Starting phenix.real_space_refine on Wed Apr 10 01:20:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/04_2024/6v93_21115_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/04_2024/6v93_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_21115/04_2024/6v93_21115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/04_2024/6v93_21115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/04_2024/6v93_21115_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v93_21115/04_2024/6v93_21115_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 14.13, per 1000 atoms: 0.78 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: 7.11 Conformation dependent library (CDL) restraints added in 4.8 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: 8.48 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: 6.86 Time building geometry restraints manager: 7.69 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: 10049 16.93 - 33.86: 691 33.86 - 50.79: 168 50.79 - 67.72: 38 67.72 - 84.65: 10 Dihedral angle restraints: 10956 sinusoidal: 4449 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 10953 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 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: 1.080 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: 4.620 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 63.350 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.090 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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= 0.282 Angle : 0.738 17.368 25016 Z= 0.461 Chirality : 0.755 20.237 2858 Planarity : 0.004 0.058 3046 Dihedral : 12.686 84.650 6732 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 881 HIS 0.007 0.001 HIS F 316 PHE 0.019 0.001 PHE G 94 TYR 0.017 0.001 TYR D 16 ARG 0.003 0.000 ARG F 237 *********************** 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 : 1.837 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7859 (mt0) cc_final: 0.7654 (mt0) REVERT: A 784 ILE cc_start: 0.9075 (mm) cc_final: 0.8794 (mm) REVERT: A 951 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8386 (tttm) REVERT: A 994 MET cc_start: 0.8217 (mtm) cc_final: 0.8004 (mtm) REVERT: A 1087 LEU cc_start: 0.8784 (tp) cc_final: 0.8580 (tp) REVERT: A 1142 ASP cc_start: 0.7542 (t0) cc_final: 0.7224 (t0) REVERT: D 135 ASN cc_start: 0.7474 (p0) cc_final: 0.6944 (p0) REVERT: D 142 GLU cc_start: 0.8218 (tt0) cc_final: 0.7866 (tt0) REVERT: E 1 MET cc_start: 0.6658 (mmt) cc_final: 0.6021 (mmp) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3160 time to fit residues: 138.5001 Evaluate side-chains 220 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 44 HIS A 52 GLN 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.253 18351 Z= 0.346 Angle : 1.266 50.347 25016 Z= 0.813 Chirality : 0.243 6.473 2858 Planarity : 0.004 0.056 3046 Dihedral : 10.778 66.031 2671 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.86 % Favored : 93.09 % Rotamer: Outliers : 0.73 % Allowed : 7.33 % Favored : 91.95 % 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: -1.76 (0.17), residues: 2160 helix: 0.77 (0.19), residues: 755 sheet: -1.83 (0.27), residues: 299 loop : -2.46 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 210 HIS 0.004 0.001 HIS F 316 PHE 0.013 0.001 PHE G 94 TYR 0.023 0.001 TYR F 419 ARG 0.006 0.000 ARG E 158 *********************** 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 224 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 211 time to evaluate : 2.041 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7929 (mt0) cc_final: 0.7698 (mt0) REVERT: A 98 HIS cc_start: 0.7560 (t70) cc_final: 0.7349 (t-90) REVERT: A 784 ILE cc_start: 0.9107 (mm) cc_final: 0.8830 (mm) REVERT: A 994 MET cc_start: 0.8227 (mtm) cc_final: 0.8025 (mtm) REVERT: A 1142 ASP cc_start: 0.7678 (t0) cc_final: 0.7418 (t0) REVERT: D 135 ASN cc_start: 0.7517 (p0) cc_final: 0.6967 (p0) REVERT: E 1 MET cc_start: 0.6694 (mmt) cc_final: 0.6086 (mmp) outliers start: 13 outliers final: 11 residues processed: 217 average time/residue: 0.2930 time to fit residues: 99.4613 Evaluate side-chains 209 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 198 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 1100 PHE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- 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: 0.8286 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.242 18351 Z= 0.626 Angle : 1.363 50.687 25016 Z= 0.855 Chirality : 0.244 6.453 2858 Planarity : 0.006 0.068 3046 Dihedral : 11.374 68.688 2671 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.04 % Favored : 90.82 % Rotamer: Outliers : 1.62 % Allowed : 9.12 % Favored : 89.26 % 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: -1.66 (0.17), residues: 2160 helix: 0.65 (0.18), residues: 765 sheet: -1.88 (0.27), residues: 286 loop : -2.22 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 103 HIS 0.024 0.002 HIS A 44 PHE 0.020 0.002 PHE D 40 TYR 0.021 0.002 TYR E 16 ARG 0.010 0.001 ARG A1447 *********************** 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 218 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 2.063 Fit side-chains REVERT: A 98 HIS cc_start: 0.7827 (t70) cc_final: 0.7610 (t-90) REVERT: F 277 MET cc_start: 0.8448 (tpp) cc_final: 0.8094 (tpt) REVERT: G 21 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8895 (mt) outliers start: 29 outliers final: 23 residues processed: 208 average time/residue: 0.2855 time to fit residues: 94.2356 Evaluate side-chains 198 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 174 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1100 PHE Chi-restraints excluded: chain A residue 1292 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 272 ASN Chi-restraints excluded: chain F residue 359 ASN Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 133 optimal weight: 0.2980 chunk 199 optimal weight: 3.9990 chunk 211 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8191 moved from start: 0.1588 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= 0.334 Angle : 1.272 50.492 25016 Z= 0.817 Chirality : 0.240 6.354 2858 Planarity : 0.004 0.053 3046 Dihedral : 10.866 67.716 2671 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.14 % Rotamer: Outliers : 1.12 % Allowed : 11.07 % Favored : 87.81 % 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: -1.06 (0.18), residues: 2160 helix: 1.25 (0.19), residues: 756 sheet: -1.34 (0.27), residues: 302 loop : -2.00 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 155 HIS 0.003 0.001 HIS A 288 PHE 0.016 0.001 PHE A1013 TYR 0.016 0.001 TYR D 16 ARG 0.007 0.000 ARG A 791 *********************** 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 207 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.672 Fit side-chains REVERT: A 98 HIS cc_start: 0.7582 (t70) cc_final: 0.7360 (t-90) REVERT: A 1087 LEU cc_start: 0.8814 (tp) cc_final: 0.8506 (tp) REVERT: D 135 ASN cc_start: 0.7336 (p0) cc_final: 0.6721 (p0) REVERT: E 1 MET cc_start: 0.6550 (mmp) cc_final: 0.6232 (mmp) REVERT: F 277 MET cc_start: 0.8094 (tpp) cc_final: 0.7827 (tpt) outliers start: 20 outliers final: 14 residues processed: 199 average time/residue: 0.2795 time to fit residues: 88.5647 Evaluate side-chains 195 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 1100 PHE Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8194 moved from start: 0.1607 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 : 1.269 50.492 25016 Z= 0.815 Chirality : 0.240 6.361 2858 Planarity : 0.004 0.091 3046 Dihedral : 10.622 68.590 2671 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.25 % Rotamer: Outliers : 1.34 % Allowed : 11.35 % Favored : 87.30 % 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: -0.80 (0.18), residues: 2160 helix: 1.47 (0.19), residues: 754 sheet: -1.10 (0.28), residues: 295 loop : -1.88 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 155 HIS 0.004 0.001 HIS A 288 PHE 0.013 0.001 PHE A1013 TYR 0.017 0.001 TYR D 16 ARG 0.005 0.000 ARG A1484 *********************** 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 202 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 2.160 Fit side-chains REVERT: A 1087 LEU cc_start: 0.8812 (tp) cc_final: 0.8489 (tp) REVERT: D 135 ASN cc_start: 0.7507 (p0) cc_final: 0.6937 (p0) REVERT: E 1 MET cc_start: 0.6720 (mmp) cc_final: 0.6232 (mmp) REVERT: F 277 MET cc_start: 0.8089 (tpp) cc_final: 0.7875 (tpt) REVERT: G 12 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8048 (ttpp) outliers start: 24 outliers final: 16 residues processed: 196 average time/residue: 0.2657 time to fit residues: 85.5276 Evaluate side-chains 193 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP 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: 1.9990 chunk 41 optimal weight: 0.0270 chunk 124 optimal weight: 0.0010 chunk 52 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.9848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8179 moved from start: 0.1633 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= 0.334 Angle : 1.265 50.495 25016 Z= 0.813 Chirality : 0.240 6.355 2858 Planarity : 0.004 0.085 3046 Dihedral : 10.512 67.853 2671 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.45 % Allowed : 11.80 % Favored : 86.74 % 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: -0.62 (0.18), residues: 2160 helix: 1.65 (0.19), residues: 749 sheet: -0.97 (0.28), residues: 305 loop : -1.79 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 155 HIS 0.003 0.000 HIS A 288 PHE 0.012 0.001 PHE A1013 TYR 0.017 0.001 TYR D 16 ARG 0.006 0.000 ARG A1484 *********************** 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 206 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 2.107 Fit side-chains REVERT: A 1087 LEU cc_start: 0.8815 (tp) cc_final: 0.8485 (tp) REVERT: D 135 ASN cc_start: 0.7472 (p0) cc_final: 0.6927 (p0) REVERT: E 1 MET cc_start: 0.6685 (mmp) cc_final: 0.6199 (mmp) REVERT: G 12 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8060 (ttpp) outliers start: 26 outliers final: 18 residues processed: 200 average time/residue: 0.2701 time to fit residues: 87.6084 Evaluate side-chains 195 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8176 moved from start: 0.1663 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= 0.334 Angle : 1.265 50.504 25016 Z= 0.813 Chirality : 0.240 6.356 2858 Planarity : 0.004 0.081 3046 Dihedral : 10.454 67.740 2671 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.37 % Favored : 92.58 % Rotamer: Outliers : 1.34 % Allowed : 11.74 % Favored : 86.91 % 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: -0.51 (0.18), residues: 2160 helix: 1.72 (0.19), residues: 750 sheet: -0.88 (0.28), residues: 306 loop : -1.72 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 155 HIS 0.003 0.000 HIS A 288 PHE 0.011 0.001 PHE A1013 TYR 0.017 0.001 TYR D 16 ARG 0.006 0.000 ARG A1484 *********************** 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 204 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 2.053 Fit side-chains REVERT: A 236 ASP cc_start: 0.7671 (t0) cc_final: 0.7390 (t0) REVERT: A 1087 LEU cc_start: 0.8820 (tp) cc_final: 0.8492 (tp) REVERT: D 135 ASN cc_start: 0.7464 (p0) cc_final: 0.6911 (p0) REVERT: E 1 MET cc_start: 0.6675 (mmp) cc_final: 0.6180 (mmp) REVERT: G 12 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8060 (ttpp) outliers start: 24 outliers final: 19 residues processed: 199 average time/residue: 0.2666 time to fit residues: 86.3698 Evaluate side-chains 198 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 178 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 272 ASN Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 0.0170 chunk 40 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8190 moved from start: 0.1723 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= 0.352 Angle : 1.273 50.514 25016 Z= 0.816 Chirality : 0.240 6.364 2858 Planarity : 0.004 0.080 3046 Dihedral : 10.510 67.437 2671 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.37 % Favored : 92.58 % Rotamer: Outliers : 1.57 % Allowed : 11.80 % Favored : 86.63 % 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: 1.70 (0.19), residues: 751 sheet: -0.84 (0.29), residues: 295 loop : -1.72 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 881 HIS 0.004 0.001 HIS A 288 PHE 0.010 0.001 PHE D 40 TYR 0.017 0.001 TYR D 16 ARG 0.005 0.000 ARG A1484 *********************** 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 209 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 2.186 Fit side-chains REVERT: A 236 ASP cc_start: 0.7661 (t0) cc_final: 0.7419 (t0) REVERT: A 1087 LEU cc_start: 0.8810 (tp) cc_final: 0.8495 (tp) REVERT: D 135 ASN cc_start: 0.7506 (p0) cc_final: 0.6912 (p0) REVERT: E 1 MET cc_start: 0.6603 (mmp) cc_final: 0.6099 (mmp) REVERT: G 12 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8069 (ttpp) outliers start: 28 outliers final: 21 residues processed: 203 average time/residue: 0.2901 time to fit residues: 96.9607 Evaluate side-chains 202 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 272 ASN Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 0.3980 chunk 202 optimal weight: 0.3980 chunk 184 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 129 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8177 moved from start: 0.1728 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= 0.336 Angle : 1.270 50.509 25016 Z= 0.814 Chirality : 0.240 6.359 2858 Planarity : 0.004 0.078 3046 Dihedral : 10.468 67.222 2671 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.28 % Favored : 92.67 % Rotamer: Outliers : 1.29 % Allowed : 12.19 % Favored : 86.52 % 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: -0.42 (0.18), residues: 2160 helix: 1.77 (0.19), residues: 748 sheet: -0.74 (0.29), residues: 306 loop : -1.67 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 155 HIS 0.003 0.001 HIS A 288 PHE 0.009 0.001 PHE F 345 TYR 0.017 0.001 TYR D 16 ARG 0.005 0.000 ARG A1484 *********************** 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 203 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 2.030 Fit side-chains REVERT: A 236 ASP cc_start: 0.7661 (t0) cc_final: 0.7382 (t0) REVERT: A 358 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.8077 (t-90) REVERT: A 1087 LEU cc_start: 0.8822 (tp) cc_final: 0.8490 (tp) REVERT: D 135 ASN cc_start: 0.7549 (p0) cc_final: 0.6995 (p0) REVERT: E 1 MET cc_start: 0.6628 (mmp) cc_final: 0.6009 (mmp) REVERT: G 12 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8064 (ttpp) outliers start: 23 outliers final: 20 residues processed: 198 average time/residue: 0.2836 time to fit residues: 92.1086 Evaluate side-chains 200 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 358 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 272 ASN Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 200 optimal weight: 0.3980 chunk 173 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 106 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1846 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= 0.414 Angle : 1.292 50.521 25016 Z= 0.824 Chirality : 0.241 6.374 2858 Planarity : 0.005 0.082 3046 Dihedral : 10.643 67.657 2671 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.12 % Favored : 91.84 % Rotamer: Outliers : 1.34 % Allowed : 12.36 % Favored : 86.30 % 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: -0.62 (0.18), residues: 2160 helix: 1.53 (0.19), residues: 761 sheet: -0.88 (0.29), residues: 301 loop : -1.75 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 881 HIS 0.012 0.001 HIS A 358 PHE 0.017 0.001 PHE A 528 TYR 0.018 0.001 TYR D 16 ARG 0.005 0.000 ARG A1484 ********************** 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 201 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 2.257 Fit side-chains REVERT: A 236 ASP cc_start: 0.7707 (t0) cc_final: 0.7472 (t0) REVERT: D 135 ASN cc_start: 0.7571 (p0) cc_final: 0.6949 (p0) REVERT: E 1 MET cc_start: 0.6811 (mmp) cc_final: 0.6157 (mmp) REVERT: G 12 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8084 (ttpp) outliers start: 24 outliers final: 21 residues processed: 196 average time/residue: 0.2721 time to fit residues: 86.8285 Evaluate side-chains 198 residues out of total 2027 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 272 ASN Chi-restraints excluded: chain F residue 371 ASN Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 418 CYS Chi-restraints excluded: chain F residue 419 TYR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 92 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 160 optimal weight: 0.0000 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3406 r_free = 0.3406 target = 0.113348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.092948 restraints weight = 53206.042| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.58 r_work: 0.2980 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1879 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= 0.383 Angle : 1.287 50.516 25016 Z= 0.821 Chirality : 0.241 6.371 2858 Planarity : 0.004 0.079 3046 Dihedral : 10.697 67.223 2671 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.75 % Favored : 92.21 % Rotamer: Outliers : 1.29 % Allowed : 12.53 % Favored : 86.19 % 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: -0.58 (0.18), residues: 2160 helix: 1.55 (0.19), residues: 760 sheet: -0.86 (0.29), residues: 291 loop : -1.71 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 881 HIS 0.004 0.001 HIS A 105 PHE 0.013 0.001 PHE A 528 TYR 0.018 0.001 TYR D 16 ARG 0.005 0.000 ARG A1484 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3571.48 seconds wall clock time: 66 minutes 17.23 seconds (3977.23 seconds total)