Starting phenix.real_space_refine on Sat Aug 23 13:38:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8u_42027/08_2025/8u8u_42027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8u_42027/08_2025/8u8u_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 { model { file = "/net/cci-nas-00/data/ceres_data/8u8u_42027/08_2025/8u8u_42027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8u_42027/08_2025/8u8u_42027.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u8u_42027/08_2025/8u8u_42027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8u_42027/08_2025/8u8u_42027.map" } 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-2.0-5787/lib/python3.9/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: 2.66, per 1000 atoms: 0.22 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: 0.83 Conformation dependent library (CDL) restraints added in 370.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.94 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: 1.98 Time building geometry restraints manager: 1.14 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=" 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 bond pdb=" CA SER E1130 " pdb=" CB SER E1130 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.56e-02 4.11e+03 1.20e+01 ... (remaining 12751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 17025 2.21 - 4.41: 425 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 - 0.126: 1933 0.126 - 0.253: 30 0.253 - 0.379: 3 0.379 - 0.505: 3 0.505 - 0.632: 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 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.97e+00 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 2.35 -2.97 -0.63 2.00e-01 2.50e+01 9.85e+00 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 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.86e+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: 1.700 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.520 Find NCS groups from input model: 0.100 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 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= 0.287 Angle : 0.842 11.032 17575 Z= 0.499 Chirality : 0.072 0.632 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 aren 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 covalent geometry : bond 0.00479 (12756) covalent geometry : angle 0.84168 (17575) hydrogen bonds : bond 0.16925 ( 616) hydrogen bonds : angle 6.27147 ( 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 : 0.273 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: 0.5529 time to fit residues: 174.9208 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 : 0.428 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.164835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.130259 restraints weight = 16580.611| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.20 r_work: 0.3513 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12756 Z= 0.147 Angle : 0.592 10.010 17575 Z= 0.310 Chirality : 0.039 0.164 1988 Planarity : 0.006 0.057 2028 Dihedral : 19.166 136.805 2259 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.79 % Allowed : 11.26 % Favored : 85.94 % 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 aren not related in a simple way. whole: 0.70 (0.22), residues: 1386 helix: 1.49 (0.19), residues: 735 sheet: -0.04 (0.53), residues: 86 loop : -0.81 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1003 TYR 0.017 0.001 TYR E 610 PHE 0.016 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 covalent geometry : bond 0.00316 (12756) covalent geometry : angle 0.59202 (17575) hydrogen bonds : bond 0.05427 ( 616) hydrogen bonds : angle 3.66293 ( 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 282 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.448 Fit side-chains REVERT: A 232 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: B 256 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8220 (mmt) REVERT: B 276 MET cc_start: 0.6880 (ttm) cc_final: 0.6655 (ppp) REVERT: E 304 GLN cc_start: 0.7368 (tt0) cc_final: 0.7079 (tp40) REVERT: E 370 THR cc_start: 0.7897 (p) cc_final: 0.7594 (m) REVERT: E 372 LYS cc_start: 0.8629 (tttp) cc_final: 0.8407 (ttpp) REVERT: E 394 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7735 (mmmt) REVERT: E 401 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: E 529 HIS cc_start: 0.7829 (m90) cc_final: 0.7599 (t-170) REVERT: E 585 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7928 (tm-30) REVERT: E 629 GLN cc_start: 0.7907 (tp40) cc_final: 0.7684 (tp40) REVERT: E 636 GLU cc_start: 0.7360 (mp0) cc_final: 0.7010 (mp0) REVERT: E 638 THR cc_start: 0.7904 (p) cc_final: 0.7687 (m) REVERT: E 639 LEU cc_start: 0.8276 (mt) cc_final: 0.7977 (mp) REVERT: E 770 ARG cc_start: 0.7703 (mtm110) cc_final: 0.7446 (mtm-85) REVERT: E 861 LEU cc_start: 0.8535 (tp) cc_final: 0.8207 (tt) REVERT: E 865 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7322 (mp0) REVERT: E 987 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6992 (ttt180) REVERT: E 1016 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6886 (mp0) REVERT: E 1056 GLU cc_start: 0.7887 (tp30) cc_final: 0.7656 (mm-30) outliers start: 33 outliers final: 13 residues processed: 257 average time/residue: 0.5210 time to fit residues: 144.7071 Evaluate side-chains 235 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 256 MET 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 949 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 1109 LYS 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: 0.9990 chunk 78 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 105 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS E 238 GLN E 249 HIS E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 680 HIS E 920 HIS E1030 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.161677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127163 restraints weight = 16625.666| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.98 r_work: 0.3455 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12756 Z= 0.180 Angle : 0.611 10.607 17575 Z= 0.319 Chirality : 0.040 0.153 1988 Planarity : 0.006 0.057 2028 Dihedral : 18.906 136.234 2256 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.05 % Allowed : 14.82 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.22), residues: 1386 helix: 1.60 (0.19), residues: 732 sheet: -0.27 (0.55), residues: 81 loop : -0.92 (0.23), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1003 TYR 0.022 0.002 TYR E 610 PHE 0.017 0.002 PHE E 802 TRP 0.029 0.002 TRP A 200 HIS 0.008 0.002 HIS E1150 Details of bonding type rmsd covalent geometry : bond 0.00412 (12756) covalent geometry : angle 0.61140 (17575) hydrogen bonds : bond 0.05911 ( 616) hydrogen bonds : angle 3.64693 ( 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 281 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 0.385 Fit side-chains REVERT: A 232 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: E 370 THR cc_start: 0.7975 (p) cc_final: 0.7657 (m) REVERT: E 372 LYS cc_start: 0.8659 (tttp) cc_final: 0.8411 (ttpp) REVERT: E 394 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7739 (mmmt) REVERT: E 401 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: E 529 HIS cc_start: 0.7777 (m90) cc_final: 0.7487 (t-90) REVERT: E 585 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7957 (tm-30) REVERT: E 636 GLU cc_start: 0.7482 (mp0) cc_final: 0.7034 (mp0) REVERT: E 638 THR cc_start: 0.7940 (p) cc_final: 0.7738 (m) REVERT: E 770 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7495 (mtm-85) REVERT: E 861 LEU cc_start: 0.8553 (tp) cc_final: 0.8230 (tt) REVERT: E 865 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7454 (mp0) REVERT: E 987 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6943 (ttt180) REVERT: E 1016 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7049 (mp0) REVERT: E 1056 GLU cc_start: 0.7959 (tp30) cc_final: 0.7726 (mm-30) outliers start: 36 outliers final: 17 residues processed: 251 average time/residue: 0.5538 time to fit residues: 150.0732 Evaluate side-chains 254 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR 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 340 LEU 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 536 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 678 THR 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 999 TYR Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1109 LYS Chi-restraints excluded: chain E residue 1128 ASP Chi-restraints excluded: chain E residue 1132 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 140 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.162907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.127797 restraints weight = 16531.812| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.21 r_work: 0.3472 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12756 Z= 0.141 Angle : 0.565 12.434 17575 Z= 0.295 Chirality : 0.038 0.148 1988 Planarity : 0.005 0.048 2028 Dihedral : 18.637 135.677 2256 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.39 % Allowed : 16.68 % Favored : 79.93 % 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 aren not related in a simple way. whole: 0.83 (0.22), residues: 1386 helix: 1.76 (0.19), residues: 739 sheet: -0.15 (0.55), residues: 79 loop : -0.99 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E1003 TYR 0.019 0.001 TYR E 913 PHE 0.016 0.001 PHE B 265 TRP 0.019 0.002 TRP A 200 HIS 0.006 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00310 (12756) covalent geometry : angle 0.56513 (17575) hydrogen bonds : bond 0.05059 ( 616) hydrogen bonds : angle 3.46827 ( 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 265 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.277 Fit side-chains REVERT: A 232 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8031 (tt0) REVERT: E 370 THR cc_start: 0.8041 (p) cc_final: 0.7697 (m) REVERT: E 372 LYS cc_start: 0.8636 (tttp) cc_final: 0.8425 (ttpp) REVERT: E 394 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7732 (mmmt) REVERT: E 529 HIS cc_start: 0.7743 (m90) cc_final: 0.7467 (t-90) REVERT: E 585 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7929 (tm-30) REVERT: E 636 GLU cc_start: 0.7440 (mp0) cc_final: 0.6987 (mp0) REVERT: E 770 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7431 (mtm-85) REVERT: E 987 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6962 (ttt180) REVERT: E 1013 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.6272 (mpt180) REVERT: E 1016 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6980 (mp0) REVERT: E 1056 GLU cc_start: 0.7978 (tp30) cc_final: 0.7748 (mm-30) outliers start: 40 outliers final: 16 residues processed: 241 average time/residue: 0.5553 time to fit residues: 144.0990 Evaluate side-chains 235 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 242 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 429 HIS 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 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 1132 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 0.0770 chunk 109 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.0020 overall best weight: 0.7548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 195 GLN E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 680 HIS E 847 ASN 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 = 0.162427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127271 restraints weight = 16555.381| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.16 r_work: 0.3465 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12756 Z= 0.149 Angle : 0.562 11.367 17575 Z= 0.294 Chirality : 0.038 0.150 1988 Planarity : 0.005 0.048 2028 Dihedral : 18.307 136.340 2256 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.39 % Allowed : 16.51 % Favored : 80.10 % 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 aren not related in a simple way. whole: 0.88 (0.22), residues: 1386 helix: 1.84 (0.19), residues: 738 sheet: -0.13 (0.56), residues: 79 loop : -1.02 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E1003 TYR 0.015 0.001 TYR A 229 PHE 0.016 0.001 PHE E 229 TRP 0.018 0.002 TRP A 200 HIS 0.006 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00333 (12756) covalent geometry : angle 0.56159 (17575) hydrogen bonds : bond 0.05111 ( 616) hydrogen bonds : angle 3.44792 ( 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 260 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.273 Fit side-chains REVERT: B 328 MET cc_start: 0.7664 (mtt) cc_final: 0.7453 (ttt) REVERT: E 370 THR cc_start: 0.8045 (p) cc_final: 0.7692 (m) REVERT: E 372 LYS cc_start: 0.8646 (tttp) cc_final: 0.8420 (ttpp) REVERT: E 394 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7742 (mmmt) REVERT: E 401 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: E 529 HIS cc_start: 0.7738 (m90) cc_final: 0.7447 (t-90) REVERT: E 585 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 636 GLU cc_start: 0.7433 (mp0) cc_final: 0.6991 (mp0) REVERT: E 770 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7431 (mtm-85) REVERT: E 987 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6927 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6231 (mpt180) REVERT: E 1016 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7029 (mp0) outliers start: 40 outliers final: 22 residues processed: 238 average time/residue: 0.5562 time to fit residues: 142.7541 Evaluate side-chains 242 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 208 SER 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 A residue 340 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 429 HIS Chi-restraints excluded: chain E residue 437 LEU 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 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 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 Chi-restraints excluded: chain E residue 1150 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 128 optimal weight: 0.0770 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS E 405 HIS E 493 GLN E 515 GLN E 680 HIS E 847 ASN E1030 HIS E1165 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128389 restraints weight = 16514.101| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.14 r_work: 0.3484 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12756 Z= 0.124 Angle : 0.540 12.810 17575 Z= 0.280 Chirality : 0.037 0.145 1988 Planarity : 0.005 0.046 2028 Dihedral : 18.143 135.750 2256 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.71 % Allowed : 18.12 % Favored : 79.17 % 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 aren not related in a simple way. whole: 1.02 (0.22), residues: 1386 helix: 1.96 (0.19), residues: 739 sheet: 0.00 (0.54), residues: 85 loop : -1.01 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E1190 TYR 0.023 0.001 TYR E 913 PHE 0.014 0.001 PHE B 265 TRP 0.014 0.001 TRP A 200 HIS 0.006 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00261 (12756) covalent geometry : angle 0.54022 (17575) hydrogen bonds : bond 0.04576 ( 616) hydrogen bonds : angle 3.33633 ( 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 254 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.305 Fit side-chains REVERT: B 328 MET cc_start: 0.7626 (mtt) cc_final: 0.7416 (ttt) REVERT: E 304 GLN cc_start: 0.7361 (tt0) cc_final: 0.7071 (tp40) REVERT: E 370 THR cc_start: 0.8040 (p) cc_final: 0.7681 (m) REVERT: E 372 LYS cc_start: 0.8636 (tttp) cc_final: 0.8416 (ttpp) REVERT: E 394 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7746 (mmmt) REVERT: E 529 HIS cc_start: 0.7743 (m90) cc_final: 0.7498 (t-90) REVERT: E 585 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7922 (tm-30) REVERT: E 636 GLU cc_start: 0.7371 (mp0) cc_final: 0.6911 (mp0) REVERT: E 770 ARG cc_start: 0.7701 (mtm110) cc_final: 0.7418 (mtt90) REVERT: E 987 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6901 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6394 (mpt180) REVERT: E 1016 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6978 (mp0) REVERT: E 1056 GLU cc_start: 0.7947 (tp30) cc_final: 0.7701 (mm-30) outliers start: 32 outliers final: 16 residues processed: 238 average time/residue: 0.5680 time to fit residues: 145.6256 Evaluate side-chains 234 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 B residue 323 VAL Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 437 LEU 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 1013 ARG Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1150 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 346 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 HIS E 680 HIS E 847 ASN E1009 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.162257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126677 restraints weight = 16374.997| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.20 r_work: 0.3449 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12756 Z= 0.170 Angle : 0.581 12.920 17575 Z= 0.301 Chirality : 0.039 0.153 1988 Planarity : 0.005 0.052 2028 Dihedral : 18.051 135.520 2256 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.56 % Allowed : 18.29 % Favored : 78.15 % 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 aren not related in a simple way. whole: 0.88 (0.22), residues: 1386 helix: 1.84 (0.19), residues: 739 sheet: -0.21 (0.55), residues: 81 loop : -1.01 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1190 TYR 0.017 0.002 TYR E 627 PHE 0.019 0.001 PHE E 229 TRP 0.019 0.002 TRP A 200 HIS 0.006 0.001 HIS E 624 Details of bonding type rmsd covalent geometry : bond 0.00394 (12756) covalent geometry : angle 0.58051 (17575) hydrogen bonds : bond 0.05485 ( 616) hydrogen bonds : angle 3.45917 ( 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 274 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.312 Fit side-chains REVERT: E 370 THR cc_start: 0.8092 (p) cc_final: 0.7728 (m) REVERT: E 372 LYS cc_start: 0.8648 (tttp) cc_final: 0.8407 (ttpp) REVERT: E 394 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7731 (mmmt) REVERT: E 401 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7498 (mt-10) REVERT: E 493 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7448 (pm20) REVERT: E 500 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7917 (mp) REVERT: E 529 HIS cc_start: 0.7778 (m90) cc_final: 0.7443 (t-170) REVERT: E 585 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7931 (tm-30) REVERT: E 636 GLU cc_start: 0.7400 (mp0) cc_final: 0.6893 (mp0) REVERT: E 770 ARG cc_start: 0.7765 (mtm110) cc_final: 0.7449 (mtm-85) REVERT: E 987 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6871 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6298 (mpt180) REVERT: E 1016 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7019 (mp0) REVERT: E 1203 GLN cc_start: 0.6619 (pm20) cc_final: 0.6246 (pm20) outliers start: 42 outliers final: 22 residues processed: 249 average time/residue: 0.5518 time to fit residues: 148.5534 Evaluate side-chains 256 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 500 LEU 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 939 VAL 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 Chi-restraints excluded: chain E residue 1128 ASP Chi-restraints excluded: chain E residue 1150 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 69 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS E 405 HIS E 680 HIS E 847 ASN E1165 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.163085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127711 restraints weight = 16465.486| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.27 r_work: 0.3455 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2815 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= 0.148 Angle : 0.574 13.603 17575 Z= 0.296 Chirality : 0.038 0.151 1988 Planarity : 0.005 0.055 2028 Dihedral : 17.939 135.202 2256 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.30 % Allowed : 19.22 % Favored : 77.48 % 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 aren not related in a simple way. whole: 0.90 (0.22), residues: 1386 helix: 1.87 (0.19), residues: 737 sheet: -0.07 (0.53), residues: 85 loop : -1.05 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1190 TYR 0.024 0.001 TYR E 913 PHE 0.016 0.001 PHE E 229 TRP 0.015 0.002 TRP A 200 HIS 0.006 0.001 HIS E 405 Details of bonding type rmsd covalent geometry : bond 0.00334 (12756) covalent geometry : angle 0.57377 (17575) hydrogen bonds : bond 0.05043 ( 616) hydrogen bonds : angle 3.40673 ( 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 266 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.334 Fit side-chains REVERT: E 268 MET cc_start: 0.8447 (ttm) cc_final: 0.8152 (ttt) REVERT: E 304 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.7140 (tp40) REVERT: E 370 THR cc_start: 0.8098 (p) cc_final: 0.7729 (m) REVERT: E 372 LYS cc_start: 0.8658 (tttp) cc_final: 0.8423 (ttpp) REVERT: E 394 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7739 (mmmt) REVERT: E 401 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: E 493 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7454 (pm20) REVERT: E 500 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7868 (mp) REVERT: E 529 HIS cc_start: 0.7754 (m90) cc_final: 0.7452 (t-90) REVERT: E 585 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7985 (tm-30) REVERT: E 636 GLU cc_start: 0.7365 (mp0) cc_final: 0.6856 (mp0) REVERT: E 770 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7474 (mtt90) REVERT: E 924 SER cc_start: 0.8160 (p) cc_final: 0.7473 (t) REVERT: E 987 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6900 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6249 (mpt180) REVERT: E 1016 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6992 (mp0) REVERT: E 1203 GLN cc_start: 0.6622 (pm20) cc_final: 0.6250 (pm20) outliers start: 39 outliers final: 21 residues processed: 245 average time/residue: 0.5714 time to fit residues: 150.8724 Evaluate side-chains 253 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 500 LEU 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 939 VAL 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 Chi-restraints excluded: chain E residue 1128 ASP Chi-restraints excluded: chain E residue 1150 HIS 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: 0.6980 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 118 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS E 405 HIS E 680 HIS E 847 ASN E1030 HIS E1165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.163146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.127601 restraints weight = 16418.776| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.28 r_work: 0.3454 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2874 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= 0.147 Angle : 0.576 14.006 17575 Z= 0.297 Chirality : 0.038 0.149 1988 Planarity : 0.005 0.055 2028 Dihedral : 17.866 135.006 2256 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.13 % Allowed : 19.39 % Favored : 77.48 % 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 aren not related in a simple way. whole: 0.91 (0.22), residues: 1386 helix: 1.87 (0.19), residues: 738 sheet: -0.11 (0.53), residues: 85 loop : -1.04 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1190 TYR 0.015 0.001 TYR E 627 PHE 0.016 0.001 PHE E 229 TRP 0.017 0.002 TRP B 182 HIS 0.007 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00330 (12756) covalent geometry : angle 0.57598 (17575) hydrogen bonds : bond 0.04982 ( 616) hydrogen bonds : angle 3.40090 ( 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 266 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.339 Fit side-chains REVERT: E 268 MET cc_start: 0.8441 (ttm) cc_final: 0.8144 (ttt) REVERT: E 304 GLN cc_start: 0.7443 (tt0) cc_final: 0.7184 (tp40) REVERT: E 370 THR cc_start: 0.8085 (p) cc_final: 0.7698 (m) REVERT: E 372 LYS cc_start: 0.8656 (tttp) cc_final: 0.8420 (ttpp) REVERT: E 394 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7742 (mmmt) REVERT: E 401 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: E 447 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.7030 (ttm110) REVERT: E 493 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: E 500 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7875 (mp) REVERT: E 511 ARG cc_start: 0.8585 (mpt-90) cc_final: 0.8364 (mtt180) REVERT: E 529 HIS cc_start: 0.7773 (m90) cc_final: 0.7496 (t-90) REVERT: E 585 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8001 (tm-30) REVERT: E 636 GLU cc_start: 0.7336 (mp0) cc_final: 0.6817 (mp0) REVERT: E 770 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7470 (mtt90) REVERT: E 924 SER cc_start: 0.8179 (p) cc_final: 0.7493 (t) REVERT: E 987 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6872 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6244 (mpt180) REVERT: E 1016 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6987 (mp0) REVERT: E 1203 GLN cc_start: 0.6625 (pm20) cc_final: 0.6256 (pm20) outliers start: 37 outliers final: 20 residues processed: 245 average time/residue: 0.5189 time to fit residues: 137.6498 Evaluate side-chains 248 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 429 HIS Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 500 LEU 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 992 GLN 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 1150 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS E 405 HIS E 680 HIS E 847 ASN E1030 HIS E1165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128451 restraints weight = 16503.837| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.25 r_work: 0.3468 rms_B_bonded: 2.90 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: 0.7642 moved from start: 0.2917 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= 0.137 Angle : 0.574 14.255 17575 Z= 0.295 Chirality : 0.037 0.147 1988 Planarity : 0.005 0.055 2028 Dihedral : 17.762 134.656 2256 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 20.07 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.22), residues: 1386 helix: 1.93 (0.19), residues: 739 sheet: -0.17 (0.53), residues: 85 loop : -1.03 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E1190 TYR 0.025 0.001 TYR E 913 PHE 0.023 0.001 PHE A 228 TRP 0.015 0.002 TRP B 182 HIS 0.007 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00301 (12756) covalent geometry : angle 0.57410 (17575) hydrogen bonds : bond 0.04694 ( 616) hydrogen bonds : angle 3.34619 ( 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 257 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.275 Fit side-chains REVERT: E 268 MET cc_start: 0.8463 (ttm) cc_final: 0.8172 (ttt) REVERT: E 304 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7177 (tp40) REVERT: E 370 THR cc_start: 0.8076 (p) cc_final: 0.7680 (m) REVERT: E 372 LYS cc_start: 0.8655 (tttp) cc_final: 0.8419 (ttpp) REVERT: E 394 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7750 (mmmt) REVERT: E 401 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: E 493 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: E 529 HIS cc_start: 0.7737 (m90) cc_final: 0.7490 (t-90) REVERT: E 582 MET cc_start: 0.8101 (ttp) cc_final: 0.7830 (ttm) REVERT: E 585 GLN cc_start: 0.8291 (tm-30) cc_final: 0.8005 (tm-30) REVERT: E 636 GLU cc_start: 0.7296 (mp0) cc_final: 0.6764 (mp0) REVERT: E 770 ARG cc_start: 0.7700 (mtm110) cc_final: 0.7422 (mtt90) REVERT: E 924 SER cc_start: 0.8167 (p) cc_final: 0.7477 (t) REVERT: E 987 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6877 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.6407 (mpt180) REVERT: E 1016 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6963 (mp0) REVERT: E 1203 GLN cc_start: 0.6621 (pm20) cc_final: 0.6254 (pm20) outliers start: 35 outliers final: 19 residues processed: 237 average time/residue: 0.5503 time to fit residues: 140.8387 Evaluate side-chains 242 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 429 HIS 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 939 VAL 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 1013 ARG Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1128 ASP Chi-restraints excluded: chain E residue 1150 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 5.9990 chunk 125 optimal weight: 0.3980 chunk 100 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS E 405 HIS 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 = 0.4059 r_free = 0.4059 target = 0.162519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126938 restraints weight = 16408.200| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.24 r_work: 0.3440 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12756 Z= 0.178 Angle : 0.607 14.281 17575 Z= 0.312 Chirality : 0.039 0.171 1988 Planarity : 0.005 0.055 2028 Dihedral : 17.734 135.041 2256 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.54 % Allowed : 20.07 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.22), residues: 1386 helix: 1.82 (0.19), residues: 738 sheet: -0.18 (0.54), residues: 85 loop : -1.08 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 511 TYR 0.017 0.001 TYR E 627 PHE 0.024 0.002 PHE A 228 TRP 0.017 0.002 TRP A 200 HIS 0.007 0.001 HIS E 920 Details of bonding type rmsd covalent geometry : bond 0.00418 (12756) covalent geometry : angle 0.60689 (17575) hydrogen bonds : bond 0.05317 ( 616) hydrogen bonds : angle 3.44301 ( 1730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4696.19 seconds wall clock time: 80 minutes 14.24 seconds (4814.24 seconds total)