Starting phenix.real_space_refine on Fri Jul 3 05:43:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8u_42027/07_2026/8u8u_42027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8u_42027/07_2026/8u8u_42027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u8u_42027/07_2026/8u8u_42027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8u_42027/07_2026/8u8u_42027.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8u_42027/07_2026/8u8u_42027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8u_42027/07_2026/8u8u_42027.cif" } resolution = 2.9 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= 0.002 sd= 0.029 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: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 59 5.16 5 C 7687 2.51 5 N 2195 2.21 5 O 2339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12344 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1730 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 206} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1570 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 4, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 7752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 985, 7752 Classifications: {'peptide': 985} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 67, 'TRANS': 917} Chain breaks: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 4, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 72 Chain: "N" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 453 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain breaks: 1 Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "T" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 613 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'APC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.90, per 1000 atoms: 0.23 Number of scatterers: 12344 At special positions: 0 Unit cell: (108.712, 105.288, 129.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 64 15.00 O 2339 8.00 N 2195 7.00 C 7687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 525.0 milliseconds 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 11 sheets defined 59.6% alpha, 6.9% beta 26 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 166 removed outlier: 3.693A pdb=" N ALA A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 removed outlier: 3.718A pdb=" N GLU A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 262 removed outlier: 3.522A pdb=" N ASN A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 285 removed outlier: 3.524A pdb=" N HIS A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 321 through 332 Processing helix chain 'A' and resid 338 through 354 removed outlier: 3.842A pdb=" N ASP A 342 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 removed outlier: 3.560A pdb=" N LYS B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 223 removed outlier: 3.692A pdb=" N TYR B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET B 223 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.668A pdb=" N ASN B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 267 removed outlier: 4.239A pdb=" N ALA B 266 " --> pdb=" O LYS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 321 through 331 removed outlier: 3.557A pdb=" N SER B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 removed outlier: 3.566A pdb=" N LEU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 236 Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.841A pdb=" N ALA E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 4.093A pdb=" N LYS E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.511A pdb=" N TYR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 290 removed outlier: 3.706A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 310 removed outlier: 3.625A pdb=" N TYR E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.814A pdb=" N ILE E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 336 removed outlier: 3.570A pdb=" N LEU E 333 " --> pdb=" O LYS E 329 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 355 Processing helix chain 'E' and resid 392 through 409 removed outlier: 3.737A pdb=" N CYS E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU E 399 " --> pdb=" O THR E 395 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 401 " --> pdb=" O GLN E 397 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA E 409 " --> pdb=" O HIS E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 461 removed outlier: 3.507A pdb=" N LYS E 428 " --> pdb=" O SER E 424 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 458 " --> pdb=" O ASN E 454 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 475 through 490 removed outlier: 3.693A pdb=" N VAL E 479 " --> pdb=" O ASP E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 520 removed outlier: 4.294A pdb=" N GLN E 517 " --> pdb=" O VAL E 513 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL E 519 " --> pdb=" O GLN E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 538 removed outlier: 3.910A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N CYS E 535 " --> pdb=" O ARG E 531 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU E 536 " --> pdb=" O LYS E 532 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU E 537 " --> pdb=" O TYR E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 587 removed outlier: 3.529A pdb=" N LEU E 575 " --> pdb=" O VAL E 571 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 577 " --> pdb=" O MET E 573 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU E 583 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL E 584 " --> pdb=" O ALA E 580 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN E 585 " --> pdb=" O GLU E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 634 Processing helix chain 'E' and resid 678 through 687 removed outlier: 3.632A pdb=" N CYS E 687 " --> pdb=" O LEU E 683 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 691 Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 711 through 723 removed outlier: 3.851A pdb=" N ALA E 723 " --> pdb=" O GLN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 738 Processing helix chain 'E' and resid 747 through 750 Processing helix chain 'E' and resid 751 through 789 removed outlier: 3.559A pdb=" N ARG E 759 " --> pdb=" O LYS E 755 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG E 760 " --> pdb=" O ALA E 756 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 774 " --> pdb=" O ARG E 770 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E 775 " --> pdb=" O GLU E 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG E 776 " --> pdb=" O MET E 772 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR E 781 " --> pdb=" O ALA E 777 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU E 785 " --> pdb=" O TYR E 781 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA E 786 " --> pdb=" O ARG E 782 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN E 787 " --> pdb=" O LEU E 783 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 836 through 850 removed outlier: 3.613A pdb=" N TRP E 840 " --> pdb=" O HIS E 836 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 867 removed outlier: 3.662A pdb=" N GLU E 866 " --> pdb=" O ALA E 862 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL E 867 " --> pdb=" O PHE E 863 " (cutoff:3.500A) Processing helix chain 'E' and resid 867 through 877 Processing helix chain 'E' and resid 884 through 888 removed outlier: 3.556A pdb=" N GLY E 887 " --> pdb=" O TRP E 884 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 907 removed outlier: 3.651A pdb=" N GLU E 900 " --> pdb=" O ALA E 896 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG E 906 " --> pdb=" O ALA E 902 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA E 907 " --> pdb=" O ASN E 903 " (cutoff:3.500A) Processing helix chain 'E' and resid 909 through 912 Processing helix chain 'E' and resid 925 through 936 removed outlier: 3.531A pdb=" N ALA E 933 " --> pdb=" O GLN E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 944 removed outlier: 3.959A pdb=" N ALA E 942 " --> pdb=" O SER E 938 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER E 943 " --> pdb=" O VAL E 939 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 944 " --> pdb=" O GLY E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 973 removed outlier: 3.531A pdb=" N GLY E 958 " --> pdb=" O ASP E 954 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN E 972 " --> pdb=" O ARG E 968 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG E 973 " --> pdb=" O GLN E 969 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 981 removed outlier: 3.716A pdb=" N VAL E 980 " --> pdb=" O ARG E 976 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 981 " --> pdb=" O VAL E 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 976 through 981' Processing helix chain 'E' and resid 986 through 996 removed outlier: 3.938A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1017 Processing helix chain 'E' and resid 1024 through 1044 removed outlier: 3.729A pdb=" N GLN E1041 " --> pdb=" O PHE E1037 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU E1042 " --> pdb=" O LYS E1038 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET E1043 " --> pdb=" O SER E1039 " (cutoff:3.500A) Processing helix chain 'E' and resid 1045 through 1064 Processing helix chain 'E' and resid 1111 through 1142 Proline residue: E1120 - end of helix removed outlier: 3.599A pdb=" N ILE E1124 " --> pdb=" O PRO E1120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS E1125 " --> pdb=" O PRO E1121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER E1126 " --> pdb=" O ASN E1122 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU E1137 " --> pdb=" O MET E1133 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS E1142 " --> pdb=" O HIS E1138 " (cutoff:3.500A) Processing helix chain 'E' and resid 1159 through 1177 removed outlier: 4.025A pdb=" N GLU E1177 " --> pdb=" O ARG E1173 " (cutoff:3.500A) Processing helix chain 'E' and resid 1179 through 1191 Processing helix chain 'E' and resid 1197 through 1209 removed outlier: 4.053A pdb=" N GLN E1203 " --> pdb=" O LEU E1199 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU E1204 " --> pdb=" O GLU E1200 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1225 removed outlier: 3.887A pdb=" N GLN E1221 " --> pdb=" O ASP E1218 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS E1223 " --> pdb=" O GLU E1220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 197 removed outlier: 3.548A pdb=" N ALA A 183 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 172 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 185 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 170 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER A 169 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL A 230 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 171 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLU A 232 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE A 173 " --> pdb=" O GLU A 232 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR A 229 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET A 276 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 231 " --> pdb=" O MET A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA3, first strand: chain 'B' and resid 191 through 196 removed outlier: 6.472A pdb=" N HIS B 184 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TRP B 194 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TRP B 182 " --> pdb=" O TRP B 194 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN B 196 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ILE B 180 " --> pdb=" O GLN B 196 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE B 228 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 232 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N PHE B 175 " --> pdb=" O GLU B 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 412 through 415 Processing sheet with id=AA5, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.633A pdb=" N GLU E 495 " --> pdb=" O LEU E 621 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 588 through 590 Processing sheet with id=AA7, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AA8, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AA9, first strand: chain 'E' and resid 831 through 832 Processing sheet with id=AB1, first strand: chain 'E' and resid 919 through 922 Processing sheet with id=AB2, first strand: chain 'E' and resid 1069 through 1071 546 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2635 1.33 - 1.45: 3098 1.45 - 1.58: 6807 1.58 - 1.70: 120 1.70 - 1.82: 96 Bond restraints: 12756 Sorted by residual: bond pdb=" CA SER E1126 " pdb=" CB SER E1126 " ideal model delta sigma weight residual 1.528 1.451 0.078 1.56e-02 4.11e+03 2.47e+01 bond pdb=" C1' DC T 4 " pdb=" N1 DC T 4 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.34e+01 bond pdb=" CA SER E1129 " pdb=" CB SER E1129 " ideal model delta sigma weight residual 1.528 1.472 0.056 1.56e-02 4.11e+03 1.29e+01 bond pdb=" CA SER A 292 " pdb=" CB SER A 292 " ideal model delta sigma weight residual 1.533 1.452 0.081 2.29e-02 1.91e+03 1.26e+01 bond pdb=" N ASP A 193 " pdb=" CA ASP A 193 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.25e-02 6.40e+03 1.22e+01 ... (remaining 12751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 16997 2.21 - 4.41: 453 4.41 - 6.62: 111 6.62 - 8.83: 12 8.83 - 11.03: 2 Bond angle restraints: 17575 Sorted by residual: angle pdb=" O LEU E 569 " pdb=" C LEU E 569 " pdb=" N PRO E 570 " ideal model delta sigma weight residual 120.71 127.94 -7.23 9.40e-01 1.13e+00 5.92e+01 angle pdb=" N TYR E 999 " pdb=" CA TYR E 999 " pdb=" C TYR E 999 " ideal model delta sigma weight residual 110.48 99.45 11.03 1.48e+00 4.57e-01 5.56e+01 angle pdb=" C HIS E1131 " pdb=" N MET E1132 " pdb=" CA MET E1132 " ideal model delta sigma weight residual 120.29 111.14 9.15 1.42e+00 4.96e-01 4.16e+01 angle pdb=" CA LEU E 569 " pdb=" C LEU E 569 " pdb=" N PRO E 570 " ideal model delta sigma weight residual 120.93 114.50 6.43 1.06e+00 8.90e-01 3.68e+01 angle pdb=" N HIS E1131 " pdb=" CA HIS E1131 " pdb=" C HIS E1131 " ideal model delta sigma weight residual 111.71 104.81 6.90 1.15e+00 7.56e-01 3.60e+01 ... (remaining 17570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.86: 7001 26.86 - 53.72: 464 53.72 - 80.58: 123 80.58 - 107.44: 3 107.44 - 134.30: 2 Dihedral angle restraints: 7593 sinusoidal: 3486 harmonic: 4107 Sorted by residual: dihedral pdb=" CA SER E1148 " pdb=" C SER E1148 " pdb=" N VAL E1149 " pdb=" CA VAL E1149 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" O1A APC E1301 " pdb=" C3A APC E1301 " pdb=" PA APC E1301 " pdb=" PB APC E1301 " ideal model delta sinusoidal sigma weight residual 59.99 -51.84 111.83 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" CA GLY E 661 " pdb=" C GLY E 661 " pdb=" N ALA E 662 " pdb=" CA ALA E 662 " ideal model delta harmonic sigma weight residual -180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1935 0.128 - 0.257: 28 0.257 - 0.385: 3 0.385 - 0.514: 3 0.514 - 0.642: 19 Chirality restraints: 1988 Sorted by residual: chirality pdb=" P DA N -24 " pdb=" OP1 DA N -24 " pdb=" OP2 DA N -24 " pdb=" O5' DA N -24 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DG T -12 " pdb=" OP1 DG T -12 " pdb=" OP2 DG T -12 " pdb=" O5' DG T -12 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DC T -9 " pdb=" OP1 DC T -9 " pdb=" OP2 DC T -9 " pdb=" O5' DC T -9 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.15e+00 ... (remaining 1985 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 287 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C LEU A 287 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU A 287 " 0.024 2.00e-02 2.50e+03 pdb=" N MET A 288 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 455 " 0.261 9.50e-02 1.11e+02 1.17e-01 8.38e+00 pdb=" NE ARG E 455 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG E 455 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG E 455 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 455 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 200 " -0.020 2.00e-02 2.50e+03 1.68e-02 7.10e+00 pdb=" CG TRP A 200 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 200 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 200 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 200 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 200 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 200 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 200 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 200 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 200 " -0.001 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1981 2.77 - 3.30: 11261 3.30 - 3.83: 19547 3.83 - 4.37: 22295 4.37 - 4.90: 37852 Nonbonded interactions: 92936 Sorted by model distance: nonbonded pdb=" OE2 GLU E 900 " pdb=" OG SER E 915 " model vdw 2.234 3.040 nonbonded pdb=" O VAL E1025 " pdb=" OG SER E1029 " model vdw 2.341 3.040 nonbonded pdb=" NH1 ARG E 967 " pdb=" O ALA E 978 " model vdw 2.344 3.120 nonbonded pdb=" NE2 GLN E1080 " pdb=" OE1 GLN E1115 " model vdw 2.346 3.120 nonbonded pdb=" O GLU E 890 " pdb=" OG1 THR E 894 " model vdw 2.364 3.040 ... (remaining 92931 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 151 or (resid 152 and (name N or name CA or name C or name \ O or name CB )) or resid 153 through 160 or (resid 161 through 162 and (name N \ or name CA or name C or name O or name CB )) or resid 163 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throug \ h 187 or (resid 188 and (name N or name CA or name C or name O or name CB )) or \ resid 189 through 198 or (resid 199 and (name N or name CA or name C or name O o \ r name CB )) or resid 200 through 266 or (resid 267 and (name N or name CA or na \ me C or name O or name CB )) or resid 268 through 282 or (resid 283 and (name N \ or name CA or name C or name O or name CB )) or resid 284 through 285 or (resid \ 286 and (name N or name CA or name C or name O or name CB )) or resid 287 or (re \ sid 288 and (name N or name CA or name C or name O or name CB )) or resid 289 th \ rough 296 or (resid 297 and (name N or name CA or name C or name O or name CB )) \ or resid 298 or (resid 299 and (name N or name CA or name C or name O or name C \ B )) or resid 300 through 301 or (resid 302 and (name N or name CA or name C or \ name O or name CB )) or resid 303 through 306 or resid 313 through 316 or (resid \ 317 and (name N or name CA or name C or name O or name CB )) or resid 318 throu \ gh 326 or (resid 327 and (name N or name CA or name C or name O or name CB )) or \ resid 328 through 332 or (resid 333 and (name N or name CA or name C or name O \ or name CB )) or resid 334 or (resid 335 through 336 and (name N or name CA or n \ ame C or name O or name CB )) or resid 337 through 351 or (resid 352 and (name N \ or name CA or name C or name O or name CB )) or resid 353 through 357)) selection = (chain 'B' and (resid 151 through 319 or (resid 320 and (name N or name CA or na \ me C or name O or name CB )) or resid 321 through 357)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.000 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:8.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5937 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 : 0.005 0.081 12756 Z= 0.354 Angle : 0.854 11.032 17575 Z= 0.542 Chirality : 0.074 0.642 1988 Planarity : 0.007 0.117 2028 Dihedral : 17.580 134.297 4917 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.17 % Allowed : 1.69 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.14 (0.21), residues: 1386 helix: 0.89 (0.18), residues: 711 sheet: 0.24 (0.54), residues: 87 loop : -0.87 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1007 TYR 0.017 0.001 TYR E 610 PHE 0.020 0.001 PHE E 802 TRP 0.046 0.002 TRP A 200 HIS 0.011 0.002 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.35 (12756) covalent geometry : angle 0.85419 / 0.54 (17575) hydrogen bonds : bond 0.16925 / 11.42 ( 616) hydrogen bonds : angle 6.27147 / 4.38 ( 1730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 293 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.6900 (tp) cc_final: 0.6686 (tt) REVERT: A 227 ASP cc_start: 0.7453 (t70) cc_final: 0.7124 (t0) REVERT: B 164 LEU cc_start: 0.8006 (tp) cc_final: 0.7734 (tm) REVERT: B 172 SER cc_start: 0.7968 (p) cc_final: 0.7626 (p) REVERT: E 372 LYS cc_start: 0.7805 (tttp) cc_final: 0.7401 (ttpp) REVERT: E 394 LYS cc_start: 0.7043 (mmmt) cc_final: 0.6568 (mmmt) REVERT: E 413 CYS cc_start: 0.7799 (m) cc_final: 0.7244 (t) REVERT: E 482 MET cc_start: 0.5985 (ttp) cc_final: 0.5765 (ttm) REVERT: E 495 GLU cc_start: 0.6859 (tt0) cc_final: 0.6180 (tt0) REVERT: E 529 HIS cc_start: 0.6464 (m-70) cc_final: 0.5932 (t-170) REVERT: E 585 GLN cc_start: 0.6949 (tm-30) cc_final: 0.6511 (tm-30) REVERT: E 611 SER cc_start: 0.7036 (t) cc_final: 0.6801 (p) REVERT: E 614 ASN cc_start: 0.5821 (m-40) cc_final: 0.5587 (m-40) REVERT: E 636 GLU cc_start: 0.7171 (mp0) cc_final: 0.6609 (mp0) REVERT: E 638 THR cc_start: 0.7022 (p) cc_final: 0.6719 (m) REVERT: E 770 ARG cc_start: 0.5823 (mtm110) cc_final: 0.5558 (mtm-85) REVERT: E 781 TYR cc_start: 0.6903 (m-80) cc_final: 0.6648 (m-80) REVERT: E 854 ARG cc_start: 0.7396 (mtt-85) cc_final: 0.6989 (mtt-85) REVERT: E 861 LEU cc_start: 0.6716 (tp) cc_final: 0.6353 (tt) REVERT: E 865 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6229 (mp0) REVERT: E 866 GLU cc_start: 0.7173 (tt0) cc_final: 0.6961 (tt0) REVERT: E 982 GLU cc_start: 0.7351 (tt0) cc_final: 0.7091 (tt0) REVERT: E 1012 LYS cc_start: 0.5306 (mtpt) cc_final: 0.5040 (mtmt) REVERT: E 1016 GLU cc_start: 0.6360 (mm-30) cc_final: 0.5880 (mp0) REVERT: E 1042 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6616 (mm-30) REVERT: E 1213 LYS cc_start: 0.8038 (mttm) cc_final: 0.7644 (mmmm) outliers start: 2 outliers final: 1 residues processed: 293 average time/residue: 0.6035 time to fit residues: 191.5351 Evaluate side-chains 237 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.0000 chunk 55 optimal weight: 8.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS A 267 GLN B 262 ASN E 223 GLN E 249 HIS E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 529 HIS E 617 GLN E 659 HIS E 680 HIS E 722 GLN E 812 HIS E1030 HIS E1150 HIS E1165 GLN E1175 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130821 restraints weight = 16631.353| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.20 r_work: 0.3520 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12756 Z= 0.150 Angle : 0.611 10.872 17575 Z= 0.327 Chirality : 0.041 0.189 1988 Planarity : 0.005 0.058 2028 Dihedral : 19.355 135.612 2259 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.46 % Allowed : 11.35 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.62 (0.22), residues: 1386 helix: 1.39 (0.19), residues: 734 sheet: 0.03 (0.53), residues: 86 loop : -0.81 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1003 TYR 0.015 0.001 TYR E 610 PHE 0.015 0.001 PHE E 802 TRP 0.028 0.002 TRP A 200 HIS 0.007 0.001 HIS A 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (12756) covalent geometry : angle 0.61143 / 0.33 (17575) hydrogen bonds : bond 0.05905 / 4.08 ( 616) hydrogen bonds : angle 3.85649 / 2.80 ( 1730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 255 time to evaluate : 0.427 Fit side-chains REVERT: B 164 LEU cc_start: 0.8376 (tp) cc_final: 0.8171 (tm) REVERT: B 169 SER cc_start: 0.8006 (p) cc_final: 0.7789 (t) REVERT: E 304 GLN cc_start: 0.7370 (tt0) cc_final: 0.7093 (tp40) REVERT: E 370 THR cc_start: 0.7891 (p) cc_final: 0.7589 (m) REVERT: E 394 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7688 (mmmt) REVERT: E 401 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: E 529 HIS cc_start: 0.7836 (m90) cc_final: 0.7596 (t-170) REVERT: E 536 LEU cc_start: 0.8617 (tt) cc_final: 0.8399 (tt) REVERT: E 585 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7956 (tm-30) REVERT: E 636 GLU cc_start: 0.7351 (mp0) cc_final: 0.7006 (mp0) REVERT: E 638 THR cc_start: 0.7921 (p) cc_final: 0.7692 (m) REVERT: E 639 LEU cc_start: 0.8278 (mt) cc_final: 0.7947 (mp) REVERT: E 770 ARG cc_start: 0.7690 (mtm110) cc_final: 0.7427 (mtm-85) REVERT: E 861 LEU cc_start: 0.8558 (tp) cc_final: 0.8274 (tt) REVERT: E 865 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7443 (mp0) REVERT: E 987 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.6958 (ttt180) REVERT: E 1013 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.6025 (mpt180) REVERT: E 1016 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6956 (mp0) REVERT: E 1056 GLU cc_start: 0.7897 (tp30) cc_final: 0.7666 (mm-30) outliers start: 29 outliers final: 12 residues processed: 262 average time/residue: 0.6133 time to fit residues: 174.1954 Evaluate side-chains 243 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 228 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1109 LYS Chi-restraints excluded: chain E residue 1128 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 23 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 78 optimal weight: 0.0040 chunk 127 optimal weight: 4.9990 chunk 106 optimal weight: 0.0570 chunk 105 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 120 optimal weight: 0.0870 chunk 101 optimal weight: 0.0970 overall best weight: 0.2486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 238 GLN E 249 HIS E 265 ASN E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E1030 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.131307 restraints weight = 16781.797| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.25 r_work: 0.3529 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12756 Z= 0.123 Angle : 0.575 11.557 17575 Z= 0.303 Chirality : 0.039 0.185 1988 Planarity : 0.005 0.047 2028 Dihedral : 19.071 135.023 2256 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.79 % Allowed : 14.65 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.95 (0.22), residues: 1386 helix: 1.76 (0.19), residues: 736 sheet: -0.07 (0.52), residues: 86 loop : -0.78 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1003 TYR 0.014 0.001 TYR E 461 PHE 0.016 0.001 PHE B 250 TRP 0.031 0.001 TRP E 271 HIS 0.006 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 (12756) covalent geometry : angle 0.57467 / 0.30 (17575) hydrogen bonds : bond 0.04757 / 3.31 ( 616) hydrogen bonds : angle 3.54823 / 2.57 ( 1730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.426 Fit side-chains REVERT: E 232 CYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6485 (m) REVERT: E 370 THR cc_start: 0.7900 (p) cc_final: 0.7607 (m) REVERT: E 394 LYS cc_start: 0.7877 (mmmt) cc_final: 0.7616 (mmmt) REVERT: E 401 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7158 (mp0) REVERT: E 585 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7925 (tm-30) REVERT: E 629 GLN cc_start: 0.7893 (tp40) cc_final: 0.7653 (tp40) REVERT: E 636 GLU cc_start: 0.7329 (mp0) cc_final: 0.6985 (mp0) REVERT: E 639 LEU cc_start: 0.8181 (mt) cc_final: 0.7951 (mp) REVERT: E 770 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7313 (mtt90) REVERT: E 861 LEU cc_start: 0.8512 (tp) cc_final: 0.8142 (tt) REVERT: E 865 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7393 (mp0) REVERT: E 987 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7030 (ttt180) REVERT: E 1016 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6868 (mp0) REVERT: E 1056 GLU cc_start: 0.7884 (tp30) cc_final: 0.7671 (mm-30) REVERT: E 1117 ASN cc_start: 0.8150 (m-40) cc_final: 0.7922 (m110) outliers start: 33 outliers final: 12 residues processed: 231 average time/residue: 0.6665 time to fit residues: 166.0475 Evaluate side-chains 225 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1128 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 140 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 118 optimal weight: 0.0670 chunk 113 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 617 GLN E 680 HIS E 920 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.161476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127211 restraints weight = 16564.189| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.94 r_work: 0.3458 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12756 Z= 0.194 Angle : 0.626 13.332 17575 Z= 0.331 Chirality : 0.042 0.183 1988 Planarity : 0.006 0.050 2028 Dihedral : 18.910 135.099 2256 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.56 % Allowed : 14.82 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.22), residues: 1386 helix: 1.62 (0.19), residues: 735 sheet: 0.13 (0.54), residues: 86 loop : -0.93 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 854 TYR 0.023 0.002 TYR E 610 PHE 0.020 0.002 PHE E 229 TRP 0.032 0.002 TRP A 200 HIS 0.016 0.002 HIS E1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (12756) covalent geometry : angle 0.62619 / 0.33 (17575) hydrogen bonds : bond 0.06188 / 4.26 ( 616) hydrogen bonds : angle 3.69348 / 2.66 ( 1730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.444 Fit side-chains REVERT: A 232 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.8010 (tt0) REVERT: E 370 THR cc_start: 0.7960 (p) cc_final: 0.7654 (m) REVERT: E 394 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7772 (mmmt) REVERT: E 401 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: E 511 ARG cc_start: 0.8576 (mpt-90) cc_final: 0.8308 (mmt-90) REVERT: E 585 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7922 (tm-30) REVERT: E 629 GLN cc_start: 0.7966 (tp40) cc_final: 0.7759 (tp40) REVERT: E 636 GLU cc_start: 0.7472 (mp0) cc_final: 0.7085 (mp0) REVERT: E 678 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7864 (m) REVERT: E 770 ARG cc_start: 0.7761 (mtm110) cc_final: 0.7485 (mtm-85) REVERT: E 861 LEU cc_start: 0.8560 (tp) cc_final: 0.8235 (tt) REVERT: E 865 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7465 (mp0) REVERT: E 987 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6904 (ttt180) REVERT: E 1016 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7093 (mp0) REVERT: E 1056 GLU cc_start: 0.7932 (tp30) cc_final: 0.7730 (mm-30) outliers start: 42 outliers final: 19 residues processed: 249 average time/residue: 0.6335 time to fit residues: 170.6550 Evaluate side-chains 252 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1064 MET Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1129 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 128 optimal weight: 0.0770 chunk 36 optimal weight: 8.9990 chunk 13 optimal weight: 0.1980 chunk 58 optimal weight: 0.0570 chunk 109 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 92 optimal weight: 0.1980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS A 284 HIS E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E 847 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.164573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.129325 restraints weight = 16654.298| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.32 r_work: 0.3487 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 12756 Z= 0.123 Angle : 0.559 11.770 17575 Z= 0.295 Chirality : 0.038 0.180 1988 Planarity : 0.005 0.046 2028 Dihedral : 18.721 134.573 2256 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.96 % Allowed : 17.02 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.98 (0.22), residues: 1386 helix: 1.88 (0.19), residues: 736 sheet: 0.17 (0.55), residues: 85 loop : -0.95 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 854 TYR 0.025 0.001 TYR E 913 PHE 0.012 0.001 PHE E 229 TRP 0.055 0.002 TRP E 271 HIS 0.006 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (12756) covalent geometry : angle 0.55859 / 0.29 (17575) hydrogen bonds : bond 0.04752 / 3.29 ( 616) hydrogen bonds : angle 3.47956 / 2.51 ( 1730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.428 Fit side-chains REVERT: A 232 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: E 370 THR cc_start: 0.8021 (p) cc_final: 0.7698 (m) REVERT: E 394 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7766 (mmmt) REVERT: E 511 ARG cc_start: 0.8606 (mpt-90) cc_final: 0.8351 (mmt-90) REVERT: E 585 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7958 (tm-30) REVERT: E 629 GLN cc_start: 0.7971 (tp40) cc_final: 0.7757 (tp40) REVERT: E 636 GLU cc_start: 0.7407 (mp0) cc_final: 0.7041 (mp0) REVERT: E 770 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7446 (mtm-85) REVERT: E 987 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6973 (ttt-90) REVERT: E 1016 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6972 (mp0) REVERT: E 1056 GLU cc_start: 0.8002 (tp30) cc_final: 0.7781 (mm-30) outliers start: 35 outliers final: 12 residues processed: 227 average time/residue: 0.6557 time to fit residues: 160.4231 Evaluate side-chains 221 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1072 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS A 270 GLN B 195 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 680 HIS E 847 ASN E1165 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.160629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124878 restraints weight = 16547.749| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.28 r_work: 0.3418 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12756 Z= 0.204 Angle : 0.630 13.514 17575 Z= 0.332 Chirality : 0.043 0.196 1988 Planarity : 0.006 0.049 2028 Dihedral : 18.545 134.706 2256 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.96 % Allowed : 17.61 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.66 (0.22), residues: 1386 helix: 1.62 (0.19), residues: 738 sheet: 0.10 (0.57), residues: 79 loop : -1.11 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 854 TYR 0.019 0.002 TYR E 610 PHE 0.021 0.002 PHE E 229 TRP 0.026 0.002 TRP A 200 HIS 0.014 0.002 HIS E1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (12756) covalent geometry : angle 0.63009 / 0.33 (17575) hydrogen bonds : bond 0.06353 / 4.38 ( 616) hydrogen bonds : angle 3.68315 / 2.64 ( 1730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.518 Fit side-chains REVERT: A 211 VAL cc_start: 0.8663 (m) cc_final: 0.8388 (p) REVERT: E 370 THR cc_start: 0.8097 (p) cc_final: 0.7752 (m) REVERT: E 394 LYS cc_start: 0.8009 (mmmt) cc_final: 0.7771 (mmmt) REVERT: E 401 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: E 493 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7563 (pm20) REVERT: E 585 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7960 (tm-30) REVERT: E 629 GLN cc_start: 0.8079 (tp40) cc_final: 0.7863 (tp40) REVERT: E 636 GLU cc_start: 0.7521 (mp0) cc_final: 0.7085 (mp0) REVERT: E 770 ARG cc_start: 0.7831 (mtm110) cc_final: 0.7484 (mtt90) REVERT: E 865 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7814 (mm-30) REVERT: E 987 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6913 (ttt-90) REVERT: E 1016 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7114 (mp0) outliers start: 35 outliers final: 16 residues processed: 242 average time/residue: 0.6241 time to fit residues: 163.4578 Evaluate side-chains 250 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 573 MET Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1064 MET Chi-restraints excluded: chain E residue 1072 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 109 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 84 optimal weight: 0.0070 chunk 1 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS B 195 GLN E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E 847 ASN E1030 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.163655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128179 restraints weight = 16458.098| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.25 r_work: 0.3466 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12756 Z= 0.129 Angle : 0.560 13.306 17575 Z= 0.296 Chirality : 0.039 0.194 1988 Planarity : 0.005 0.047 2028 Dihedral : 18.370 134.363 2256 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.71 % Allowed : 18.88 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.89 (0.22), residues: 1386 helix: 1.86 (0.19), residues: 740 sheet: 0.03 (0.57), residues: 79 loop : -1.07 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 854 TYR 0.025 0.001 TYR E 913 PHE 0.015 0.001 PHE E 802 TRP 0.022 0.002 TRP E 271 HIS 0.006 0.001 HIS E1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (12756) covalent geometry : angle 0.55953 / 0.30 (17575) hydrogen bonds : bond 0.04909 / 3.41 ( 616) hydrogen bonds : angle 3.48335 / 2.50 ( 1730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 0.437 Fit side-chains REVERT: E 370 THR cc_start: 0.8041 (p) cc_final: 0.7701 (m) REVERT: E 394 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7761 (mmmt) REVERT: E 493 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: E 585 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7927 (tm-30) REVERT: E 629 GLN cc_start: 0.8029 (tp40) cc_final: 0.7814 (tp40) REVERT: E 636 GLU cc_start: 0.7398 (mp0) cc_final: 0.6959 (mp0) REVERT: E 770 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7437 (mtm-85) REVERT: E 987 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6831 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.6230 (mpt180) REVERT: E 1016 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7007 (mp0) REVERT: E 1056 GLU cc_start: 0.7992 (tp30) cc_final: 0.7763 (mm-30) outliers start: 32 outliers final: 17 residues processed: 232 average time/residue: 0.6246 time to fit residues: 156.7360 Evaluate side-chains 233 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1064 MET Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1128 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 143 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS A 270 GLN E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E 847 ASN E1030 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.162532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126840 restraints weight = 16490.564| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.28 r_work: 0.3452 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12756 Z= 0.157 Angle : 0.582 13.707 17575 Z= 0.307 Chirality : 0.040 0.193 1988 Planarity : 0.005 0.053 2028 Dihedral : 18.305 134.196 2256 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.79 % Allowed : 18.88 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.87 (0.22), residues: 1386 helix: 1.84 (0.19), residues: 739 sheet: 0.04 (0.57), residues: 79 loop : -1.08 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E1003 TYR 0.017 0.001 TYR E 627 PHE 0.017 0.001 PHE E 229 TRP 0.017 0.002 TRP E 271 HIS 0.008 0.001 HIS E1150 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (12756) covalent geometry : angle 0.58246 / 0.31 (17575) hydrogen bonds : bond 0.05242 / 3.63 ( 616) hydrogen bonds : angle 3.49093 / 2.51 ( 1730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.461 Fit side-chains REVERT: E 370 THR cc_start: 0.8096 (p) cc_final: 0.7752 (m) REVERT: E 394 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7765 (mmmt) REVERT: E 401 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: E 493 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7603 (pm20) REVERT: E 585 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7968 (tm-30) REVERT: E 629 GLN cc_start: 0.8060 (tp40) cc_final: 0.7851 (tp40) REVERT: E 636 GLU cc_start: 0.7411 (mp0) cc_final: 0.6972 (mp0) REVERT: E 770 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7450 (mtm-85) REVERT: E 987 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7093 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.6353 (mpt180) REVERT: E 1016 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7032 (mp0) REVERT: E 1056 GLU cc_start: 0.8006 (tp30) cc_final: 0.7778 (mm-30) outliers start: 33 outliers final: 20 residues processed: 238 average time/residue: 0.6281 time to fit residues: 161.8118 Evaluate side-chains 247 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 767 LYS Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1064 MET Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1128 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 103 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 118 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E 847 ASN E1030 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.164183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128609 restraints weight = 16472.952| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.27 r_work: 0.3468 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12756 Z= 0.132 Angle : 0.567 14.254 17575 Z= 0.297 Chirality : 0.039 0.188 1988 Planarity : 0.005 0.054 2028 Dihedral : 18.180 133.911 2256 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.71 % Allowed : 19.31 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.00 (0.22), residues: 1386 helix: 1.96 (0.19), residues: 740 sheet: -0.05 (0.56), residues: 79 loop : -1.03 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E1003 TYR 0.026 0.001 TYR E 913 PHE 0.015 0.001 PHE E 802 TRP 0.023 0.002 TRP E 271 HIS 0.005 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (12756) covalent geometry : angle 0.56651 / 0.30 (17575) hydrogen bonds : bond 0.04795 / 3.32 ( 616) hydrogen bonds : angle 3.39635 / 2.44 ( 1730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 0.385 Fit side-chains REVERT: E 370 THR cc_start: 0.8064 (p) cc_final: 0.7728 (m) REVERT: E 394 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7794 (mmmt) REVERT: E 493 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7576 (pm20) REVERT: E 585 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7967 (tm-30) REVERT: E 629 GLN cc_start: 0.8055 (tp40) cc_final: 0.7849 (tp40) REVERT: E 636 GLU cc_start: 0.7365 (mp0) cc_final: 0.6946 (mp0) REVERT: E 639 LEU cc_start: 0.8329 (mt) cc_final: 0.8044 (mp) REVERT: E 770 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7424 (mtm-85) REVERT: E 987 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7096 (ttt180) REVERT: E 1013 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.6290 (mpt180) REVERT: E 1016 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7015 (mp0) REVERT: E 1056 GLU cc_start: 0.8016 (tp30) cc_final: 0.7781 (mm-30) outliers start: 32 outliers final: 17 residues processed: 235 average time/residue: 0.6120 time to fit residues: 155.5426 Evaluate side-chains 235 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 215 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 767 LYS Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1128 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 136 optimal weight: 0.0770 chunk 101 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 HIS E 680 HIS E 847 ASN E1009 GLN E1030 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.163913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.128484 restraints weight = 16547.436| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.24 r_work: 0.3473 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12756 Z= 0.130 Angle : 0.569 14.406 17575 Z= 0.297 Chirality : 0.039 0.186 1988 Planarity : 0.005 0.055 2028 Dihedral : 18.141 133.818 2256 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.46 % Allowed : 19.56 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.02 (0.22), residues: 1386 helix: 1.99 (0.19), residues: 740 sheet: -0.10 (0.56), residues: 79 loop : -1.02 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1003 TYR 0.017 0.001 TYR E 627 PHE 0.014 0.001 PHE E 802 TRP 0.019 0.002 TRP E 271 HIS 0.006 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (12756) covalent geometry : angle 0.56861 / 0.30 (17575) hydrogen bonds : bond 0.04735 / 3.30 ( 616) hydrogen bonds : angle 3.39176 / 2.43 ( 1730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2772 Ramachandran restraints generated. 1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.428 Fit side-chains REVERT: E 304 GLN cc_start: 0.7340 (tt0) cc_final: 0.7047 (tp40) REVERT: E 370 THR cc_start: 0.8064 (p) cc_final: 0.7721 (m) REVERT: E 394 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7751 (mmmt) REVERT: E 401 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7536 (mt-10) REVERT: E 493 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: E 585 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7935 (tm-30) REVERT: E 629 GLN cc_start: 0.8039 (tp40) cc_final: 0.7827 (tp40) REVERT: E 636 GLU cc_start: 0.7371 (mp0) cc_final: 0.6935 (mp0) REVERT: E 639 LEU cc_start: 0.8307 (mt) cc_final: 0.8001 (mp) REVERT: E 770 ARG cc_start: 0.7697 (mtm110) cc_final: 0.7424 (mtt90) REVERT: E 987 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7069 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6292 (mpt180) REVERT: E 1016 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6968 (mp0) REVERT: E 1056 GLU cc_start: 0.8016 (tp30) cc_final: 0.7760 (mm-30) REVERT: E 1203 GLN cc_start: 0.6519 (pm20) cc_final: 0.6159 (pm20) outliers start: 29 outliers final: 15 residues processed: 232 average time/residue: 0.5759 time to fit residues: 144.3329 Evaluate side-chains 238 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1072 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 10.0000 chunk 125 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 117 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E 847 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.163056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127487 restraints weight = 16486.042| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.17 r_work: 0.3463 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12756 Z= 0.148 Angle : 0.586 14.424 17575 Z= 0.306 Chirality : 0.039 0.184 1988 Planarity : 0.005 0.056 2028 Dihedral : 18.092 133.921 2256 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.20 % Allowed : 19.73 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.97 (0.22), residues: 1386 helix: 1.94 (0.19), residues: 739 sheet: -0.12 (0.56), residues: 79 loop : -1.03 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 511 TYR 0.027 0.001 TYR E 913 PHE 0.017 0.001 PHE E 229 TRP 0.022 0.002 TRP E 271 HIS 0.006 0.001 HIS E 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (12756) covalent geometry : angle 0.58632 / 0.31 (17575) hydrogen bonds : bond 0.05053 / 3.50 ( 616) hydrogen bonds : angle 3.43000 / 2.45 ( 1730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5149.52 seconds wall clock time: 88 minutes 21.88 seconds (5301.88 seconds total)