Starting phenix.real_space_refine on Sun Sep 13 01:26:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6yuf_10930/09_2026/6yuf_10930.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yuf_10930/09_2026/6yuf_10930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6yuf_10930/09_2026/6yuf_10930.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6yuf_10930/09_2026/6yuf_10930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6yuf_10930/09_2026/6yuf_10930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yuf_10930/09_2026/6yuf_10930.map" model { file = "/net/cci-nas-00/data/ceres_data/6yuf_10930/09_2026/6yuf_10930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yuf_10930/09_2026/6yuf_10930.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.065 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 P 68 5.49 5 S 72 5.16 5 Be 2 3.05 5 C 12233 2.51 5 N 3307 2.21 5 O 3840 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19528 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1195 Classifications: {'peptide': 152} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Chain: "D" Number of atoms: 10247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1272, 10247 Classifications: {'peptide': 1272} Link IDs: {'PTRANS': 36, 'TRANS': 1235} Chain breaks: 4 Chain: "A" Number of atoms: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3047 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 13, 'TRANS': 370} Chain breaks: 2 Chain: "C" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3665 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 10, 'TRANS': 445} Chain breaks: 2 Chain: "X" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "Y" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 654 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.96, per 1000 atoms: 0.20 Number of scatterers: 19528 At special positions: 0 Unit cell: (129.71, 130.8, 179.85, 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) S 72 16.00 P 68 15.00 F 6 9.00 O 3840 8.00 N 3307 7.00 C 12233 6.00 Be 2 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 844.0 milliseconds 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4380 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 9 sheets defined 63.3% alpha, 4.7% beta 31 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.816A pdb=" N LYS B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.747A pdb=" N HIS B 34 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 54 through 88 removed outlier: 4.000A pdb=" N MET B 88 " --> pdb=" O MET B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 584 through 600 Processing helix chain 'D' and resid 215 through 240 Processing helix chain 'D' and resid 260 through 278 removed outlier: 3.779A pdb=" N ARG D 276 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.651A pdb=" N LEU D 283 " --> pdb=" O CYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 301 Processing helix chain 'D' and resid 321 through 338 removed outlier: 3.582A pdb=" N PHE D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 365 removed outlier: 3.801A pdb=" N TYR D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 376 removed outlier: 3.973A pdb=" N ALA D 370 " --> pdb=" O THR D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 385 removed outlier: 3.500A pdb=" N SER D 385 " --> pdb=" O ALA D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 411 removed outlier: 3.796A pdb=" N LEU D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 439 Proline residue: D 426 - end of helix Processing helix chain 'D' and resid 444 through 465 Proline residue: D 453 - end of helix removed outlier: 4.503A pdb=" N GLN D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 457 " --> pdb=" O PRO D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 477 removed outlier: 3.776A pdb=" N ILE D 472 " --> pdb=" O GLN D 468 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE D 473 " --> pdb=" O ARG D 469 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 477 " --> pdb=" O ILE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 486 through 491 Processing helix chain 'D' and resid 502 through 504 No H-bonds generated for 'chain 'D' and resid 502 through 504' Processing helix chain 'D' and resid 505 through 515 removed outlier: 4.055A pdb=" N VAL D 509 " --> pdb=" O SER D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 547 through 576 removed outlier: 3.596A pdb=" N ILE D 551 " --> pdb=" O THR D 547 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU D 558 " --> pdb=" O LYS D 554 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR D 560 " --> pdb=" O ARG D 556 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG D 561 " --> pdb=" O HIS D 557 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS D 565 " --> pdb=" O ARG D 561 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE D 566 " --> pdb=" O ILE D 562 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA D 568 " --> pdb=" O ASN D 564 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR D 569 " --> pdb=" O HIS D 565 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS D 576 " --> pdb=" O SER D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 600 removed outlier: 3.838A pdb=" N THR D 590 " --> pdb=" O PHE D 586 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 591 " --> pdb=" O ALA D 587 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU D 595 " --> pdb=" O LYS D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 626 removed outlier: 4.043A pdb=" N GLN D 615 " --> pdb=" O THR D 611 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE D 616 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET D 622 " --> pdb=" O MET D 618 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 625 " --> pdb=" O VAL D 621 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN D 626 " --> pdb=" O MET D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 649 removed outlier: 3.539A pdb=" N LYS D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 644 " --> pdb=" O LEU D 640 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS D 647 " --> pdb=" O LEU D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 685 removed outlier: 3.866A pdb=" N ASN D 682 " --> pdb=" O ILE D 678 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU D 683 " --> pdb=" O THR D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 695 removed outlier: 3.859A pdb=" N LEU D 695 " --> pdb=" O HIS D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 712 Processing helix chain 'D' and resid 713 through 723 removed outlier: 3.610A pdb=" N VAL D 723 " --> pdb=" O GLN D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 741 Processing helix chain 'D' and resid 742 through 745 Processing helix chain 'D' and resid 760 through 767 removed outlier: 3.788A pdb=" N PHE D 764 " --> pdb=" O ASP D 760 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 767 " --> pdb=" O ILE D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 771 through 776 Processing helix chain 'D' and resid 776 through 786 removed outlier: 4.904A pdb=" N LEU D 783 " --> pdb=" O PHE D 779 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE D 784 " --> pdb=" O PHE D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 804 removed outlier: 3.695A pdb=" N LEU D 800 " --> pdb=" O ARG D 796 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 813 removed outlier: 3.606A pdb=" N ILE D 812 " --> pdb=" O ILE D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.570A pdb=" N LYS D 826 " --> pdb=" O GLN D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 827 through 829 No H-bonds generated for 'chain 'D' and resid 827 through 829' Processing helix chain 'D' and resid 831 through 849 removed outlier: 3.907A pdb=" N ASP D 836 " --> pdb=" O ALA D 832 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR D 837 " --> pdb=" O ILE D 833 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 846 " --> pdb=" O LEU D 842 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 848 " --> pdb=" O THR D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 852 through 862 removed outlier: 4.063A pdb=" N GLY D 858 " --> pdb=" O PRO D 854 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N CYS D 859 " --> pdb=" O GLN D 855 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE D 860 " --> pdb=" O ILE D 856 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 861 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER D 862 " --> pdb=" O GLY D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 886 removed outlier: 3.852A pdb=" N ARG D 872 " --> pdb=" O SER D 868 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS D 877 " --> pdb=" O LYS D 873 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 881 " --> pdb=" O LYS D 877 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 884 " --> pdb=" O CYS D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 901 removed outlier: 4.169A pdb=" N ASP D 894 " --> pdb=" O ASN D 890 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 898 " --> pdb=" O ASP D 894 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 923 removed outlier: 4.828A pdb=" N LEU D 915 " --> pdb=" O SER D 911 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU D 916 " --> pdb=" O GLU D 912 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 918 " --> pdb=" O SER D 914 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE D 923 " --> pdb=" O GLU D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 951 removed outlier: 3.671A pdb=" N GLN D 950 " --> pdb=" O LYS D 946 " (cutoff:3.500A) Processing helix chain 'D' and resid 951 through 956 removed outlier: 4.016A pdb=" N LEU D 955 " --> pdb=" O TYR D 951 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS D 956 " --> pdb=" O PHE D 952 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 951 through 956' Processing helix chain 'D' and resid 964 through 978 removed outlier: 4.419A pdb=" N VAL D 970 " --> pdb=" O HIS D 966 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 972 " --> pdb=" O LEU D 968 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS D 974 " --> pdb=" O VAL D 970 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 978 " --> pdb=" O LYS D 974 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1005 removed outlier: 3.635A pdb=" N GLN D 991 " --> pdb=" O THR D 987 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D1000 " --> pdb=" O LEU D 996 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1033 removed outlier: 4.163A pdb=" N TYR D1021 " --> pdb=" O LYS D1017 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D1026 " --> pdb=" O GLU D1022 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D1029 " --> pdb=" O SER D1025 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1045 Processing helix chain 'D' and resid 1045 through 1050 removed outlier: 4.157A pdb=" N TYR D1049 " --> pdb=" O LEU D1045 " (cutoff:3.500A) Processing helix chain 'D' and resid 1056 through 1061 removed outlier: 3.935A pdb=" N PHE D1061 " --> pdb=" O GLU D1058 " (cutoff:3.500A) Processing helix chain 'D' and resid 1062 through 1073 removed outlier: 4.395A pdb=" N ALA D1067 " --> pdb=" O TYR D1063 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE D1068 " --> pdb=" O TYR D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1083 through 1093 removed outlier: 3.849A pdb=" N GLU D1088 " --> pdb=" O LEU D1084 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER D1089 " --> pdb=" O ARG D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1099 through 1118 removed outlier: 3.759A pdb=" N LEU D1103 " --> pdb=" O GLY D1099 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET D1104 " --> pdb=" O THR D1100 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLU D1105 " --> pdb=" O ALA D1101 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D1106 " --> pdb=" O THR D1102 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL D1107 " --> pdb=" O LEU D1103 " (cutoff:3.500A) Proline residue: D1108 - end of helix removed outlier: 4.560A pdb=" N SER D1112 " --> pdb=" O PRO D1108 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR D1115 " --> pdb=" O CYS D1111 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG D1116 " --> pdb=" O SER D1112 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1139 removed outlier: 4.833A pdb=" N VAL D1127 " --> pdb=" O LEU D1123 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D1138 " --> pdb=" O LEU D1134 " (cutoff:3.500A) Processing helix chain 'D' and resid 1147 through 1152 Processing helix chain 'D' and resid 1152 through 1161 removed outlier: 3.894A pdb=" N TYR D1160 " --> pdb=" O LEU D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1167 through 1172 Processing helix chain 'D' and resid 1183 through 1194 removed outlier: 3.846A pdb=" N ILE D1187 " --> pdb=" O ASP D1183 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D1194 " --> pdb=" O GLY D1190 " (cutoff:3.500A) Processing helix chain 'D' and resid 1201 through 1218 removed outlier: 3.568A pdb=" N ILE D1205 " --> pdb=" O GLY D1201 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN D1210 " --> pdb=" O HIS D1206 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS D1215 " --> pdb=" O MET D1211 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG D1217 " --> pdb=" O ARG D1213 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU D1218 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1223 removed outlier: 3.840A pdb=" N ILE D1223 " --> pdb=" O SER D1220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1223' Processing helix chain 'D' and resid 1224 through 1238 removed outlier: 3.593A pdb=" N THR D1230 " --> pdb=" O LEU D1226 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D1236 " --> pdb=" O ASP D1232 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU D1237 " --> pdb=" O MET D1233 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN D1238 " --> pdb=" O ILE D1234 " (cutoff:3.500A) Processing helix chain 'D' and resid 1239 through 1259 removed outlier: 3.621A pdb=" N VAL D1245 " --> pdb=" O ASN D1241 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER D1249 " --> pdb=" O VAL D1245 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D1256 " --> pdb=" O GLU D1252 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP D1257 " --> pdb=" O LEU D1253 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU D1258 " --> pdb=" O LEU D1254 " (cutoff:3.500A) Processing helix chain 'D' and resid 1262 through 1269 Processing helix chain 'D' and resid 1295 through 1298 Processing helix chain 'D' and resid 1299 through 1304 Processing helix chain 'D' and resid 1307 through 1315 removed outlier: 3.747A pdb=" N ILE D1311 " --> pdb=" O PHE D1307 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D1312 " --> pdb=" O LEU D1308 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP D1313 " --> pdb=" O PRO D1309 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N CYS D1315 " --> pdb=" O ILE D1311 " (cutoff:3.500A) Processing helix chain 'D' and resid 1319 through 1337 removed outlier: 4.403A pdb=" N ILE D1329 " --> pdb=" O LEU D1325 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D1334 " --> pdb=" O LEU D1330 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS D1335 " --> pdb=" O LYS D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1340 through 1345 removed outlier: 3.847A pdb=" N CYS D1344 " --> pdb=" O ASN D1340 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1352 removed outlier: 5.029A pdb=" N ILE D1349 " --> pdb=" O SER D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1356 through 1358 No H-bonds generated for 'chain 'D' and resid 1356 through 1358' Processing helix chain 'D' and resid 1359 through 1374 removed outlier: 4.029A pdb=" N ILE D1364 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS D1371 " --> pdb=" O HIS D1367 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG D1372 " --> pdb=" O THR D1368 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG D1373 " --> pdb=" O GLU D1369 " (cutoff:3.500A) Processing helix chain 'D' and resid 1381 through 1393 removed outlier: 4.174A pdb=" N ASP D1387 " --> pdb=" O ALA D1383 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D1388 " --> pdb=" O GLN D1384 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D1389 " --> pdb=" O SER D1385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE D1390 " --> pdb=" O ALA D1386 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D1393 " --> pdb=" O ILE D1389 " (cutoff:3.500A) Processing helix chain 'D' and resid 1411 through 1417 Processing helix chain 'D' and resid 1423 through 1433 removed outlier: 3.970A pdb=" N ILE D1429 " --> pdb=" O ARG D1425 " (cutoff:3.500A) Processing helix chain 'D' and resid 1447 through 1463 removed outlier: 3.588A pdb=" N VAL D1454 " --> pdb=" O LYS D1450 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D1459 " --> pdb=" O SER D1455 " (cutoff:3.500A) Processing helix chain 'D' and resid 1470 through 1486 removed outlier: 3.804A pdb=" N MET D1474 " --> pdb=" O GLU D1470 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE D1475 " --> pdb=" O GLU D1471 " (cutoff:3.500A) Processing helix chain 'D' and resid 1486 through 1491 removed outlier: 3.750A pdb=" N ILE D1490 " --> pdb=" O ILE D1486 " (cutoff:3.500A) Processing helix chain 'D' and resid 1503 through 1525 removed outlier: 3.510A pdb=" N ILE D1508 " --> pdb=" O ILE D1504 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN D1509 " --> pdb=" O LEU D1505 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D1513 " --> pdb=" O ASN D1509 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D1514 " --> pdb=" O LEU D1510 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D1515 " --> pdb=" O CYS D1511 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE D1524 " --> pdb=" O ILE D1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.592A pdb=" N TYR A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.887A pdb=" N ALA A 154 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.772A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 205 removed outlier: 3.574A pdb=" N GLU A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1078 Processing helix chain 'A' and resid 1080 through 1090 removed outlier: 3.925A pdb=" N ILE A1084 " --> pdb=" O GLN A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1152 removed outlier: 3.719A pdb=" N TYR A1151 " --> pdb=" O ALA A1147 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A1152 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1182 removed outlier: 3.662A pdb=" N VAL A1171 " --> pdb=" O ASP A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 3.527A pdb=" N PHE A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 59 through 64 Processing helix chain 'C' and resid 117 through 128 removed outlier: 3.830A pdb=" N VAL C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.502A pdb=" N ARG C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 238 removed outlier: 3.826A pdb=" N ASN C 218 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 967 Processing helix chain 'C' and resid 973 through 1036 Processing helix chain 'C' and resid 1098 through 1117 removed outlier: 3.851A pdb=" N LYS C1102 " --> pdb=" O SER C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1150 Processing helix chain 'C' and resid 1158 through 1163 removed outlier: 3.873A pdb=" N VAL C1162 " --> pdb=" O ARG C1158 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LYS C1163 " --> pdb=" O PRO C1159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1158 through 1163' Processing helix chain 'C' and resid 1186 through 1191 Processing sheet with id=AA1, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AA2, first strand: chain 'D' and resid 248 through 250 Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 21 removed outlier: 7.061A pdb=" N GLY A 17 " --> pdb=" O ASN A 11 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 11 " --> pdb=" O GLY A 17 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU A 4 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A 94 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 6 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET A 92 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU A 10 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 88 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A 114 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1157 through 1159 removed outlier: 6.540A pdb=" N THR A 28 " --> pdb=" O VAL A1190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1099 through 1103 Processing sheet with id=AA6, first strand: chain 'C' and resid 18 through 19 removed outlier: 3.551A pdb=" N VAL C 78 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG C 99 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 30 removed outlier: 6.329A pdb=" N ASN C 28 " --> pdb=" O CYS C1154 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 139 " --> pdb=" O ILE C1123 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP C1125 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1040 through 1044 removed outlier: 3.646A pdb=" N GLU C1042 " --> pdb=" O ARG C1081 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1170 through 1174 removed outlier: 3.799A pdb=" N GLY C1170 " --> pdb=" O GLU C1181 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 4.90 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.02: 2 1.02 - 1.24: 2078 1.24 - 1.46: 7918 1.46 - 1.68: 9876 1.68 - 1.89: 113 Bond restraints: 19987 Sorted by residual: bond pdb=" CD GLN C 9 " pdb=" NE2 GLN C 9 " ideal model delta sigma weight residual 1.328 0.800 0.528 2.10e-02 2.27e+03 6.33e+02 bond pdb=" CB GLN C 9 " pdb=" CG GLN C 9 " ideal model delta sigma weight residual 1.520 1.093 0.427 3.00e-02 1.11e+03 2.03e+02 bond pdb=" O5' ADP C1202 " pdb=" PA ADP C1202 " ideal model delta sigma weight residual 1.610 1.895 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" O5' ADP A1302 " pdb=" PA ADP A1302 " ideal model delta sigma weight residual 1.610 1.894 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" CG1 ILE D1520 " pdb=" CD1 ILE D1520 " ideal model delta sigma weight residual 1.513 0.998 0.515 3.90e-02 6.57e+02 1.74e+02 ... (remaining 19982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.80: 26984 6.80 - 13.60: 218 13.60 - 20.40: 28 20.40 - 27.21: 12 27.21 - 34.01: 4 Bond angle restraints: 27246 Sorted by residual: angle pdb=" CG GLN C 9 " pdb=" CD GLN C 9 " pdb=" NE2 GLN C 9 " ideal model delta sigma weight residual 116.40 93.95 22.45 1.50e+00 4.44e-01 2.24e+02 angle pdb=" NE ARG C 220 " pdb=" CZ ARG C 220 " pdb=" NH2 ARG C 220 " ideal model delta sigma weight residual 119.20 105.85 13.35 9.00e-01 1.23e+00 2.20e+02 angle pdb=" CG MET D1211 " pdb=" SD MET D1211 " pdb=" CE MET D1211 " ideal model delta sigma weight residual 100.90 68.85 32.05 2.20e+00 2.07e-01 2.12e+02 angle pdb=" NE ARG C 220 " pdb=" CZ ARG C 220 " pdb=" NH1 ARG C 220 " ideal model delta sigma weight residual 121.50 134.07 -12.57 1.00e+00 1.00e+00 1.58e+02 angle pdb=" CG GLN C 9 " pdb=" CD GLN C 9 " pdb=" OE1 GLN C 9 " ideal model delta sigma weight residual 120.80 142.74 -21.94 2.00e+00 2.50e-01 1.20e+02 ... (remaining 27241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 11497 33.75 - 67.50: 546 67.50 - 101.26: 35 101.26 - 135.01: 1 135.01 - 168.76: 4 Dihedral angle restraints: 12083 sinusoidal: 5379 harmonic: 6704 Sorted by residual: dihedral pdb=" CA SER D1178 " pdb=" C SER D1178 " pdb=" N PRO D1179 " pdb=" CA PRO D1179 " ideal model delta harmonic sigma weight residual -180.00 -142.80 -37.20 0 5.00e+00 4.00e-02 5.54e+01 dihedral pdb=" CA LYS D 722 " pdb=" C LYS D 722 " pdb=" N VAL D 723 " pdb=" CA VAL D 723 " ideal model delta harmonic sigma weight residual -180.00 -145.18 -34.82 0 5.00e+00 4.00e-02 4.85e+01 dihedral pdb=" O1B ADP C1202 " pdb=" O3A ADP C1202 " pdb=" PB ADP C1202 " pdb=" PA ADP C1202 " ideal model delta sinusoidal sigma weight residual 300.00 132.53 167.47 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 12080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 3114 0.238 - 0.476: 40 0.476 - 0.713: 2 0.713 - 0.951: 2 0.951 - 1.189: 1 Chirality restraints: 3159 Sorted by residual: chirality pdb=" CG LEU D1189 " pdb=" CB LEU D1189 " pdb=" CD1 LEU D1189 " pdb=" CD2 LEU D1189 " both_signs ideal model delta sigma weight residual False -2.59 -1.40 -1.19 2.00e-01 2.50e+01 3.53e+01 chirality pdb=" CG LEU C 964 " pdb=" CB LEU C 964 " pdb=" CD1 LEU C 964 " pdb=" CD2 LEU C 964 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CG LEU D 999 " pdb=" CB LEU D 999 " pdb=" CD1 LEU D 999 " pdb=" CD2 LEU D 999 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 ... (remaining 3156 not shown) Planarity restraints: 3214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 922 " -0.009 2.00e-02 2.50e+03 6.10e-02 9.30e+01 pdb=" CG TRP D 922 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 922 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP D 922 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP D 922 " 0.102 2.00e-02 2.50e+03 pdb=" CE2 TRP D 922 " -0.056 2.00e-02 2.50e+03 pdb=" CE3 TRP D 922 " -0.035 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 922 " -0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 922 " 0.085 2.00e-02 2.50e+03 pdb=" CH2 TRP D 922 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 85 " 0.225 9.50e-02 1.11e+02 1.27e-01 8.01e+01 pdb=" NE ARG B 85 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 85 " 0.146 2.00e-02 2.50e+03 pdb=" NH1 ARG B 85 " -0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG B 85 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1149 " 0.089 2.00e-02 2.50e+03 6.81e-02 6.95e+01 pdb=" CG HIS A1149 " -0.119 2.00e-02 2.50e+03 pdb=" ND1 HIS A1149 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 HIS A1149 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A1149 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS A1149 " 0.062 2.00e-02 2.50e+03 ... (remaining 3211 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 383 2.61 - 3.18: 18092 3.18 - 3.75: 31941 3.75 - 4.33: 41339 4.33 - 4.90: 62135 Nonbonded interactions: 153890 Sorted by model distance: nonbonded pdb=" OE1 GLN C 141 " pdb=" F3 BEF C1201 " model vdw 2.033 2.990 nonbonded pdb=" O ARG C 143 " pdb=" OG SER C 146 " model vdw 2.110 3.040 nonbonded pdb=" O GLN D 502 " pdb=" OG SER D 505 " model vdw 2.160 3.040 nonbonded pdb=" O THR D 272 " pdb=" OG SER D 275 " model vdw 2.162 3.040 nonbonded pdb=" NH2 ARG D 801 " pdb=" OD1 ASN D 804 " model vdw 2.182 3.120 ... (remaining 153885 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.560 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.960 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.019 0.623 19989 Z= 1.003 Angle : 1.722 34.008 27246 Z= 0.924 Chirality : 0.083 1.189 3159 Planarity : 0.011 0.179 3214 Dihedral : 18.162 168.761 7703 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.24 % Allowed : 1.41 % Favored : 98.35 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.16), residues: 2238 helix: -1.64 (0.13), residues: 1189 sheet: -1.87 (0.44), residues: 128 loop : -3.04 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.149 0.003 ARG B 85 TYR 0.106 0.005 TYR C 17 PHE 0.096 0.006 PHE C 981 TRP 0.102 0.012 TRP D 922 HIS 0.027 0.003 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.01778 / 0.79 (19987) covalent geometry : angle 1.72175 / 0.92 (27246) hydrogen bonds : bond 0.17698 / 12.12 ( 997) hydrogen bonds : angle 7.14979 / 5.04 ( 2845) Misc. bond : bond 0.62312 / 31.27 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 247 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 600 LYS cc_start: 0.8591 (pttt) cc_final: 0.8290 (pttp) REVERT: B 616 THR cc_start: 0.7554 (m) cc_final: 0.6883 (m) REVERT: D 299 GLU cc_start: 0.4917 (OUTLIER) cc_final: 0.4695 (mt-10) REVERT: D 428 VAL cc_start: 0.9426 (t) cc_final: 0.9216 (t) REVERT: D 618 MET cc_start: 0.8447 (mmt) cc_final: 0.8180 (mmt) REVERT: D 806 MET cc_start: 0.8385 (tmm) cc_final: 0.7991 (tmm) REVERT: D 1503 LYS cc_start: 0.8157 (ptpt) cc_final: 0.7577 (pttp) REVERT: A 13 LYS cc_start: 0.8831 (pttm) cc_final: 0.8547 (pttp) REVERT: A 92 MET cc_start: 0.7789 (mpp) cc_final: 0.7423 (mmm) REVERT: A 1131 GLN cc_start: 0.8573 (pt0) cc_final: 0.8058 (pt0) REVERT: C 74 MET cc_start: 0.8183 (mpp) cc_final: 0.7911 (mmm) outliers start: 5 outliers final: 3 residues processed: 252 average time/residue: 0.1500 time to fit residues: 59.3947 Evaluate side-chains 171 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain D residue 299 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 562 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1059 GLN D1336 GLN A 167 GLN C 34 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.094899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079651 restraints weight = 85806.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.081478 restraints weight = 51914.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.082727 restraints weight = 36084.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.083597 restraints weight = 27733.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.084190 restraints weight = 22779.098| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19989 Z= 0.196 Angle : 0.816 17.050 27246 Z= 0.430 Chirality : 0.047 0.231 3159 Planarity : 0.006 0.079 3214 Dihedral : 18.745 167.550 3169 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.61 % Allowed : 11.05 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.16), residues: 2238 helix: -0.92 (0.14), residues: 1224 sheet: -1.46 (0.44), residues: 128 loop : -3.03 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 85 TYR 0.024 0.002 TYR D 493 PHE 0.024 0.002 PHE C1121 TRP 0.020 0.003 TRP D 922 HIS 0.009 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (19987) covalent geometry : angle 0.81596 / 0.43 (27246) hydrogen bonds : bond 0.07394 / 4.97 ( 997) hydrogen bonds : angle 5.73590 / 4.06 ( 2845) Misc. bond : bond 0.02506 / 1.30 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.9126 (tmm) cc_final: 0.8581 (tmm) REVERT: B 562 ASN cc_start: 0.6719 (m-40) cc_final: 0.6459 (m110) REVERT: B 584 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7257 (mpt180) REVERT: D 423 TYR cc_start: 0.8017 (m-80) cc_final: 0.7591 (m-80) REVERT: D 459 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8701 (tm-30) REVERT: D 593 LEU cc_start: 0.9032 (tp) cc_final: 0.8803 (tt) REVERT: D 595 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8283 (pt0) REVERT: D 718 LEU cc_start: 0.6335 (tt) cc_final: 0.6099 (mm) REVERT: D 775 LEU cc_start: 0.9120 (tp) cc_final: 0.8843 (mp) REVERT: D 1047 LYS cc_start: 0.7735 (mtmt) cc_final: 0.7468 (mttt) REVERT: D 1104 MET cc_start: 0.8662 (mpp) cc_final: 0.8426 (mpp) REVERT: D 1508 ILE cc_start: 0.8763 (mm) cc_final: 0.8469 (mm) REVERT: D 1511 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7972 (p) REVERT: D 1521 LYS cc_start: 0.8879 (ptpp) cc_final: 0.8440 (pttt) REVERT: A 92 MET cc_start: 0.7849 (mpp) cc_final: 0.7604 (mmm) REVERT: A 149 ASP cc_start: 0.8410 (t0) cc_final: 0.8168 (t0) REVERT: A 1109 GLU cc_start: 0.9346 (mm-30) cc_final: 0.8964 (mp0) REVERT: A 1131 GLN cc_start: 0.8745 (pt0) cc_final: 0.8141 (pt0) REVERT: A 1149 HIS cc_start: 0.6472 (m90) cc_final: 0.6219 (m90) REVERT: C 74 MET cc_start: 0.8100 (mpp) cc_final: 0.7838 (mmm) REVERT: C 126 GLU cc_start: 0.8871 (tp30) cc_final: 0.8560 (tp30) REVERT: C 205 GLU cc_start: 0.8404 (tp30) cc_final: 0.8062 (mt-10) outliers start: 33 outliers final: 19 residues processed: 252 average time/residue: 0.1371 time to fit residues: 55.1230 Evaluate side-chains 202 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 567 TYR Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain B residue 584 ARG Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 459 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 1044 HIS Chi-restraints excluded: chain D residue 1222 PHE Chi-restraints excluded: chain D residue 1476 ILE Chi-restraints excluded: chain D residue 1483 LEU Chi-restraints excluded: chain D residue 1511 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 1142 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 187 optimal weight: 2.9990 chunk 227 optimal weight: 20.0000 chunk 221 optimal weight: 0.7980 chunk 135 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 213 GLN ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1118 HIS ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.094779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.079435 restraints weight = 85678.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.081328 restraints weight = 51615.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.082607 restraints weight = 35721.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.083415 restraints weight = 27278.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.084072 restraints weight = 22625.749| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19989 Z= 0.166 Angle : 0.721 10.437 27246 Z= 0.382 Chirality : 0.044 0.232 3159 Planarity : 0.005 0.074 3214 Dihedral : 18.359 169.431 3163 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.29 % Allowed : 15.13 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.17), residues: 2238 helix: -0.64 (0.14), residues: 1244 sheet: -1.32 (0.43), residues: 134 loop : -2.80 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1058 TYR 0.018 0.001 TYR D 857 PHE 0.022 0.002 PHE D1034 TRP 0.009 0.001 TRP B 18 HIS 0.011 0.001 HIS D 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (19987) covalent geometry : angle 0.72124 / 0.38 (27246) hydrogen bonds : bond 0.06454 / 4.32 ( 997) hydrogen bonds : angle 5.37518 / 3.81 ( 2845) Misc. bond : bond 0.01544 / 0.81 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 TRP cc_start: 0.9203 (t-100) cc_final: 0.8997 (t60) REVERT: B 562 ASN cc_start: 0.6916 (m-40) cc_final: 0.6638 (m110) REVERT: D 423 TYR cc_start: 0.8008 (m-80) cc_final: 0.7558 (m-80) REVERT: D 575 LEU cc_start: 0.8473 (tp) cc_final: 0.8083 (mt) REVERT: D 595 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8319 (pt0) REVERT: D 775 LEU cc_start: 0.9126 (tp) cc_final: 0.8850 (mp) REVERT: D 1104 MET cc_start: 0.8667 (mpp) cc_final: 0.8321 (mpp) REVERT: D 1170 TRP cc_start: 0.6687 (t60) cc_final: 0.6156 (t60) REVERT: D 1427 LYS cc_start: 0.9407 (tppp) cc_final: 0.8628 (tppt) REVERT: D 1511 CYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7992 (p) REVERT: A 92 MET cc_start: 0.7913 (mpp) cc_final: 0.7711 (mmm) REVERT: A 149 ASP cc_start: 0.8476 (t0) cc_final: 0.8251 (t0) REVERT: C 74 MET cc_start: 0.8023 (mpp) cc_final: 0.7772 (mmm) REVERT: C 120 GLU cc_start: 0.8357 (mp0) cc_final: 0.8091 (mp0) REVERT: C 126 GLU cc_start: 0.8787 (tp30) cc_final: 0.8516 (tp30) REVERT: C 143 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.7861 (mmm-85) REVERT: C 205 GLU cc_start: 0.8394 (tp30) cc_final: 0.8005 (mt-10) outliers start: 47 outliers final: 29 residues processed: 237 average time/residue: 0.1254 time to fit residues: 48.8651 Evaluate side-chains 207 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 567 TYR Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 518 GLN Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1044 HIS Chi-restraints excluded: chain D residue 1049 TYR Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1222 PHE Chi-restraints excluded: chain D residue 1333 ILE Chi-restraints excluded: chain D residue 1511 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 967 TYR Chi-restraints excluded: chain C residue 1017 ILE Chi-restraints excluded: chain C residue 1107 LEU Chi-restraints excluded: chain C residue 1142 MET Chi-restraints excluded: chain C residue 1161 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 92 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 98 optimal weight: 0.3980 chunk 161 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.080253 restraints weight = 86227.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.082110 restraints weight = 52399.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.083372 restraints weight = 36523.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.084210 restraints weight = 28064.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084700 restraints weight = 23220.326| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19989 Z= 0.146 Angle : 0.707 12.972 27246 Z= 0.366 Chirality : 0.044 0.239 3159 Planarity : 0.004 0.073 3214 Dihedral : 18.204 169.370 3159 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.48 % Allowed : 15.96 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.17), residues: 2238 helix: -0.44 (0.14), residues: 1254 sheet: -1.24 (0.43), residues: 134 loop : -2.74 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1049 TYR 0.020 0.001 TYR D 857 PHE 0.024 0.002 PHE D 714 TRP 0.007 0.001 TRP D 606 HIS 0.008 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.15 (19987) covalent geometry : angle 0.70699 / 0.37 (27246) hydrogen bonds : bond 0.05936 / 3.97 ( 997) hydrogen bonds : angle 5.12992 / 3.65 ( 2845) Misc. bond : bond 0.00244 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 200 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 TRP cc_start: 0.9224 (t-100) cc_final: 0.8075 (t60) REVERT: D 423 TYR cc_start: 0.7919 (m-80) cc_final: 0.7474 (m-80) REVERT: D 521 PHE cc_start: 0.7178 (t80) cc_final: 0.6813 (t80) REVERT: D 575 LEU cc_start: 0.8508 (tp) cc_final: 0.8131 (mt) REVERT: D 595 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8331 (pt0) REVERT: D 775 LEU cc_start: 0.9116 (tp) cc_final: 0.8882 (mp) REVERT: D 1024 MET cc_start: 0.8643 (mpp) cc_final: 0.8160 (mpp) REVERT: D 1104 MET cc_start: 0.8642 (mpp) cc_final: 0.8256 (mpp) REVERT: D 1170 TRP cc_start: 0.6766 (t60) cc_final: 0.6279 (t60) REVERT: D 1427 LYS cc_start: 0.9299 (tppp) cc_final: 0.8868 (tptm) REVERT: D 1511 CYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 92 MET cc_start: 0.7892 (mpp) cc_final: 0.7653 (mmm) REVERT: A 149 ASP cc_start: 0.8456 (t0) cc_final: 0.8230 (t0) REVERT: C 74 MET cc_start: 0.8006 (mpp) cc_final: 0.7774 (mmm) REVERT: C 120 GLU cc_start: 0.8321 (mp0) cc_final: 0.8037 (mp0) REVERT: C 126 GLU cc_start: 0.8737 (tp30) cc_final: 0.8496 (tp30) REVERT: C 143 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.7792 (mmm-85) REVERT: C 205 GLU cc_start: 0.8411 (tp30) cc_final: 0.7987 (mt-10) REVERT: C 220 ARG cc_start: 0.6500 (ttt90) cc_final: 0.5980 (ttt90) REVERT: C 957 LEU cc_start: 0.6935 (OUTLIER) cc_final: 0.6465 (mt) outliers start: 51 outliers final: 24 residues processed: 235 average time/residue: 0.1282 time to fit residues: 48.9484 Evaluate side-chains 212 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 567 TYR Chi-restraints excluded: chain B residue 582 CYS Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 1044 HIS Chi-restraints excluded: chain D residue 1049 TYR Chi-restraints excluded: chain D residue 1059 GLN Chi-restraints excluded: chain D residue 1143 ASN Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1222 PHE Chi-restraints excluded: chain D residue 1325 LEU Chi-restraints excluded: chain D residue 1333 ILE Chi-restraints excluded: chain D residue 1511 CYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 967 TYR Chi-restraints excluded: chain C residue 1142 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 197 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 108 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 154 optimal weight: 0.0050 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 HIS D 459 GLN D 513 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.095902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.080662 restraints weight = 85242.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.082593 restraints weight = 51326.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083876 restraints weight = 35506.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084777 restraints weight = 27132.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.085326 restraints weight = 22244.827| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19989 Z= 0.141 Angle : 0.693 14.066 27246 Z= 0.358 Chirality : 0.043 0.246 3159 Planarity : 0.004 0.070 3214 Dihedral : 18.074 169.291 3159 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.19 % Allowed : 17.91 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.17), residues: 2238 helix: -0.32 (0.14), residues: 1265 sheet: -1.09 (0.45), residues: 125 loop : -2.66 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1049 TYR 0.020 0.001 TYR D 857 PHE 0.020 0.001 PHE C1121 TRP 0.037 0.003 TRP B 18 HIS 0.010 0.001 HIS B 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (19987) covalent geometry : angle 0.69256 / 0.36 (27246) hydrogen bonds : bond 0.05614 / 3.75 ( 997) hydrogen bonds : angle 5.00293 / 3.56 ( 2845) Misc. bond : bond 0.00107 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 HIS cc_start: 0.7081 (m90) cc_final: 0.6808 (m170) REVERT: D 423 TYR cc_start: 0.7853 (m-80) cc_final: 0.7396 (m-80) REVERT: D 513 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8332 (pp30) REVERT: D 575 LEU cc_start: 0.8509 (tp) cc_final: 0.8138 (mt) REVERT: D 595 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8319 (pt0) REVERT: D 921 LEU cc_start: 0.9357 (mt) cc_final: 0.9152 (mp) REVERT: D 1020 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8846 (pp) REVERT: D 1024 MET cc_start: 0.8724 (mpp) cc_final: 0.7891 (mpp) REVERT: D 1104 MET cc_start: 0.8629 (mpp) cc_final: 0.8175 (mpp) REVERT: D 1233 MET cc_start: 0.8857 (tmm) cc_final: 0.8606 (ppp) REVERT: D 1427 LYS cc_start: 0.9388 (tppp) cc_final: 0.8707 (tppt) REVERT: D 1511 CYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8153 (p) REVERT: A 92 MET cc_start: 0.7957 (mpp) cc_final: 0.7693 (mmm) REVERT: A 149 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8191 (t0) REVERT: A 1058 ARG cc_start: 0.8417 (mmt180) cc_final: 0.8166 (mmt180) REVERT: A 1221 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8837 (tp) REVERT: C 120 GLU cc_start: 0.8332 (mp0) cc_final: 0.8002 (mp0) REVERT: C 126 GLU cc_start: 0.8752 (tp30) cc_final: 0.8541 (tp30) REVERT: C 143 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.7839 (mmm-85) REVERT: C 205 GLU cc_start: 0.8380 (tp30) cc_final: 0.7961 (mt-10) REVERT: C 957 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6509 (mt) outliers start: 45 outliers final: 24 residues processed: 240 average time/residue: 0.1227 time to fit residues: 47.9180 Evaluate side-chains 215 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 567 TYR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 513 GLN Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 1020 LEU Chi-restraints excluded: chain D residue 1044 HIS Chi-restraints excluded: chain D residue 1049 TYR Chi-restraints excluded: chain D residue 1143 ASN Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1222 PHE Chi-restraints excluded: chain D residue 1511 CYS Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 967 TYR Chi-restraints excluded: chain C residue 1142 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 152 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 221 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 ASN ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.094210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.079356 restraints weight = 86150.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.081136 restraints weight = 53216.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.082366 restraints weight = 37631.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.083222 restraints weight = 29149.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.083735 restraints weight = 24151.174| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19989 Z= 0.177 Angle : 0.722 13.034 27246 Z= 0.374 Chirality : 0.044 0.227 3159 Planarity : 0.004 0.073 3214 Dihedral : 18.024 170.305 3158 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.34 % Allowed : 18.88 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.17), residues: 2238 helix: -0.18 (0.14), residues: 1271 sheet: -1.12 (0.43), residues: 135 loop : -2.61 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 207 TYR 0.020 0.001 TYR D 857 PHE 0.024 0.002 PHE A1157 TRP 0.008 0.001 TRP D 922 HIS 0.007 0.001 HIS A1149 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.18 (19987) covalent geometry : angle 0.72202 / 0.37 (27246) hydrogen bonds : bond 0.05669 / 3.77 ( 997) hydrogen bonds : angle 5.00389 / 3.55 ( 2845) Misc. bond : bond 0.00113 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 185 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 423 TYR cc_start: 0.7899 (m-80) cc_final: 0.7467 (m-80) REVERT: D 518 GLN cc_start: 0.8008 (tp40) cc_final: 0.7751 (tm-30) REVERT: D 575 LEU cc_start: 0.8560 (tp) cc_final: 0.8192 (mt) REVERT: D 595 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8348 (pt0) REVERT: D 741 MET cc_start: 0.6671 (mmm) cc_final: 0.6316 (mmm) REVERT: D 939 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7755 (mm) REVERT: D 1020 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8836 (pp) REVERT: D 1024 MET cc_start: 0.8700 (mpp) cc_final: 0.7880 (mpp) REVERT: D 1427 LYS cc_start: 0.9336 (tppp) cc_final: 0.8888 (tptm) REVERT: D 1511 CYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8250 (p) REVERT: A 92 MET cc_start: 0.7996 (mpp) cc_final: 0.7735 (mmm) REVERT: A 149 ASP cc_start: 0.8419 (t0) cc_final: 0.8210 (t0) REVERT: A 1058 ARG cc_start: 0.8455 (mmt180) cc_final: 0.8175 (mmt180) REVERT: A 1221 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8664 (tp) REVERT: C 120 GLU cc_start: 0.8396 (mp0) cc_final: 0.7936 (mp0) REVERT: C 126 GLU cc_start: 0.8747 (tp30) cc_final: 0.8524 (tp30) REVERT: C 143 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: C 179 MET cc_start: 0.8494 (tpp) cc_final: 0.8241 (tmm) REVERT: C 205 GLU cc_start: 0.8378 (tp30) cc_final: 0.8009 (mt-10) REVERT: C 1161 MET cc_start: 0.7482 (ppp) cc_final: 0.6923 (ppp) outliers start: 48 outliers final: 34 residues processed: 218 average time/residue: 0.1169 time to fit residues: 41.5969 Evaluate side-chains 218 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 567 TYR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 421 ILE Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 513 GLN Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 976 MET Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1020 LEU Chi-restraints excluded: chain D residue 1044 HIS Chi-restraints excluded: chain D residue 1049 TYR Chi-restraints excluded: chain D residue 1091 LEU Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1222 PHE Chi-restraints excluded: chain D residue 1483 LEU Chi-restraints excluded: chain D residue 1511 CYS Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 967 TYR Chi-restraints excluded: chain C residue 1142 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 162 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.080153 restraints weight = 85642.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.082075 restraints weight = 51792.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.083400 restraints weight = 35950.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.084308 restraints weight = 27402.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.084915 restraints weight = 22464.528| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19989 Z= 0.141 Angle : 0.699 14.429 27246 Z= 0.358 Chirality : 0.043 0.236 3159 Planarity : 0.004 0.070 3214 Dihedral : 17.923 169.555 3158 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.06 % Favored : 92.90 % Rotamer: Outliers : 2.14 % Allowed : 19.66 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.17), residues: 2238 helix: -0.10 (0.14), residues: 1276 sheet: -0.96 (0.42), residues: 136 loop : -2.58 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1125 TYR 0.021 0.001 TYR D 857 PHE 0.020 0.001 PHE A1157 TRP 0.013 0.002 TRP B 18 HIS 0.003 0.001 HIS D 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (19987) covalent geometry : angle 0.69896 / 0.36 (27246) hydrogen bonds : bond 0.05383 / 3.60 ( 997) hydrogen bonds : angle 4.86760 / 3.44 ( 2845) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 HIS cc_start: 0.7637 (m170) cc_final: 0.7176 (m90) REVERT: B 616 THR cc_start: 0.7733 (m) cc_final: 0.7350 (p) REVERT: D 423 TYR cc_start: 0.7806 (m-80) cc_final: 0.7251 (m-80) REVERT: D 575 LEU cc_start: 0.8522 (tp) cc_final: 0.8106 (mt) REVERT: D 595 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8316 (pt0) REVERT: D 720 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7720 (mt) REVERT: D 740 ASN cc_start: 0.8289 (t160) cc_final: 0.7798 (p0) REVERT: D 939 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7722 (mm) REVERT: D 1020 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8830 (pp) REVERT: D 1024 MET cc_start: 0.8712 (mpp) cc_final: 0.7893 (mpp) REVERT: D 1047 LYS cc_start: 0.7261 (mtmt) cc_final: 0.6785 (mtpt) REVERT: D 1427 LYS cc_start: 0.9382 (tppp) cc_final: 0.9021 (tppt) REVERT: A 149 ASP cc_start: 0.8460 (t0) cc_final: 0.8209 (t0) REVERT: A 1058 ARG cc_start: 0.8473 (mmt180) cc_final: 0.8216 (mmt180) REVERT: A 1221 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8678 (tp) REVERT: C 120 GLU cc_start: 0.8383 (mp0) cc_final: 0.7956 (mp0) REVERT: C 143 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.8177 (mmm-85) REVERT: C 205 GLU cc_start: 0.8353 (tp30) cc_final: 0.8129 (mt-10) REVERT: C 957 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6419 (mm) REVERT: C 1161 MET cc_start: 0.7474 (ppp) cc_final: 0.7030 (ppp) outliers start: 44 outliers final: 29 residues processed: 237 average time/residue: 0.1252 time to fit residues: 48.6078 Evaluate side-chains 216 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 567 TYR Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1020 LEU Chi-restraints excluded: chain D residue 1044 HIS Chi-restraints excluded: chain D residue 1049 TYR Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1222 PHE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 967 TYR Chi-restraints excluded: chain C residue 1014 ASP Chi-restraints excluded: chain C residue 1142 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 61 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 740 ASN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1143 ASN D1145 GLN ** D1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.094616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.079819 restraints weight = 85937.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.081638 restraints weight = 52902.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.082902 restraints weight = 37227.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.083748 restraints weight = 28664.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.084268 restraints weight = 23748.149| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19989 Z= 0.156 Angle : 0.720 13.528 27246 Z= 0.369 Chirality : 0.044 0.252 3159 Planarity : 0.004 0.071 3214 Dihedral : 17.887 170.225 3158 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.13 % Favored : 91.82 % Rotamer: Outliers : 2.68 % Allowed : 20.44 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.18), residues: 2238 helix: -0.02 (0.14), residues: 1278 sheet: -1.00 (0.42), residues: 136 loop : -2.60 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1049 TYR 0.021 0.001 TYR D 857 PHE 0.039 0.002 PHE D1144 TRP 0.016 0.002 TRP B 18 HIS 0.009 0.001 HIS D 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (19987) covalent geometry : angle 0.71991 / 0.37 (27246) hydrogen bonds : bond 0.05391 / 3.60 ( 997) hydrogen bonds : angle 4.86279 / 3.44 ( 2845) Misc. bond : bond 0.00096 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 HIS cc_start: 0.7729 (m170) cc_final: 0.7164 (m90) REVERT: B 616 THR cc_start: 0.7717 (m) cc_final: 0.7310 (p) REVERT: D 423 TYR cc_start: 0.7939 (m-80) cc_final: 0.7398 (m-80) REVERT: D 595 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8332 (pt0) REVERT: D 740 ASN cc_start: 0.8359 (t0) cc_final: 0.7861 (p0) REVERT: D 939 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7848 (mm) REVERT: D 1020 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8812 (pp) REVERT: D 1024 MET cc_start: 0.8729 (mpp) cc_final: 0.7984 (mpp) REVERT: D 1427 LYS cc_start: 0.9397 (tppp) cc_final: 0.9039 (tppt) REVERT: D 1511 CYS cc_start: 0.8890 (m) cc_final: 0.8196 (p) REVERT: A 149 ASP cc_start: 0.8436 (t0) cc_final: 0.8180 (t0) REVERT: A 1058 ARG cc_start: 0.8475 (mmt180) cc_final: 0.8218 (mmt180) REVERT: A 1109 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8879 (mp0) REVERT: A 1221 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8686 (tp) REVERT: C 120 GLU cc_start: 0.8382 (mp0) cc_final: 0.7941 (mp0) REVERT: C 143 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.8132 (mmm-85) REVERT: C 957 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6557 (mt) REVERT: C 1161 MET cc_start: 0.7665 (ppp) cc_final: 0.7068 (ppp) outliers start: 55 outliers final: 34 residues processed: 229 average time/residue: 0.1264 time to fit residues: 47.0210 Evaluate side-chains 219 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 567 TYR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1020 LEU Chi-restraints excluded: chain D residue 1044 HIS Chi-restraints excluded: chain D residue 1049 TYR Chi-restraints excluded: chain D residue 1091 LEU Chi-restraints excluded: chain D residue 1143 ASN Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1222 PHE Chi-restraints excluded: chain D residue 1483 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 1014 ASP Chi-restraints excluded: chain C residue 1142 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 188 optimal weight: 0.4980 chunk 164 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 200 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 230 optimal weight: 20.0000 chunk 186 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 HIS A1195 ASN C 979 ASN ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.095453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.080469 restraints weight = 84364.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.082359 restraints weight = 50832.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.083660 restraints weight = 35274.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.084554 restraints weight = 27019.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.085159 restraints weight = 22179.674| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 19989 Z= 0.142 Angle : 0.729 15.319 27246 Z= 0.369 Chirality : 0.044 0.275 3159 Planarity : 0.004 0.071 3214 Dihedral : 17.830 169.694 3158 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.15 % Favored : 92.81 % Rotamer: Outliers : 2.43 % Allowed : 20.88 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2238 helix: 0.03 (0.14), residues: 1274 sheet: -1.11 (0.41), residues: 140 loop : -2.45 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 220 TYR 0.037 0.001 TYR D 493 PHE 0.030 0.002 PHE D 449 TRP 0.019 0.001 TRP B 18 HIS 0.005 0.001 HIS D 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (19987) covalent geometry : angle 0.72861 / 0.37 (27246) hydrogen bonds : bond 0.05195 / 3.47 ( 997) hydrogen bonds : angle 4.79854 / 3.40 ( 2845) Misc. bond : bond 0.00079 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 HIS cc_start: 0.7715 (m170) cc_final: 0.7202 (m90) REVERT: B 616 THR cc_start: 0.7697 (m) cc_final: 0.7309 (p) REVERT: D 423 TYR cc_start: 0.7871 (m-80) cc_final: 0.7339 (m-80) REVERT: D 521 PHE cc_start: 0.7251 (t80) cc_final: 0.6941 (t80) REVERT: D 595 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8314 (pt0) REVERT: D 720 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7706 (mt) REVERT: D 939 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7766 (mm) REVERT: D 1020 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8803 (pp) REVERT: D 1024 MET cc_start: 0.8690 (mpp) cc_final: 0.8011 (mpp) REVERT: D 1397 GLU cc_start: 0.3950 (mp0) cc_final: 0.3554 (mp0) REVERT: D 1427 LYS cc_start: 0.9419 (tppp) cc_final: 0.9033 (tppt) REVERT: D 1511 CYS cc_start: 0.8890 (m) cc_final: 0.8325 (p) REVERT: A 149 ASP cc_start: 0.8480 (t0) cc_final: 0.8231 (t0) REVERT: A 1109 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8841 (mp0) REVERT: A 1221 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8677 (tp) REVERT: C 120 GLU cc_start: 0.8378 (mp0) cc_final: 0.7930 (mp0) REVERT: C 957 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6440 (mt) REVERT: C 1161 MET cc_start: 0.7652 (ppp) cc_final: 0.7046 (ppp) outliers start: 50 outliers final: 30 residues processed: 224 average time/residue: 0.1318 time to fit residues: 47.3104 Evaluate side-chains 212 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 567 TYR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1020 LEU Chi-restraints excluded: chain D residue 1044 HIS Chi-restraints excluded: chain D residue 1049 TYR Chi-restraints excluded: chain D residue 1059 GLN Chi-restraints excluded: chain D residue 1091 LEU Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1222 PHE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 1014 ASP Chi-restraints excluded: chain C residue 1142 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 576 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 ASN D 804 ASN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1143 ASN ** D1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 ASN ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.095164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.080173 restraints weight = 85369.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.082103 restraints weight = 51342.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.083400 restraints weight = 35636.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.084288 restraints weight = 27171.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.084934 restraints weight = 22336.791| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19989 Z= 0.147 Angle : 0.743 14.259 27246 Z= 0.376 Chirality : 0.044 0.282 3159 Planarity : 0.004 0.071 3214 Dihedral : 17.788 170.121 3158 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.64 % Favored : 92.31 % Rotamer: Outliers : 2.19 % Allowed : 21.51 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.18), residues: 2238 helix: 0.10 (0.15), residues: 1270 sheet: -1.12 (0.41), residues: 140 loop : -2.38 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1321 TYR 0.030 0.001 TYR D 493 PHE 0.036 0.001 PHE D 449 TRP 0.021 0.002 TRP B 18 HIS 0.005 0.001 HIS D1371 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (19987) covalent geometry : angle 0.74265 / 0.38 (27246) hydrogen bonds : bond 0.05174 / 3.46 ( 997) hydrogen bonds : angle 4.78343 / 3.38 ( 2845) Misc. bond : bond 0.00077 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4476 Ramachandran restraints generated. 2238 Oldfield, 0 Emsley, 2238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 HIS cc_start: 0.7764 (m170) cc_final: 0.7233 (m90) REVERT: B 616 THR cc_start: 0.7720 (m) cc_final: 0.7339 (p) REVERT: D 423 TYR cc_start: 0.7891 (m-80) cc_final: 0.7339 (m-80) REVERT: D 521 PHE cc_start: 0.7235 (t80) cc_final: 0.7003 (t80) REVERT: D 595 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8318 (pt0) REVERT: D 720 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7716 (mt) REVERT: D 939 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7798 (mm) REVERT: D 1020 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8786 (pp) REVERT: D 1024 MET cc_start: 0.8638 (mpp) cc_final: 0.7915 (mpp) REVERT: D 1320 LEU cc_start: 0.9222 (tp) cc_final: 0.8895 (mm) REVERT: D 1397 GLU cc_start: 0.3958 (mp0) cc_final: 0.3549 (mp0) REVERT: D 1427 LYS cc_start: 0.9427 (tppp) cc_final: 0.8991 (tppt) REVERT: D 1511 CYS cc_start: 0.8919 (m) cc_final: 0.8205 (p) REVERT: A 149 ASP cc_start: 0.8457 (t0) cc_final: 0.8221 (t0) REVERT: A 1109 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8858 (mp0) REVERT: A 1163 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.6946 (p0) REVERT: A 1221 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8684 (tp) REVERT: C 120 GLU cc_start: 0.8381 (mp0) cc_final: 0.7918 (mp0) REVERT: C 957 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6478 (mt) REVERT: C 1160 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7032 (mp0) REVERT: C 1161 MET cc_start: 0.7626 (ppp) cc_final: 0.7046 (ppp) outliers start: 45 outliers final: 34 residues processed: 220 average time/residue: 0.1250 time to fit residues: 44.6995 Evaluate side-chains 219 residues out of total 2055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 567 TYR Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 553 SER Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain D residue 631 VAL Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 992 ILE Chi-restraints excluded: chain D residue 1020 LEU Chi-restraints excluded: chain D residue 1044 HIS Chi-restraints excluded: chain D residue 1049 TYR Chi-restraints excluded: chain D residue 1059 GLN Chi-restraints excluded: chain D residue 1091 LEU Chi-restraints excluded: chain D residue 1211 MET Chi-restraints excluded: chain D residue 1222 PHE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1163 ASP Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 957 LEU Chi-restraints excluded: chain C residue 967 TYR Chi-restraints excluded: chain C residue 1014 ASP Chi-restraints excluded: chain C residue 1142 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 57 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.080062 restraints weight = 85448.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.081927 restraints weight = 52020.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.083188 restraints weight = 36404.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.084085 restraints weight = 28018.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.084685 restraints weight = 23074.229| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19989 Z= 0.149 Angle : 0.741 13.942 27246 Z= 0.375 Chirality : 0.044 0.249 3159 Planarity : 0.004 0.072 3214 Dihedral : 17.758 170.134 3158 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.09 % Allowed : 21.56 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.18), residues: 2238 helix: 0.16 (0.15), residues: 1270 sheet: -1.19 (0.40), residues: 147 loop : -2.35 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 220 TYR 0.027 0.001 TYR D 493 PHE 0.033 0.002 PHE D 449 TRP 0.022 0.002 TRP B 18 HIS 0.004 0.001 HIS D 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (19987) covalent geometry : angle 0.74076 / 0.38 (27246) hydrogen bonds : bond 0.05120 / 3.42 ( 997) hydrogen bonds : angle 4.75966 / 3.35 ( 2845) Misc. bond : bond 0.00075 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3246.27 seconds wall clock time: 57 minutes 6.49 seconds (3426.49 seconds total)