Starting phenix.real_space_refine on Tue Dec 31 20:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vdt_31925/12_2024/7vdt_31925.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vdt_31925/12_2024/7vdt_31925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vdt_31925/12_2024/7vdt_31925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vdt_31925/12_2024/7vdt_31925.map" model { file = "/net/cci-nas-00/data/ceres_data/7vdt_31925/12_2024/7vdt_31925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vdt_31925/12_2024/7vdt_31925.cif" } resolution = 2.8 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 20 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians P 274 5.49 5 Mg 1 5.21 5 S 39 5.16 5 Be 1 3.05 5 C 9682 2.51 5 N 3077 2.21 5 O 3627 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16704 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 5057 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 20, 'TRANS': 596} Chain breaks: 3 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 717 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2752 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "J" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2827 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 10.38, per 1000 atoms: 0.62 Number of scatterers: 16704 At special positions: 0 Unit cell: (132.065, 116.91, 150.467, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 39 16.00 P 274 15.00 Mg 1 11.99 F 3 9.00 O 3627 8.00 N 3077 7.00 C 9682 6.00 Be 1 4.00 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 - 3.00 Amino acid : True - 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2614 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 63.0% alpha, 4.3% beta 118 base pairs and 250 stacking pairs defined. Time for finding SS restraints: 7.65 Creating SS restraints... Processing helix chain 'A' and resid 542 through 558 removed outlier: 3.718A pdb=" N LYS A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 736 Processing helix chain 'A' and resid 755 through 771 removed outlier: 3.518A pdb=" N LYS A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 799 Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 814 through 826 Processing helix chain 'A' and resid 837 through 844 removed outlier: 3.589A pdb=" N ALA A 843 " --> pdb=" O ALA A 839 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 851 Processing helix chain 'A' and resid 860 through 866 removed outlier: 3.752A pdb=" N ILE A 864 " --> pdb=" O TYR A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.368A pdb=" N ASN A 888 " --> pdb=" O ARG A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 901 Processing helix chain 'A' and resid 918 through 929 removed outlier: 3.915A pdb=" N TRP A 922 " --> pdb=" O LEU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 972 removed outlier: 3.605A pdb=" N LEU A 968 " --> pdb=" O ILE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 1001 through 1014 Processing helix chain 'A' and resid 1037 through 1048 Processing helix chain 'A' and resid 1049 through 1053 removed outlier: 4.079A pdb=" N PHE A1052 " --> pdb=" O PRO A1049 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A1053 " --> pdb=" O TYR A1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1053' Processing helix chain 'A' and resid 1054 through 1063 Processing helix chain 'A' and resid 1072 through 1079 removed outlier: 4.042A pdb=" N TYR A1076 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1095 removed outlier: 3.514A pdb=" N ARG A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Proline residue: A1090 - end of helix removed outlier: 3.537A pdb=" N THR A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1119 removed outlier: 3.707A pdb=" N MET A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A1111 " --> pdb=" O SER A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1144 removed outlier: 4.263A pdb=" N GLY A1136 " --> pdb=" O ALA A1132 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET A1137 " --> pdb=" O GLU A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1160 Processing helix chain 'A' and resid 1179 through 1188 removed outlier: 4.181A pdb=" N ASP A1183 " --> pdb=" O ASN A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1229 removed outlier: 4.121A pdb=" N LYS A1213 " --> pdb=" O SER A1209 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A1223 " --> pdb=" O LYS A1219 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A1224 " --> pdb=" O TYR A1220 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP A1225 " --> pdb=" O LYS A1221 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1253 removed outlier: 3.600A pdb=" N ALA A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A1250 " --> pdb=" O PHE A1246 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A1251 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A1252 " --> pdb=" O GLN A1248 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS A1253 " --> pdb=" O ALA A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1274 removed outlier: 3.830A pdb=" N GLN A1271 " --> pdb=" O GLU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1276 through 1295 removed outlier: 3.653A pdb=" N PHE A1280 " --> pdb=" O HIS A1276 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET A1286 " --> pdb=" O LEU A1282 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP A1287 " --> pdb=" O PHE A1283 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A1288 " --> pdb=" O MET A1284 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A1291 " --> pdb=" O ASP A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1316 removed outlier: 4.057A pdb=" N LYS A1316 " --> pdb=" O SER A1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 22 removed outlier: 3.822A pdb=" N LYS B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 16 through 22' Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.531A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.474A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.511A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.656A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.584A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.017A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.512A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.587A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.500A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.500A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.641A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.518A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 52 removed outlier: 3.884A pdb=" N GLU K 50 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 79 removed outlier: 4.117A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.628A pdb=" N LEU K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA K 114 " --> pdb=" O CYS K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.566A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 776 through 777 removed outlier: 6.559A pdb=" N LEU A 807 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASP A 881 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 809 " --> pdb=" O ASP A 881 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 808 " --> pdb=" O THR A 858 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 832 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N THR A 859 " --> pdb=" O VAL A 832 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 992 through 996 removed outlier: 6.767A pdb=" N VAL A1171 " --> pdb=" O LEU A1202 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU A1204 " --> pdb=" O VAL A1171 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A1173 " --> pdb=" O LEU A1204 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A1099 " --> pdb=" O PHE A1152 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU A1154 " --> pdb=" O VAL A1099 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A1101 " --> pdb=" O LEU A1154 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A1124 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N SER A1155 " --> pdb=" O LEU A1124 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N LEU A1126 " --> pdb=" O SER A1155 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1017 through 1018 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.333A pdb=" N ARG B 45 " --> pdb=" O ILE K 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.033A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.127A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 570 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 284 hydrogen bonds 556 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 250 stacking parallelities Total time for adding SS restraints: 9.54 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3336 1.33 - 1.45: 5072 1.45 - 1.57: 8536 1.57 - 1.69: 546 1.69 - 1.81: 72 Bond restraints: 17562 Sorted by residual: bond pdb=" F2 BEF A1701 " pdb="BE BEF A1701 " ideal model delta sigma weight residual 1.476 1.711 -0.235 2.00e-02 2.50e+03 1.37e+02 bond pdb=" F1 BEF A1701 " pdb="BE BEF A1701 " ideal model delta sigma weight residual 1.476 1.703 -0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" F3 BEF A1701 " pdb="BE BEF A1701 " ideal model delta sigma weight residual 1.476 1.689 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" CG1 ILE A1151 " pdb=" CD1 ILE A1151 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.29e+00 bond pdb=" CG LEU A1100 " pdb=" CD1 LEU A1100 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.82e+00 ... (remaining 17557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 24815 4.25 - 8.51: 60 8.51 - 12.76: 2 12.76 - 17.01: 1 17.01 - 21.27: 1 Bond angle restraints: 24879 Sorted by residual: angle pdb=" F1 BEF A1701 " pdb="BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 120.12 98.85 21.27 3.00e+00 1.11e-01 5.03e+01 angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.47 108.01 5.46 1.01e+00 9.80e-01 2.93e+01 angle pdb=" F2 BEF A1701 " pdb="BE BEF A1701 " pdb=" F3 BEF A1701 " ideal model delta sigma weight residual 119.96 105.59 14.37 3.00e+00 1.11e-01 2.29e+01 angle pdb=" CA LYS A1301 " pdb=" C LYS A1301 " pdb=" N PRO A1302 " ideal model delta sigma weight residual 120.77 116.52 4.25 9.70e-01 1.06e+00 1.92e+01 angle pdb=" CA MET A 749 " pdb=" CB MET A 749 " pdb=" CG MET A 749 " ideal model delta sigma weight residual 114.10 121.41 -7.31 2.00e+00 2.50e-01 1.34e+01 ... (remaining 24874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8648 35.61 - 71.22: 1235 71.22 - 106.83: 10 106.83 - 142.44: 3 142.44 - 178.05: 2 Dihedral angle restraints: 9898 sinusoidal: 5860 harmonic: 4038 Sorted by residual: dihedral pdb=" O2A ADP A1703 " pdb=" O3A ADP A1703 " pdb=" PA ADP A1703 " pdb=" PB ADP A1703 " ideal model delta sinusoidal sigma weight residual 300.00 121.95 178.05 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP A1703 " pdb=" O3A ADP A1703 " pdb=" PB ADP A1703 " pdb=" PA ADP A1703 " ideal model delta sinusoidal sigma weight residual -60.00 65.55 -125.55 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP A1703 " pdb=" O5' ADP A1703 " pdb=" PA ADP A1703 " pdb=" O2A ADP A1703 " ideal model delta sinusoidal sigma weight residual -60.00 -151.03 91.03 1 2.00e+01 2.50e-03 2.44e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1848 0.036 - 0.073: 768 0.073 - 0.109: 147 0.109 - 0.146: 43 0.146 - 0.182: 6 Chirality restraints: 2812 Sorted by residual: chirality pdb=" CA MET A 749 " pdb=" N MET A 749 " pdb=" C MET A 749 " pdb=" CB MET A 749 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CB VAL B 43 " pdb=" CA VAL B 43 " pdb=" CG1 VAL B 43 " pdb=" CG2 VAL B 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" C3' ADP A1703 " pdb=" C2' ADP A1703 " pdb=" C4' ADP A1703 " pdb=" O3' ADP A1703 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2809 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1152 " 0.020 2.00e-02 2.50e+03 2.11e-02 7.81e+00 pdb=" CG PHE A1152 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A1152 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A1152 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A1152 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A1152 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A1152 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 804 " 0.037 5.00e-02 4.00e+02 5.67e-02 5.15e+00 pdb=" N PRO A 805 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 77 " -0.040 9.50e-02 1.11e+02 2.32e-02 2.95e+00 pdb=" NE ARG G 77 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG G 77 " -0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG G 77 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG G 77 " 0.008 2.00e-02 2.50e+03 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 7 2.02 - 2.74: 1840 2.74 - 3.46: 21785 3.46 - 4.18: 45915 4.18 - 4.90: 72934 Nonbonded interactions: 142481 Sorted by model distance: nonbonded pdb=" O LEU A 550 " pdb=" CD2 LEU A 554 " model vdw 1.303 3.460 nonbonded pdb=" O ALA A 551 " pdb=" NE2 GLN A 555 " model vdw 1.368 3.120 nonbonded pdb=" OH TYR A1076 " pdb=" NZ LYS A1301 " model vdw 1.722 3.120 nonbonded pdb=" O ALA A 551 " pdb=" CD GLN A 555 " model vdw 1.743 3.270 nonbonded pdb=" O ALA A 551 " pdb=" OE1 GLN A 555 " model vdw 1.922 3.040 ... (remaining 142476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 117 or (resid 118 and (name N or \ name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 40 through 134) } 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 46.830 Find NCS groups from input model: 0.390 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.007 0.235 17562 Z= 0.409 Angle : 0.704 21.266 24879 Z= 0.399 Chirality : 0.041 0.182 2812 Planarity : 0.004 0.057 2210 Dihedral : 23.616 178.049 7284 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.34 % Allowed : 0.42 % Favored : 99.24 % 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: -0.92 (0.21), residues: 1360 helix: -0.00 (0.18), residues: 778 sheet: -0.31 (0.73), residues: 63 loop : -1.49 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1313 HIS 0.005 0.001 HIS F 75 PHE 0.048 0.002 PHE A1152 TYR 0.025 0.002 TYR C 57 ARG 0.029 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1051 MET cc_start: 0.9168 (mtp) cc_final: 0.8799 (mtp) REVERT: A 1308 ASP cc_start: 0.7876 (m-30) cc_final: 0.7641 (p0) REVERT: B 79 LYS cc_start: 0.9022 (mmtt) cc_final: 0.8807 (mtpt) REVERT: K 80 THR cc_start: 0.9116 (p) cc_final: 0.8541 (p) REVERT: K 115 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8509 (mttp) outliers start: 4 outliers final: 2 residues processed: 218 average time/residue: 2.0181 time to fit residues: 473.8975 Evaluate side-chains 180 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 555 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 84 ASN H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.004 0.039 17562 Z= 0.228 Angle : 0.653 9.887 24879 Z= 0.367 Chirality : 0.040 0.218 2812 Planarity : 0.005 0.050 2210 Dihedral : 27.998 179.123 4516 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.61 % Allowed : 9.43 % Favored : 88.95 % 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: 0.32 (0.23), residues: 1360 helix: 1.26 (0.18), residues: 815 sheet: -0.23 (0.72), residues: 63 loop : -1.56 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 922 HIS 0.008 0.001 HIS A 969 PHE 0.025 0.002 PHE A1152 TYR 0.052 0.002 TYR A 552 ARG 0.011 0.001 ARG A1296 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 555 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.6780 (pt0) REVERT: A 874 ARG cc_start: 0.6758 (ptt180) cc_final: 0.6347 (ptt90) REVERT: A 905 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7528 (mtp85) REVERT: A 1051 MET cc_start: 0.9135 (mtp) cc_final: 0.8775 (mtp) REVERT: A 1284 MET cc_start: 0.7402 (mmm) cc_final: 0.7199 (mmm) REVERT: A 1308 ASP cc_start: 0.7696 (m-30) cc_final: 0.7382 (p0) REVERT: B 84 MET cc_start: 0.8513 (mmm) cc_final: 0.8180 (mmm) REVERT: F 93 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: K 115 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8522 (mttp) outliers start: 19 outliers final: 2 residues processed: 200 average time/residue: 1.9373 time to fit residues: 418.1975 Evaluate side-chains 179 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 GLN Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 GLN A 555 GLN ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS G 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17562 Z= 0.305 Angle : 0.644 9.881 24879 Z= 0.362 Chirality : 0.041 0.156 2812 Planarity : 0.004 0.050 2210 Dihedral : 28.055 179.868 4514 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.29 % Allowed : 12.57 % Favored : 85.13 % 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: 0.59 (0.23), residues: 1360 helix: 1.54 (0.18), residues: 816 sheet: -0.31 (0.71), residues: 62 loop : -1.57 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 922 HIS 0.005 0.001 HIS F 75 PHE 0.028 0.002 PHE A1152 TYR 0.042 0.002 TYR A 552 ARG 0.008 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 874 ARG cc_start: 0.6721 (ptt180) cc_final: 0.6418 (ptt90) REVERT: A 975 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8441 (p90) REVERT: A 1051 MET cc_start: 0.9077 (mtp) cc_final: 0.8866 (mtp) REVERT: A 1284 MET cc_start: 0.7515 (mmm) cc_final: 0.7310 (mmm) REVERT: F 93 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8313 (mp10) REVERT: H 57 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8229 (mmmm) REVERT: K 115 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8563 (mttp) outliers start: 27 outliers final: 12 residues processed: 196 average time/residue: 1.8583 time to fit residues: 393.9278 Evaluate side-chains 184 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17562 Z= 0.251 Angle : 0.611 10.712 24879 Z= 0.344 Chirality : 0.039 0.146 2812 Planarity : 0.004 0.053 2210 Dihedral : 28.004 179.517 4511 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.46 % Allowed : 14.44 % Favored : 83.09 % 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: 0.76 (0.23), residues: 1360 helix: 1.71 (0.18), residues: 817 sheet: -0.33 (0.70), residues: 62 loop : -1.56 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 764 HIS 0.023 0.001 HIS A1241 PHE 0.020 0.002 PHE A1152 TYR 0.045 0.002 TYR A 552 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 874 ARG cc_start: 0.6749 (ptt180) cc_final: 0.6372 (ptt90) REVERT: A 884 HIS cc_start: 0.8153 (OUTLIER) cc_final: 0.7747 (m90) REVERT: A 1051 MET cc_start: 0.9062 (mtp) cc_final: 0.8827 (mtp) REVERT: A 1100 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8804 (pp) REVERT: A 1280 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6325 (m-80) REVERT: B 22 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6518 (mm) REVERT: H 57 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8202 (mmmm) REVERT: K 115 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8552 (mttp) outliers start: 29 outliers final: 11 residues processed: 197 average time/residue: 1.8490 time to fit residues: 395.2652 Evaluate side-chains 189 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1280 PHE Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 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 555 GLN ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17562 Z= 0.257 Angle : 0.614 11.190 24879 Z= 0.344 Chirality : 0.038 0.149 2812 Planarity : 0.004 0.057 2210 Dihedral : 28.018 179.687 4511 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.23 % Allowed : 14.10 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.23), residues: 1360 helix: 1.81 (0.18), residues: 815 sheet: -0.38 (0.70), residues: 62 loop : -1.58 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 942 HIS 0.008 0.001 HIS A 884 PHE 0.026 0.002 PHE A1065 TYR 0.047 0.002 TYR A 552 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 1.518 Fit side-chains revert: symmetry clash REVERT: A 874 ARG cc_start: 0.6740 (ptt180) cc_final: 0.6339 (ptt90) REVERT: A 884 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.7745 (m-70) REVERT: A 886 MET cc_start: 0.9034 (mmm) cc_final: 0.8774 (mmm) REVERT: A 949 MET cc_start: 0.0060 (pmm) cc_final: -0.0324 (pmm) REVERT: A 1051 MET cc_start: 0.9058 (mtp) cc_final: 0.8855 (mtp) REVERT: A 1100 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8795 (pp) REVERT: A 1280 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6652 (m-80) REVERT: B 22 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6506 (mm) REVERT: F 93 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8308 (mp10) REVERT: H 57 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8208 (mmmm) REVERT: K 115 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8560 (mttp) outliers start: 38 outliers final: 17 residues processed: 202 average time/residue: 1.8295 time to fit residues: 400.3824 Evaluate side-chains 197 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 905 ARG Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1280 PHE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.0270 chunk 153 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 0.0050 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS G 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17562 Z= 0.196 Angle : 0.597 10.712 24879 Z= 0.333 Chirality : 0.037 0.156 2812 Planarity : 0.004 0.060 2210 Dihedral : 27.935 179.699 4511 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.12 % Allowed : 15.89 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1360 helix: 1.96 (0.18), residues: 817 sheet: -0.30 (0.71), residues: 57 loop : -1.49 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 942 HIS 0.019 0.001 HIS A1241 PHE 0.018 0.002 PHE A1116 TYR 0.050 0.002 TYR A 552 ARG 0.006 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 874 ARG cc_start: 0.6717 (ptt180) cc_final: 0.6336 (ptt90) REVERT: A 884 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7766 (m90) REVERT: A 886 MET cc_start: 0.9009 (mmm) cc_final: 0.8771 (mmm) REVERT: A 949 MET cc_start: 0.0035 (pmm) cc_final: -0.0354 (pmm) REVERT: A 1051 MET cc_start: 0.9049 (mtp) cc_final: 0.8837 (mtp) REVERT: A 1100 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8762 (pp) REVERT: A 1280 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6763 (m-80) REVERT: B 22 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6472 (mm) REVERT: F 93 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8321 (mp-120) REVERT: H 57 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8138 (mmmm) REVERT: K 115 LYS cc_start: 0.8793 (mmtm) cc_final: 0.8561 (mttp) outliers start: 25 outliers final: 11 residues processed: 201 average time/residue: 1.8911 time to fit residues: 411.5367 Evaluate side-chains 196 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1280 PHE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 63 ASN G 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17562 Z= 0.231 Angle : 0.610 13.133 24879 Z= 0.339 Chirality : 0.038 0.178 2812 Planarity : 0.004 0.063 2210 Dihedral : 27.947 179.284 4511 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.29 % Allowed : 16.31 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1360 helix: 1.98 (0.18), residues: 817 sheet: -0.33 (0.70), residues: 62 loop : -1.50 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 922 HIS 0.010 0.001 HIS A 884 PHE 0.016 0.002 PHE A1152 TYR 0.054 0.002 TYR A 552 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 874 ARG cc_start: 0.6711 (ptt180) cc_final: 0.6333 (ptt90) REVERT: A 886 MET cc_start: 0.8938 (mmm) cc_final: 0.8729 (mmm) REVERT: A 949 MET cc_start: -0.0007 (pmm) cc_final: -0.0383 (pmm) REVERT: A 1051 MET cc_start: 0.9052 (mtp) cc_final: 0.8849 (mtp) REVERT: A 1100 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8777 (pp) REVERT: A 1280 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6861 (m-80) REVERT: B 22 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6457 (mm) REVERT: H 57 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8158 (mmmm) REVERT: K 115 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8570 (mttp) outliers start: 27 outliers final: 14 residues processed: 196 average time/residue: 1.8663 time to fit residues: 396.5601 Evaluate side-chains 189 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1280 PHE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17562 Z= 0.236 Angle : 0.607 11.133 24879 Z= 0.338 Chirality : 0.038 0.169 2812 Planarity : 0.004 0.063 2210 Dihedral : 27.964 179.274 4511 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.72 % Allowed : 16.23 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1360 helix: 1.94 (0.18), residues: 823 sheet: -0.23 (0.71), residues: 62 loop : -1.48 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 922 HIS 0.004 0.001 HIS A 969 PHE 0.016 0.002 PHE A1152 TYR 0.055 0.002 TYR A 552 ARG 0.007 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 2.018 Fit side-chains REVERT: A 874 ARG cc_start: 0.6712 (ptt180) cc_final: 0.6379 (ptt90) REVERT: A 884 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7857 (m90) REVERT: A 886 MET cc_start: 0.8992 (mmm) cc_final: 0.8711 (mmm) REVERT: A 1100 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8768 (pp) REVERT: A 1280 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: B 22 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6445 (mm) REVERT: H 57 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8174 (mmmm) REVERT: K 115 LYS cc_start: 0.8796 (mmtm) cc_final: 0.8575 (mttp) outliers start: 32 outliers final: 20 residues processed: 200 average time/residue: 1.7861 time to fit residues: 388.3873 Evaluate side-chains 196 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1280 PHE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 151 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 93 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17562 Z= 0.219 Angle : 0.618 14.741 24879 Z= 0.339 Chirality : 0.037 0.166 2812 Planarity : 0.004 0.066 2210 Dihedral : 27.933 179.088 4511 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.55 % Allowed : 16.65 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1360 helix: 1.98 (0.18), residues: 823 sheet: -0.21 (0.71), residues: 62 loop : -1.46 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 942 HIS 0.006 0.001 HIS A 884 PHE 0.014 0.002 PHE A1152 TYR 0.057 0.002 TYR A 552 ARG 0.007 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 1.368 Fit side-chains REVERT: A 874 ARG cc_start: 0.6702 (ptt180) cc_final: 0.6374 (ptt90) REVERT: A 884 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7614 (m-70) REVERT: A 886 MET cc_start: 0.8983 (mmm) cc_final: 0.8750 (mmm) REVERT: A 949 MET cc_start: -0.0237 (pmm) cc_final: -0.0870 (pmm) REVERT: A 1280 PHE cc_start: 0.7149 (OUTLIER) cc_final: 0.6811 (m-80) REVERT: B 22 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6449 (mm) REVERT: H 57 LYS cc_start: 0.8431 (mmmt) cc_final: 0.8165 (mmmm) REVERT: K 115 LYS cc_start: 0.8808 (mmtm) cc_final: 0.8585 (mttp) outliers start: 30 outliers final: 22 residues processed: 197 average time/residue: 2.0481 time to fit residues: 437.1049 Evaluate side-chains 196 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1280 PHE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 76 GLN Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 GLN ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17562 Z= 0.217 Angle : 0.619 15.876 24879 Z= 0.340 Chirality : 0.037 0.171 2812 Planarity : 0.004 0.068 2210 Dihedral : 27.901 178.861 4511 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.38 % Allowed : 16.65 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1360 helix: 2.00 (0.18), residues: 821 sheet: -0.26 (0.71), residues: 62 loop : -1.46 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 942 HIS 0.004 0.001 HIS A 969 PHE 0.013 0.001 PHE A1150 TYR 0.057 0.002 TYR A 552 ARG 0.007 0.000 ARG E 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2720 Ramachandran restraints generated. 1360 Oldfield, 0 Emsley, 1360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 1.407 Fit side-chains revert: symmetry clash REVERT: A 874 ARG cc_start: 0.6720 (ptt180) cc_final: 0.6397 (ptt90) REVERT: A 884 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7597 (m90) REVERT: A 886 MET cc_start: 0.8945 (mmm) cc_final: 0.8743 (mmm) REVERT: A 949 MET cc_start: -0.0262 (pmm) cc_final: -0.0887 (pmm) REVERT: B 22 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6454 (mm) REVERT: H 57 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8145 (mmmm) REVERT: K 115 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8591 (mttp) outliers start: 28 outliers final: 20 residues processed: 194 average time/residue: 1.8554 time to fit residues: 390.7496 Evaluate side-chains 193 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 884 HIS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 975 PHE Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1170 THR Chi-restraints excluded: chain A residue 1263 VAL Chi-restraints excluded: chain A residue 1268 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 76 GLN Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 105 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 104 GLN G 110 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.110769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.077616 restraints weight = 32170.882| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.88 r_work: 0.2967 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17562 Z= 0.251 Angle : 0.637 16.002 24879 Z= 0.348 Chirality : 0.038 0.173 2812 Planarity : 0.004 0.067 2210 Dihedral : 27.945 179.029 4511 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.29 % Allowed : 17.08 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.23), residues: 1360 helix: 1.94 (0.18), residues: 823 sheet: -0.21 (0.71), residues: 62 loop : -1.44 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 942 HIS 0.005 0.001 HIS A 884 PHE 0.015 0.002 PHE A1152 TYR 0.058 0.002 TYR A 552 ARG 0.007 0.000 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6504.92 seconds wall clock time: 117 minutes 43.77 seconds (7063.77 seconds total)