.955 2627 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.33 % Favored : 92.63 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % 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: -0.77 (0.18), residues: 2160 helix: 1.46 (0.19), residues: 756 sheet: -1.04 (0.29), residues: 293 loop : -1.84 (0.18), residues: 1111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 2.183 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 184 average time/residue: 0.2994 time to fit residues: 89.5352 Evaluate side-chains 177 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 41 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.243 18351 Z= 0.380 Angle : 1.281 50.519 25016 Z= 0.820 Chirality : 0.241 6.372 2858 Planarity : 0.004 0.081 3046 Dihedral : 10.553 69.365 2627 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.21 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % 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: -0.74 (0.18), residues: 2160 helix: 1.46 (0.19), residues: 758 sheet: -1.02 (0.29), residues: 287 loop : -1.81 (0.18), residues: 1115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 2.148 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 182 average time/residue: 0.2660 time to fit residues: 79.5192 Evaluate side-chains 180 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 2.096 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1854 time to fit residues: 6.0816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 0.0000 chunk 23 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.244 18351 Z= 0.330 Angle : 1.266 50.503 25016 Z= 0.813 Chirality : 0.240 6.353 2858 Planarity : 0.004 0.076 3046 Dihedral : 10.359 68.992 2627 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.47 % Favored : 92.49 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % 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 (0.18), residues: 2160 helix: 1.68 (0.19), residues: 750 sheet: -0.86 (0.29), residues: 286 loop : -1.70 (0.18), residues: 1124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 2.297 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 188 average time/residue: 0.2741 time to fit residues: 84.6355 Evaluate side-chains 180 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 2.250 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1915 time to fit residues: 3.6939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.243 18351 Z= 0.351 Angle : 1.273 50.516 25016 Z= 0.816 Chirality : 0.240 6.360 2858 Planarity : 0.004 0.076 3046 Dihedral : 10.370 69.050 2627 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.25 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % 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: -0.48 (0.18), residues: 2160 helix: 1.68 (0.19), residues: 751 sheet: -0.81 (0.30), residues: 276 loop : -1.65 (0.18), residues: 1133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 2.227 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 182 average time/residue: 0.2600 time to fit residues: 77.8944 Evaluate side-chains 180 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 2.127 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1822 time to fit residues: 4.6278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 118 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 186 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.242 18351 Z= 0.365 Angle : 1.277 50.486 25016 Z= 0.817 Chirality : 0.241 6.365 2858 Planarity : 0.004 0.076 3046 Dihedral : 10.450 68.744 2627 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.61 % Favored : 92.35 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.05 % 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 (0.18), residues: 2160 helix: 1.60 (0.19), residues: 759 sheet: -0.79 (0.30), residues: 276 loop : -1.67 (0.18), residues: 1125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 2.087 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 181 average time/residue: 0.2869 time to fit residues: 84.6653 Evaluate side-chains 179 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 2.206 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1700 time to fit residues: 3.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.241 18351 Z= 0.484 Angle : 1.318 50.553 25016 Z= 0.835 Chirality : 0.242 6.392 2858 Planarity : 0.005 0.082 3046 Dihedral : 10.867 68.993 2627 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.49 % Favored : 91.42 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.14 % 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: -0.75 (0.18), residues: 2160 helix: 1.34 (0.19), residues: 760 sheet: -0.98 (0.30), residues: 278 loop : -1.74 (0.18), residues: 1122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 2.125 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 180 average time/residue: 0.2642 time to fit residues: 77.7652 Evaluate side-chains 177 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 172 time to evaluate : 2.129 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1883 time to fit residues: 4.5584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.094926 restraints weight = 53212.040| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.56 r_work: 0.3013 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.243 18351 Z= 0.326 Angle : 1.272 50.484 25016 Z= 0.815 Chirality : 0.240 6.358 2858 Planarity : 0.004 0.071 3046 Dihedral : 10.585 68.407 2627 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.24 % Favored : 92.72 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.95 % Twisted General : 0.10 % 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 (0.18), residues: 2160 helix: 1.62 (0.19), residues: 758 sheet: -0.76 (0.30), residues: 285 loop : -1.62 (0.18), residues: 1117 =============================================================================== Job complete usr+sys time: 3372.67 seconds wall clock time: 62 minutes 56.46 seconds (3776.46 seconds total)