Starting phenix.real_space_refine on Sat Feb 17 01:55:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0t_24793/02_2024/7s0t_24793_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0t_24793/02_2024/7s0t_24793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0t_24793/02_2024/7s0t_24793.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0t_24793/02_2024/7s0t_24793.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0t_24793/02_2024/7s0t_24793_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s0t_24793/02_2024/7s0t_24793_updated.pdb" } resolution = 3.05 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= 0.002 sd= 0.022 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 1 9.91 5 Fe 4 7.16 5 P 27 5.49 5 S 76 5.16 5 C 11076 2.51 5 N 2828 2.21 5 O 3083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 598": not complete - not flipped Residue "A TYR 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 145": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17095 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 9196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1231, 9196 Classifications: {'peptide': 1231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 161} Link IDs: {'PTRANS': 60, 'TRANS': 1170} Chain breaks: 16 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 852 Unresolved non-hydrogen angles: 1053 Unresolved non-hydrogen dihedrals: 681 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 11, 'ASP:plan': 32, 'PHE:plan': 4, 'GLU:plan': 48, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 504 Chain: "D" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1284 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 152} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1624 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3510 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 27, 'TRANS': 438} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 23, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 177 Chain: "G" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 921 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 28 Chain: "P" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 193 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} 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: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 299 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 54 Unusual residues: {' CA': 1, 'DCP': 1, 'SF4': 1} Classifications: {'undetermined': 3, 'water': 17} Link IDs: {None: 19} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9008 SG CYS A1473 41.278 82.041 85.282 1.00 64.88 S ATOM 8827 SG CYS A1449 45.629 87.243 84.420 1.00 68.55 S ATOM 8970 SG CYS A1468 38.906 88.990 82.407 1.00 62.69 S Time building chain proxies: 9.36, per 1000 atoms: 0.55 Number of scatterers: 17095 At special positions: 0 Unit cell: (87.68, 143.576, 168.784, 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 1 19.99 S 76 16.00 P 27 15.00 O 3083 8.00 N 2828 7.00 C 11076 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: 6.38 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1601 " pdb="FE1 SF4 A1601 " - pdb=" SG CYS A1473 " pdb="FE3 SF4 A1601 " - pdb=" SG CYS A1468 " pdb="FE2 SF4 A1601 " - pdb=" SG CYS A1449 " pdb="FE4 SF4 A1601 " - pdb=" SG CYS A1446 " Number of angles added : 12 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 17 sheets defined 34.7% alpha, 11.4% beta 4 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 9.15 Creating SS restraints... Processing helix chain 'A' and resid 96 through 115 Processing helix chain 'A' and resid 166 through 177 removed outlier: 4.389A pdb=" N SER A 170 " --> pdb=" O SER A 167 " (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 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' 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 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' 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 789 through 793 Processing helix chain 'A' and resid 807 through 811 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: 3.827A pdb=" N ASN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 916 removed outlier: 4.360A pdb=" N TYR A 916 " --> pdb=" O PHE A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 916' Processing helix chain 'A' and resid 920 through 935 removed outlier: 3.596A pdb=" N VAL A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A 934 " --> pdb=" O ARG A 930 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'A' and resid 979 through 987 Processing helix chain 'A' and resid 1019 through 1022 No H-bonds generated for 'chain 'A' and resid 1019 through 1022' Processing helix chain 'A' and resid 1045 through 1063 WARNING: missing atoms! Processing helix chain 'A' and resid 1073 through 1095 removed outlier: 4.137A pdb=" N TYR A1093 " --> pdb=" O ALA A1089 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A1094 " --> pdb=" O ASN A1090 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1130 Processing helix chain 'A' and resid 1155 through 1172 removed outlier: 4.122A pdb=" N PHE A1159 " --> pdb=" O ILE A1156 " (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 1296 Processing helix chain 'A' and resid 1330 through 1333 No H-bonds generated for 'chain 'A' and resid 1330 through 1333' Processing helix chain 'A' and resid 1343 through 1359 Proline residue: A1353 - end of helix Processing helix chain 'A' and resid 1366 through 1372 removed outlier: 3.590A pdb=" N GLU A1372 " --> pdb=" O ASN A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1454 removed outlier: 4.189A pdb=" N ARG A1452 " --> pdb=" O THR A1448 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR A1453 " --> pdb=" O CYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1467 removed outlier: 3.719A pdb=" N LYS A1467 " --> pdb=" O HIS A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1486 Processing helix chain 'A' and resid 1489 through 1501 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 129 Processing helix chain 'E' and resid 5 through 23 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: 4.958A pdb=" N THR E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 129 Processing helix chain 'E' and resid 165 through 174 Processing helix chain 'F' and resid 1 through 9 Processing helix chain 'F' and resid 52 through 75 removed outlier: 3.533A pdb=" N PHE F 64 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 132 through 137 removed outlier: 3.697A pdb=" N TYR F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 240 Processing helix chain 'F' and resid 248 through 253 removed outlier: 4.724A 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 364 Processing helix chain 'F' and resid 392 through 405 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 helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing sheet with id= A, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.555A pdb=" N ILE A 25 " --> pdb=" O ILE A 211 " (cutoff:3.500A) 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 81 through 85 removed outlier: 3.528A pdb=" N ILE A 84 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 696 through 698 removed outlier: 6.240A pdb=" N ILE A 763 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LEU A 672 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER A 765 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N HIS A 822 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLY A 766 " --> pdb=" O HIS A 822 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 824 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 714 through 717 Processing sheet with id= F, first strand: chain 'A' and resid 965 through 967 removed outlier: 3.721A pdb=" N ALA A 965 " --> pdb=" O LEU A1190 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG A1195 " --> pdb=" O ILE A1191 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 971 through 975 removed outlier: 3.625A pdb=" N TYR A1140 " --> pdb=" O PHE A1147 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR A1149 " --> pdb=" O VAL A1138 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL A1138 " --> pdb=" O TYR A1149 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1027 through 1029 removed outlier: 3.789A pdb=" N GLY A 996 " --> pdb=" O VAL A1035 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA A1037 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N MET A 994 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1270 through 1274 removed outlier: 3.675A pdb=" N LYS A1272 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1310 " --> pdb=" O LYS A1272 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A1308 " --> pdb=" O VAL A1274 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 198 through 202 removed outlier: 4.272A pdb=" N GLN D 214 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 86 " --> pdb=" O ASN D 81 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE D 79 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS D 90 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE D 77 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL D 92 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N PHE D 75 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP D 94 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N TYR D 73 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASN D 146 " --> pdb=" O TYR D 73 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE D 75 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL D 144 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE D 77 " --> pdb=" O GLU D 142 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU D 142 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE D 79 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR D 140 " --> pdb=" O ILE D 79 " (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 213 through 218 removed outlier: 3.633A pdb=" N HIS E 213 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE E 79 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS E 90 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE E 77 " --> pdb=" O LYS E 90 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL E 92 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE E 75 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASP E 94 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N TYR E 73 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN E 146 " --> pdb=" O TYR E 73 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N PHE E 75 " --> pdb=" O VAL E 144 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL E 144 " --> pdb=" O PHE E 75 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE E 77 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLU E 142 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ILE E 79 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR E 140 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 107 through 109 Processing sheet with id= N, first strand: chain 'F' and resid 156 through 158 Processing sheet with id= O, first strand: chain 'F' and resid 480 through 484 removed outlier: 7.482A pdb=" N ALA F 215 " --> pdb=" O GLY F 255 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU F 257 " --> pdb=" O ALA F 215 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL F 217 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE F 259 " --> pdb=" O VAL F 217 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER F 295 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE F 259 " --> pdb=" O SER F 295 " (cutoff:3.500A) removed outlier: 6.401A 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: 6.472A pdb=" N VAL F 435 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL F 355 " --> pdb=" O VAL F 435 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE F 437 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR F 436 " --> pdb=" O ASN F 455 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS F 457 " --> pdb=" O TYR F 436 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL F 438 " --> pdb=" O LYS F 457 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE F 459 " --> pdb=" O VAL F 438 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 64 through 67 removed outlier: 3.967A pdb=" N THR G 64 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE G 57 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE G 85 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N CYS G 59 " --> pdb=" O CYS G 83 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS G 83 " --> pdb=" O CYS G 59 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 6.35 Time building geometry restraints manager: 6.91 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: 6181 1.38 - 1.57: 11162 1.57 - 1.76: 53 1.76 - 1.95: 96 1.95 - 2.14: 12 Bond restraints: 17504 Sorted by residual: bond pdb=" C4' DCP A1603 " pdb=" O4' DCP A1603 " ideal model delta sigma weight residual 1.444 1.614 -0.170 1.00e-02 1.00e+04 2.91e+02 bond pdb=" C3' DCP A1603 " pdb=" C4' DCP A1603 " ideal model delta sigma weight residual 1.527 1.348 0.179 1.10e-02 8.26e+03 2.64e+02 bond pdb=" C4 DCP A1603 " pdb=" N4 DCP A1603 " ideal model delta sigma weight residual 1.334 1.475 -0.141 1.20e-02 6.94e+03 1.37e+02 bond pdb=" C1' DCP A1603 " pdb=" O4' DCP A1603 " ideal model delta sigma weight residual 1.418 1.302 0.116 1.20e-02 6.94e+03 9.34e+01 bond pdb=" C5 DCP A1603 " pdb=" C6 DCP A1603 " ideal model delta sigma weight residual 1.345 1.503 -0.158 1.80e-02 3.09e+03 7.69e+01 ... (remaining 17499 not shown) Histogram of bond angle deviations from ideal: 89.02 - 98.03: 24 98.03 - 107.03: 682 107.03 - 116.04: 11111 116.04 - 125.05: 11753 125.05 - 134.05: 351 Bond angle restraints: 23921 Sorted by residual: angle pdb=" PB DCP A1603 " pdb=" O3B DCP A1603 " pdb=" PG DCP A1603 " ideal model delta sigma weight residual 139.87 122.03 17.84 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PA DCP A1603 " pdb=" O3A DCP A1603 " pdb=" PB DCP A1603 " ideal model delta sigma weight residual 136.83 124.59 12.24 1.00e+00 1.00e+00 1.50e+02 angle pdb="FE3 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 91.00 -17.30 1.50e+00 4.44e-01 1.33e+02 angle pdb="FE2 SF4 A1601 " pdb=" S1 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.56 -16.86 1.50e+00 4.44e-01 1.26e+02 angle pdb="FE1 SF4 A1601 " pdb=" S2 SF4 A1601 " pdb="FE4 SF4 A1601 " ideal model delta sigma weight residual 73.70 90.53 -16.83 1.50e+00 4.44e-01 1.26e+02 ... (remaining 23916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 9482 17.90 - 35.79: 675 35.79 - 53.69: 180 53.69 - 71.58: 29 71.58 - 89.48: 11 Dihedral angle restraints: 10377 sinusoidal: 3942 harmonic: 6435 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 -151.50 -28.50 0 5.00e+00 4.00e-02 3.25e+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 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+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 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 10374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.044: 2794 4.044 - 8.087: 0 8.087 - 12.131: 0 12.131 - 16.174: 0 16.174 - 20.218: 4 Chirality restraints: 2798 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 9.66 -20.22 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 -9.58 20.14 2.00e-01 2.50e+01 1.01e+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 9.58 -20.13 2.00e-01 2.50e+01 1.01e+04 ... (remaining 2795 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 220 " 0.033 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 221 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 385 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO A 386 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 386 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 386 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 685 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO A 686 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 686 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 686 " 0.024 5.00e-02 4.00e+02 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 727 2.72 - 3.27: 17073 3.27 - 3.81: 27795 3.81 - 4.36: 33502 4.36 - 4.90: 58257 Nonbonded interactions: 137354 Sorted by model distance: nonbonded pdb=" O VAL F 122 " pdb=" OG1 THR F 126 " model vdw 2.181 2.440 nonbonded pdb=" OD1 ASN F 341 " pdb=" OG SER F 356 " model vdw 2.213 2.440 nonbonded pdb=" O ASP A1456 " pdb=" ND2 ASN A1461 " model vdw 2.229 2.520 nonbonded pdb=" N LYS A1316 " pdb=" OH TYR A1346 " model vdw 2.233 2.520 nonbonded pdb=" OD1 ASN G 10 " pdb=" OH TYR G 43 " model vdw 2.252 2.440 ... (remaining 137349 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.010 Extract box with map and model: 4.590 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 54.520 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.179 17504 Z= 0.351 Angle : 0.724 17.836 23921 Z= 0.450 Chirality : 0.762 20.218 2798 Planarity : 0.004 0.051 2900 Dihedral : 13.864 89.476 6189 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 2121 helix: 2.25 (0.19), residues: 771 sheet: 0.01 (0.30), residues: 299 loop : -1.41 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 343 HIS 0.009 0.001 HIS A 732 PHE 0.016 0.001 PHE A 927 TYR 0.011 0.001 TYR A 880 ARG 0.003 0.000 ARG A1309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.000 Fit side-chains REVERT: A 261 VAL cc_start: 0.8942 (m) cc_final: 0.8718 (p) REVERT: F 100 GLN cc_start: 0.8462 (pt0) cc_final: 0.8170 (pt0) REVERT: F 277 MET cc_start: 0.7849 (tpt) cc_final: 0.7511 (tpt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2638 time to fit residues: 59.3839 Evaluate side-chains 123 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN A1186 HIS E 30 GLN E 176 ASN F 221 ASN G 69 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.257 17504 Z= 0.543 Angle : 1.331 51.294 23921 Z= 0.851 Chirality : 0.240 6.490 2798 Planarity : 0.005 0.051 2900 Dihedral : 10.869 78.995 2603 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 0.57 % Allowed : 8.24 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.26 (0.18), residues: 2121 helix: 1.61 (0.18), residues: 768 sheet: -0.21 (0.29), residues: 316 loop : -1.60 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 432 HIS 0.006 0.001 HIS F 394 PHE 0.016 0.002 PHE A 787 TYR 0.015 0.002 TYR D 23 ARG 0.011 0.001 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 2.203 Fit side-chains revert: symmetry clash REVERT: D 77 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7644 (mt) outliers start: 9 outliers final: 7 residues processed: 121 average time/residue: 0.2777 time to fit residues: 54.5391 Evaluate side-chains 115 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 198 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 196 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.240 17504 Z= 0.459 Angle : 1.284 50.339 23921 Z= 0.829 Chirality : 0.244 6.365 2798 Planarity : 0.004 0.046 2900 Dihedral : 10.656 74.443 2603 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.09 % Allowed : 10.28 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.27 (0.18), residues: 2121 helix: 1.60 (0.19), residues: 772 sheet: -0.14 (0.30), residues: 295 loop : -1.63 (0.18), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 343 HIS 0.003 0.001 HIS A 732 PHE 0.012 0.001 PHE A1333 TYR 0.014 0.001 TYR A 880 ARG 0.009 0.000 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 2.057 Fit side-chains REVERT: D 16 TYR cc_start: 0.8482 (t80) cc_final: 0.7940 (t80) REVERT: D 116 GLU cc_start: 0.8290 (mp0) cc_final: 0.7853 (mp0) outliers start: 17 outliers final: 13 residues processed: 131 average time/residue: 0.2665 time to fit residues: 56.6107 Evaluate side-chains 125 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 210 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 17504 Z= 0.446 Angle : 1.277 50.408 23921 Z= 0.827 Chirality : 0.243 6.350 2798 Planarity : 0.004 0.050 2900 Dihedral : 10.568 74.930 2603 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.04 % Allowed : 10.98 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.20 (0.18), residues: 2121 helix: 1.63 (0.19), residues: 769 sheet: -0.12 (0.30), residues: 307 loop : -1.56 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 343 HIS 0.003 0.001 HIS F 394 PHE 0.014 0.001 PHE A1333 TYR 0.014 0.001 TYR A 880 ARG 0.010 0.000 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.947 Fit side-chains REVERT: D 77 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7638 (mt) REVERT: D 116 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7874 (mp0) outliers start: 32 outliers final: 23 residues processed: 136 average time/residue: 0.2648 time to fit residues: 58.4206 Evaluate side-chains 135 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 179 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 189 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.240 17504 Z= 0.498 Angle : 1.300 50.447 23921 Z= 0.837 Chirality : 0.243 6.364 2798 Planarity : 0.004 0.061 2900 Dihedral : 10.728 74.956 2603 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.23 % Allowed : 11.88 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.39 (0.18), residues: 2121 helix: 1.44 (0.19), residues: 773 sheet: -0.20 (0.30), residues: 289 loop : -1.63 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 343 HIS 0.004 0.001 HIS F 394 PHE 0.015 0.001 PHE A1333 TYR 0.017 0.001 TYR A 387 ARG 0.009 0.000 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 2.169 Fit side-chains REVERT: D 77 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7780 (mt) REVERT: D 116 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: E 33 ASP cc_start: 0.7902 (p0) cc_final: 0.7375 (p0) outliers start: 35 outliers final: 26 residues processed: 142 average time/residue: 0.2650 time to fit residues: 60.6034 Evaluate side-chains 136 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1219 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 6.9990 chunk 189 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 210 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 17504 Z= 0.444 Angle : 1.280 50.426 23921 Z= 0.828 Chirality : 0.242 6.348 2798 Planarity : 0.004 0.054 2900 Dihedral : 10.612 76.733 2603 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.11 % Allowed : 13.22 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.26 (0.18), residues: 2121 helix: 1.56 (0.19), residues: 765 sheet: -0.13 (0.30), residues: 299 loop : -1.56 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 343 HIS 0.003 0.001 HIS F 394 PHE 0.016 0.001 PHE A1333 TYR 0.015 0.001 TYR A 880 ARG 0.010 0.000 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 2.052 Fit side-chains REVERT: D 77 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7728 (mt) REVERT: D 116 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: E 33 ASP cc_start: 0.7811 (p0) cc_final: 0.5902 (p0) REVERT: F 112 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7683 (ttm) outliers start: 33 outliers final: 25 residues processed: 139 average time/residue: 0.2594 time to fit residues: 58.3324 Evaluate side-chains 136 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 968 LYS Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 154 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 177 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 210 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 17504 Z= 0.445 Angle : 1.280 50.424 23921 Z= 0.828 Chirality : 0.242 6.346 2798 Planarity : 0.004 0.056 2900 Dihedral : 10.528 76.873 2603 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.43 % Allowed : 12.77 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.26 (0.18), residues: 2121 helix: 1.58 (0.19), residues: 769 sheet: -0.13 (0.30), residues: 299 loop : -1.59 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP A 343 HIS 0.003 0.001 HIS F 394 PHE 0.018 0.001 PHE A1333 TYR 0.022 0.001 TYR D 73 ARG 0.010 0.000 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 112 time to evaluate : 1.971 Fit side-chains REVERT: A 332 PRO cc_start: 0.6418 (Cg_endo) cc_final: 0.6189 (Cg_exo) REVERT: D 16 TYR cc_start: 0.8467 (t80) cc_final: 0.7920 (t80) REVERT: D 77 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7710 (mt) REVERT: D 116 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: F 112 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7621 (ttm) outliers start: 38 outliers final: 28 residues processed: 140 average time/residue: 0.2558 time to fit residues: 59.1055 Evaluate side-chains 137 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 68 LYS Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 63 optimal weight: 0.0030 chunk 41 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 165 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.243 17504 Z= 0.425 Angle : 1.269 50.431 23921 Z= 0.823 Chirality : 0.242 6.329 2798 Planarity : 0.004 0.051 2900 Dihedral : 10.347 77.313 2603 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.92 % Allowed : 13.22 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2121 helix: 1.72 (0.19), residues: 769 sheet: -0.05 (0.29), residues: 318 loop : -1.55 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.001 TRP A 343 HIS 0.002 0.000 HIS G 27 PHE 0.021 0.001 PHE A1333 TYR 0.023 0.001 TYR D 73 ARG 0.010 0.000 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 2.028 Fit side-chains REVERT: A 332 PRO cc_start: 0.6370 (Cg_endo) cc_final: 0.6147 (Cg_exo) REVERT: D 16 TYR cc_start: 0.8357 (t80) cc_final: 0.7824 (t80) REVERT: D 77 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7600 (mt) REVERT: D 112 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: D 116 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: F 112 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7508 (ttm) outliers start: 30 outliers final: 20 residues processed: 139 average time/residue: 0.2549 time to fit residues: 58.1294 Evaluate side-chains 134 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 4 TRP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 112 MET Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 183 optimal weight: 0.0000 chunk 195 optimal weight: 0.0050 chunk 117 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 176 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 17504 Z= 0.451 Angle : 1.284 50.414 23921 Z= 0.829 Chirality : 0.242 6.345 2798 Planarity : 0.004 0.055 2900 Dihedral : 10.385 75.891 2603 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.11 % Allowed : 13.28 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2121 helix: 1.67 (0.19), residues: 770 sheet: -0.29 (0.28), residues: 329 loop : -1.51 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP A 343 HIS 0.004 0.001 HIS F 394 PHE 0.020 0.001 PHE A1333 TYR 0.026 0.001 TYR D 73 ARG 0.010 0.000 ARG A1435 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 108 time to evaluate : 1.943 Fit side-chains REVERT: A 332 PRO cc_start: 0.6416 (Cg_endo) cc_final: 0.6184 (Cg_exo) REVERT: D 16 TYR cc_start: 0.8445 (t80) cc_final: 0.7899 (t80) REVERT: D 38 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8153 (pt0) REVERT: D 77 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.7667 (mt) REVERT: D 112 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: D 116 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: F 147 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7371 (mpp) outliers start: 33 outliers final: 24 residues processed: 133 average time/residue: 0.2567 time to fit residues: 55.2857 Evaluate side-chains 137 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.242 17504 Z= 0.443 Angle : 1.281 50.419 23921 Z= 0.828 Chirality : 0.242 6.342 2798 Planarity : 0.004 0.054 2900 Dihedral : 10.395 76.127 2603 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.79 % Allowed : 13.92 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.16 (0.18), residues: 2121 helix: 1.67 (0.19), residues: 770 sheet: -0.30 (0.28), residues: 329 loop : -1.49 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 343 HIS 0.004 0.001 HIS F 394 PHE 0.021 0.001 PHE A1333 TYR 0.026 0.001 TYR D 73 ARG 0.010 0.000 ARG A1435 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 2.116 Fit side-chains REVERT: A 332 PRO cc_start: 0.6421 (Cg_endo) cc_final: 0.6182 (Cg_exo) REVERT: D 16 TYR cc_start: 0.8459 (t80) cc_final: 0.7902 (t80) REVERT: D 38 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: D 77 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7635 (mt) REVERT: D 112 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: D 116 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: F 147 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7717 (mpp) REVERT: F 403 MET cc_start: 0.8663 (tpp) cc_final: 0.8461 (mmp) outliers start: 28 outliers final: 23 residues processed: 132 average time/residue: 0.2632 time to fit residues: 57.1356 Evaluate side-chains 134 residues out of total 2013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 728 THR Chi-restraints excluded: chain A residue 911 ASP Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1424 THR Chi-restraints excluded: chain A residue 1446 CYS Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain E residue 41 ASN Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain F residue 147 MET Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 415 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 72 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 173 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 177 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 31 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.074892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063952 restraints weight = 51282.371| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.52 r_work: 0.3168 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.238 17504 Z= 0.535 Angle : 1.320 50.462 23921 Z= 0.845 Chirality : 0.244 6.373 2798 Planarity : 0.005 0.060 2900 Dihedral : 10.730 75.688 2603 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.04 % Allowed : 13.79 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: 2121 helix: 1.35 (0.19), residues: 764 sheet: -0.37 (0.29), residues: 306 loop : -1.53 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 343 HIS 0.005 0.001 HIS F 394 PHE 0.018 0.002 PHE A1333 TYR 0.028 0.002 TYR D 73 ARG 0.010 0.001 ARG A1435 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2957.98 seconds wall clock time: 55 minutes 8.64 seconds (3308.64 seconds total)