Starting phenix.real_space_refine on Wed May 14 23:27:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8u_42027/05_2025/8u8u_42027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8u_42027/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u8u_42027/05_2025/8u8u_42027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8u_42027/05_2025/8u8u_42027.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8u_42027/05_2025/8u8u_42027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8u_42027/05_2025/8u8u_42027.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 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: {'GLN:plan1': 3, 'GLU:plan': 6, 'HIS:plan': 2, 'ARG:plan': 4, 'ASP: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: 7.36, per 1000 atoms: 0.60 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 4.09 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: 5.13 Time building geometry restraints manager: 3.28 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: 1.750 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.920 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (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 TRP 0.046 0.002 TRP A 200 HIS 0.011 0.002 HIS A 284 PHE 0.020 0.001 PHE E 802 TYR 0.017 0.001 TYR E 610 ARG 0.007 0.001 ARG E1007 Details of bonding type rmsd hydrogen bonds : bond 0.16925 ( 616) hydrogen bonds : angle 6.27147 ( 1730) covalent geometry : bond 0.00479 (12756) covalent geometry : angle 0.84168 (17575) *********************** 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 : 1.134 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: 1.2901 time to fit residues: 409.4589 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 : 1.175 ------------------------------------------------------------------------------- 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 121 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 0.0010 chunk 73 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.0030 chunk 130 optimal weight: 0.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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 617 GLN E 659 HIS E 680 HIS E 722 GLN E 812 HIS E1030 HIS E1150 HIS E1165 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.166739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132328 restraints weight = 16672.253| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.45 r_work: 0.3528 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12756 Z= 0.129 Angle : 0.568 9.494 17575 Z= 0.297 Chirality : 0.038 0.159 1988 Planarity : 0.005 0.056 2028 Dihedral : 19.169 136.313 2259 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.71 % Allowed : 11.52 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1386 helix: 1.53 (0.19), residues: 740 sheet: 0.03 (0.53), residues: 86 loop : -0.76 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 200 HIS 0.006 0.001 HIS E 405 PHE 0.013 0.001 PHE E 802 TYR 0.013 0.001 TYR E 610 ARG 0.006 0.000 ARG E1003 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 616) hydrogen bonds : angle 3.62522 ( 1730) covalent geometry : bond 0.00260 (12756) covalent geometry : angle 0.56791 (17575) *********************** 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 279 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 1.151 Fit side-chains REVERT: B 169 SER cc_start: 0.7932 (p) cc_final: 0.7728 (t) REVERT: B 276 MET cc_start: 0.6893 (ttm) cc_final: 0.6646 (ppp) REVERT: E 370 THR cc_start: 0.7888 (p) cc_final: 0.7603 (m) REVERT: E 372 LYS cc_start: 0.8631 (tttp) cc_final: 0.8393 (ttpp) REVERT: E 394 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7699 (mmmt) REVERT: E 401 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: E 495 GLU cc_start: 0.7237 (tt0) cc_final: 0.7030 (tt0) REVERT: E 529 HIS cc_start: 0.7800 (m90) cc_final: 0.7569 (t-90) REVERT: E 585 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7972 (tm-30) REVERT: E 636 GLU cc_start: 0.7337 (mp0) cc_final: 0.6997 (mp0) REVERT: E 638 THR cc_start: 0.7901 (p) cc_final: 0.7675 (m) REVERT: E 639 LEU cc_start: 0.8233 (mt) cc_final: 0.7903 (mp) REVERT: E 770 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7411 (mtm-85) REVERT: E 861 LEU cc_start: 0.8513 (tp) cc_final: 0.8168 (tt) REVERT: E 865 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7285 (mp0) REVERT: E 987 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6957 (ttt180) REVERT: E 996 THR cc_start: 0.8497 (p) cc_final: 0.8164 (p) REVERT: E 1016 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6856 (mp0) REVERT: E 1056 GLU cc_start: 0.7921 (tp30) cc_final: 0.7672 (mm-30) outliers start: 32 outliers final: 11 residues processed: 255 average time/residue: 1.2429 time to fit residues: 343.3539 Evaluate side-chains 231 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 218 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 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 1128 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 26 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 617 GLN E 680 HIS E 920 HIS E1030 HIS E1175 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.161464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125749 restraints weight = 16585.490| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.25 r_work: 0.3448 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12756 Z= 0.194 Angle : 0.624 11.130 17575 Z= 0.326 Chirality : 0.041 0.156 1988 Planarity : 0.006 0.058 2028 Dihedral : 18.912 136.727 2256 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.46 % Allowed : 14.56 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1386 helix: 1.59 (0.19), residues: 732 sheet: -0.08 (0.52), residues: 86 loop : -0.95 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 200 HIS 0.009 0.002 HIS E1150 PHE 0.019 0.002 PHE E 229 TYR 0.024 0.002 TYR E 610 ARG 0.005 0.001 ARG E1003 Details of bonding type rmsd hydrogen bonds : bond 0.06217 ( 616) hydrogen bonds : angle 3.67163 ( 1730) covalent geometry : bond 0.00452 (12756) covalent geometry : angle 0.62379 (17575) *********************** 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 277 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 1.245 Fit side-chains REVERT: B 256 MET cc_start: 0.8531 (mmt) cc_final: 0.8230 (mmt) REVERT: E 370 THR cc_start: 0.7985 (p) cc_final: 0.7681 (m) REVERT: E 372 LYS cc_start: 0.8666 (tttp) cc_final: 0.8409 (ttpp) REVERT: E 394 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7738 (mmmt) REVERT: E 401 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: E 529 HIS cc_start: 0.7798 (m90) cc_final: 0.7476 (t-90) REVERT: E 585 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7953 (tm-30) REVERT: E 636 GLU cc_start: 0.7462 (mp0) cc_final: 0.7017 (mp0) REVERT: E 638 THR cc_start: 0.7901 (p) cc_final: 0.7689 (m) REVERT: E 770 ARG cc_start: 0.7781 (mtm110) cc_final: 0.7492 (mtm-85) REVERT: E 861 LEU cc_start: 0.8532 (tp) cc_final: 0.8207 (tt) REVERT: E 865 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7432 (mp0) REVERT: E 987 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6854 (ttt180) REVERT: E 996 THR cc_start: 0.8531 (p) cc_final: 0.8218 (p) REVERT: E 1016 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7056 (mp0) REVERT: E 1056 GLU cc_start: 0.7933 (tp30) cc_final: 0.7698 (mm-30) outliers start: 29 outliers final: 16 residues processed: 253 average time/residue: 1.2967 time to fit residues: 354.5728 Evaluate side-chains 255 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 437 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 1064 MET Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1132 MET Chi-restraints excluded: chain E residue 1163 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS A 284 HIS E 238 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.162142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126787 restraints weight = 16443.872| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.20 r_work: 0.3458 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12756 Z= 0.156 Angle : 0.579 12.639 17575 Z= 0.302 Chirality : 0.039 0.151 1988 Planarity : 0.005 0.048 2028 Dihedral : 18.675 136.291 2256 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.96 % Allowed : 16.43 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1386 helix: 1.72 (0.19), residues: 737 sheet: -0.11 (0.56), residues: 79 loop : -1.04 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 271 HIS 0.007 0.001 HIS E1150 PHE 0.016 0.001 PHE E 802 TYR 0.019 0.001 TYR E 913 ARG 0.008 0.000 ARG E1003 Details of bonding type rmsd hydrogen bonds : bond 0.05347 ( 616) hydrogen bonds : angle 3.51811 ( 1730) covalent geometry : bond 0.00354 (12756) covalent geometry : angle 0.57877 (17575) *********************** 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 264 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 1.293 Fit side-chains REVERT: A 352 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: B 189 LEU cc_start: 0.8127 (mm) cc_final: 0.7882 (mm) REVERT: E 370 THR cc_start: 0.8013 (p) cc_final: 0.7685 (m) REVERT: E 372 LYS cc_start: 0.8637 (tttp) cc_final: 0.8412 (ttpp) REVERT: E 394 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7700 (mmmt) REVERT: E 401 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: E 529 HIS cc_start: 0.7760 (m90) cc_final: 0.7459 (t-90) REVERT: E 585 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7894 (tm-30) REVERT: E 636 GLU cc_start: 0.7406 (mp0) cc_final: 0.6950 (mp0) REVERT: E 638 THR cc_start: 0.7916 (p) cc_final: 0.7692 (m) REVERT: E 770 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7422 (mtm-85) REVERT: E 987 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6816 (ttt180) REVERT: E 996 THR cc_start: 0.8555 (p) cc_final: 0.8231 (p) REVERT: E 1013 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6216 (mpt180) REVERT: E 1016 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6973 (mp0) REVERT: E 1056 GLU cc_start: 0.7960 (tp30) cc_final: 0.7725 (mm-30) outliers start: 35 outliers final: 13 residues processed: 243 average time/residue: 1.3443 time to fit residues: 352.4714 Evaluate side-chains 239 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 401 GLU 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 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 1132 MET Chi-restraints excluded: chain E residue 1163 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 1 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 680 HIS E 847 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.163457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.128118 restraints weight = 16549.722| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.35 r_work: 0.3473 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12756 Z= 0.135 Angle : 0.544 11.752 17575 Z= 0.285 Chirality : 0.038 0.148 1988 Planarity : 0.005 0.047 2028 Dihedral : 18.298 136.113 2256 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.05 % Allowed : 16.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.22), residues: 1386 helix: 1.87 (0.19), residues: 742 sheet: -0.01 (0.54), residues: 85 loop : -1.06 (0.23), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 271 HIS 0.006 0.001 HIS E 405 PHE 0.015 0.001 PHE E 802 TYR 0.015 0.001 TYR E 627 ARG 0.007 0.000 ARG E 511 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 616) hydrogen bonds : angle 3.36348 ( 1730) covalent geometry : bond 0.00295 (12756) covalent geometry : angle 0.54442 (17575) *********************** 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 259 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 1.276 Fit side-chains REVERT: E 370 THR cc_start: 0.8077 (p) cc_final: 0.7739 (m) REVERT: E 372 LYS cc_start: 0.8625 (tttp) cc_final: 0.8411 (ttpp) REVERT: E 394 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7729 (mmmt) REVERT: E 529 HIS cc_start: 0.7772 (m90) cc_final: 0.7500 (t-90) REVERT: E 585 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7944 (tm-30) REVERT: E 636 GLU cc_start: 0.7437 (mp0) cc_final: 0.6988 (mp0) REVERT: E 639 LEU cc_start: 0.8305 (mt) cc_final: 0.7937 (mp) REVERT: E 770 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7429 (mtm-85) REVERT: E 987 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6954 (ttt-90) REVERT: E 996 THR cc_start: 0.8567 (p) cc_final: 0.8251 (p) REVERT: E 1013 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6206 (mpt180) REVERT: E 1016 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6964 (mp0) outliers start: 36 outliers final: 18 residues processed: 242 average time/residue: 1.2823 time to fit residues: 335.4689 Evaluate side-chains 239 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain E residue 232 CYS 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 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 Chi-restraints excluded: chain E residue 1163 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 99 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 284 HIS B 346 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 680 HIS E 847 ASN E1030 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.158794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124029 restraints weight = 16565.313| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.02 r_work: 0.3413 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 12756 Z= 0.284 Angle : 0.680 15.780 17575 Z= 0.355 Chirality : 0.044 0.189 1988 Planarity : 0.006 0.053 2028 Dihedral : 18.335 137.372 2256 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.47 % Allowed : 17.95 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1386 helix: 1.42 (0.19), residues: 740 sheet: -0.27 (0.55), residues: 81 loop : -1.25 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 200 HIS 0.012 0.002 HIS E 624 PHE 0.028 0.002 PHE E 229 TYR 0.027 0.002 TYR E 913 ARG 0.007 0.001 ARG E 411 Details of bonding type rmsd hydrogen bonds : bond 0.07095 ( 616) hydrogen bonds : angle 3.77639 ( 1730) covalent geometry : bond 0.00688 (12756) covalent geometry : angle 0.68004 (17575) *********************** 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 287 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 246 time to evaluate : 1.153 Fit side-chains REVERT: A 211 VAL cc_start: 0.8654 (m) cc_final: 0.8424 (p) REVERT: B 169 SER cc_start: 0.8111 (p) cc_final: 0.7885 (t) REVERT: B 189 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8060 (mt) REVERT: E 370 THR cc_start: 0.8111 (p) cc_final: 0.7731 (m) REVERT: E 372 LYS cc_start: 0.8664 (tttp) cc_final: 0.8413 (ttpp) REVERT: E 394 LYS cc_start: 0.7945 (mmmt) cc_final: 0.7729 (mmmt) REVERT: E 401 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: E 529 HIS cc_start: 0.7845 (m90) cc_final: 0.7447 (t-170) REVERT: E 585 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7930 (tm-30) REVERT: E 636 GLU cc_start: 0.7530 (mp0) cc_final: 0.7044 (mp0) REVERT: E 770 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7457 (mtt90) REVERT: E 954 ASP cc_start: 0.7223 (t0) cc_final: 0.6806 (t0) REVERT: E 987 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7073 (ttt180) REVERT: E 996 THR cc_start: 0.8544 (p) cc_final: 0.8253 (p) REVERT: E 1016 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7130 (mp0) outliers start: 41 outliers final: 23 residues processed: 262 average time/residue: 1.2679 time to fit residues: 360.1675 Evaluate side-chains 267 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 241 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 202 LEU 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 B residue 172 SER Chi-restraints excluded: chain B residue 189 LEU 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 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 992 GLN Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1054 LEU Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1132 MET Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1163 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 139 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 680 HIS E 847 ASN E1030 HIS E1165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.161567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.125840 restraints weight = 16445.243| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.36 r_work: 0.3427 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12756 Z= 0.168 Angle : 0.598 12.827 17575 Z= 0.312 Chirality : 0.039 0.154 1988 Planarity : 0.006 0.053 2028 Dihedral : 18.140 137.518 2256 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.81 % Allowed : 19.48 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1386 helix: 1.63 (0.19), residues: 740 sheet: -0.14 (0.56), residues: 79 loop : -1.22 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 200 HIS 0.006 0.001 HIS E 624 PHE 0.018 0.001 PHE E 802 TYR 0.016 0.001 TYR E 627 ARG 0.007 0.001 ARG E1190 Details of bonding type rmsd hydrogen bonds : bond 0.05485 ( 616) hydrogen bonds : angle 3.54453 ( 1730) covalent geometry : bond 0.00386 (12756) covalent geometry : angle 0.59821 (17575) *********************** 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 281 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 1.336 Fit side-chains REVERT: B 169 SER cc_start: 0.8162 (p) cc_final: 0.7952 (t) REVERT: B 189 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7981 (mt) REVERT: E 370 THR cc_start: 0.8122 (p) cc_final: 0.7766 (m) REVERT: E 372 LYS cc_start: 0.8643 (tttp) cc_final: 0.8389 (ttpp) REVERT: E 394 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7731 (mmmt) REVERT: E 401 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: E 529 HIS cc_start: 0.7810 (m90) cc_final: 0.7436 (t-170) REVERT: E 585 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7989 (tm-30) REVERT: E 636 GLU cc_start: 0.7473 (mp0) cc_final: 0.6956 (mp0) REVERT: E 770 ARG cc_start: 0.7795 (mtm110) cc_final: 0.7504 (mtt90) REVERT: E 987 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6891 (ttt180) REVERT: E 996 THR cc_start: 0.8603 (p) cc_final: 0.8297 (p) REVERT: E 1013 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.6301 (mpt180) REVERT: E 1016 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6993 (mp0) outliers start: 45 outliers final: 26 residues processed: 256 average time/residue: 1.1914 time to fit residues: 331.1378 Evaluate side-chains 260 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU 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 238 ILE 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 333 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 858 ARG Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 943 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 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 Chi-restraints excluded: chain E residue 1163 MET Chi-restraints excluded: chain E residue 1179 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 0.3980 chunk 136 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 0.0770 chunk 89 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E 847 ASN E1030 HIS E1165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.162267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126569 restraints weight = 16497.119| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.27 r_work: 0.3445 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12756 Z= 0.141 Angle : 0.574 13.855 17575 Z= 0.299 Chirality : 0.038 0.149 1988 Planarity : 0.005 0.054 2028 Dihedral : 18.025 136.909 2256 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.73 % Allowed : 20.07 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.22), residues: 1386 helix: 1.76 (0.19), residues: 739 sheet: -0.08 (0.54), residues: 85 loop : -1.20 (0.23), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 707 HIS 0.006 0.001 HIS E 405 PHE 0.018 0.001 PHE E 802 TYR 0.027 0.001 TYR E 913 ARG 0.007 0.000 ARG E1190 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 616) hydrogen bonds : angle 3.45409 ( 1730) covalent geometry : bond 0.00309 (12756) covalent geometry : angle 0.57424 (17575) *********************** 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 280 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 1.272 Fit side-chains REVERT: B 189 LEU cc_start: 0.8178 (mm) cc_final: 0.7939 (mt) REVERT: E 304 GLN cc_start: 0.7367 (tt0) cc_final: 0.7073 (tp40) REVERT: E 370 THR cc_start: 0.8123 (p) cc_final: 0.7763 (m) REVERT: E 372 LYS cc_start: 0.8627 (tttp) cc_final: 0.8378 (ttpp) REVERT: E 394 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7750 (mmmt) REVERT: E 529 HIS cc_start: 0.7804 (m90) cc_final: 0.7475 (t-90) REVERT: E 585 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7993 (tm-30) REVERT: E 636 GLU cc_start: 0.7409 (mp0) cc_final: 0.6891 (mp0) REVERT: E 770 ARG cc_start: 0.7750 (mtm110) cc_final: 0.7457 (mtt90) REVERT: E 987 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6871 (ttt180) REVERT: E 996 THR cc_start: 0.8595 (p) cc_final: 0.8286 (p) REVERT: E 1013 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.6285 (mpt180) REVERT: E 1016 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6985 (mp0) outliers start: 44 outliers final: 24 residues processed: 256 average time/residue: 1.2254 time to fit residues: 340.5428 Evaluate side-chains 256 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU 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 333 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 858 ARG Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 943 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1128 ASP Chi-restraints excluded: chain E residue 1150 HIS Chi-restraints excluded: chain E residue 1163 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 0.3980 chunk 92 optimal weight: 0.4980 chunk 26 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E 847 ASN E1030 HIS E1165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.163580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128132 restraints weight = 16498.867| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.32 r_work: 0.3465 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12756 Z= 0.132 Angle : 0.571 14.015 17575 Z= 0.294 Chirality : 0.037 0.151 1988 Planarity : 0.005 0.054 2028 Dihedral : 17.852 135.804 2256 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.64 % Allowed : 20.41 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.22), residues: 1386 helix: 1.91 (0.19), residues: 739 sheet: -0.11 (0.54), residues: 85 loop : -1.10 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 707 HIS 0.006 0.001 HIS E 405 PHE 0.018 0.001 PHE E 802 TYR 0.016 0.001 TYR E 627 ARG 0.008 0.000 ARG E 511 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 616) hydrogen bonds : angle 3.34625 ( 1730) covalent geometry : bond 0.00287 (12756) covalent geometry : angle 0.57123 (17575) *********************** 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 272 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 1.145 Fit side-chains REVERT: E 304 GLN cc_start: 0.7374 (tt0) cc_final: 0.7092 (tp40) REVERT: E 370 THR cc_start: 0.8095 (p) cc_final: 0.7706 (m) REVERT: E 372 LYS cc_start: 0.8618 (tttp) cc_final: 0.8378 (ttpp) REVERT: E 394 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7744 (mmmt) REVERT: E 447 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.7057 (ttm110) REVERT: E 529 HIS cc_start: 0.7750 (m90) cc_final: 0.7483 (t-90) REVERT: E 585 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7991 (tm-30) REVERT: E 631 LEU cc_start: 0.8162 (mp) cc_final: 0.7935 (mt) REVERT: E 636 GLU cc_start: 0.7361 (mp0) cc_final: 0.6881 (mp0) REVERT: E 678 THR cc_start: 0.7940 (OUTLIER) cc_final: 0.7710 (m) REVERT: E 770 ARG cc_start: 0.7722 (mtm110) cc_final: 0.7439 (mtt90) REVERT: E 987 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6850 (ttt180) REVERT: E 996 THR cc_start: 0.8594 (p) cc_final: 0.8290 (p) REVERT: E 1013 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6421 (mpt180) REVERT: E 1016 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6936 (mp0) outliers start: 43 outliers final: 25 residues processed: 249 average time/residue: 1.2467 time to fit residues: 336.0569 Evaluate side-chains 250 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 SER 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 333 GLU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain E residue 249 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 762 LEU Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 858 ARG Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 943 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 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 Chi-restraints excluded: chain E residue 1163 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 58 optimal weight: 0.0370 chunk 113 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 132 optimal weight: 0.0970 chunk 141 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 92 optimal weight: 0.0020 chunk 23 optimal weight: 0.6980 overall best weight: 0.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 GLN E 405 HIS E 493 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E 847 ASN E1009 GLN E1030 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130602 restraints weight = 16394.183| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.25 r_work: 0.3499 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12756 Z= 0.114 Angle : 0.552 14.593 17575 Z= 0.281 Chirality : 0.036 0.194 1988 Planarity : 0.005 0.053 2028 Dihedral : 17.624 133.949 2256 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.79 % Allowed : 21.08 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1386 helix: 2.11 (0.19), residues: 741 sheet: -0.10 (0.55), residues: 85 loop : -1.01 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 271 HIS 0.007 0.001 HIS E 405 PHE 0.015 0.001 PHE E 802 TYR 0.023 0.001 TYR E 913 ARG 0.010 0.000 ARG E 511 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 616) hydrogen bonds : angle 3.21268 ( 1730) covalent geometry : bond 0.00238 (12756) covalent geometry : angle 0.55203 (17575) ********************** 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 253 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 1.242 Fit side-chains REVERT: A 352 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: B 203 MET cc_start: 0.8552 (mmm) cc_final: 0.8322 (mmt) REVERT: E 304 GLN cc_start: 0.7373 (tt0) cc_final: 0.7080 (tp40) REVERT: E 370 THR cc_start: 0.8055 (p) cc_final: 0.7665 (m) REVERT: E 372 LYS cc_start: 0.8601 (tttp) cc_final: 0.8375 (ttpp) REVERT: E 462 GLU cc_start: 0.7298 (mp0) cc_final: 0.6870 (mp0) REVERT: E 582 MET cc_start: 0.7866 (ttm) cc_final: 0.7613 (ttp) REVERT: E 585 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7990 (tm-30) REVERT: E 636 GLU cc_start: 0.7216 (mp0) cc_final: 0.6824 (mp0) REVERT: E 639 LEU cc_start: 0.8236 (mt) cc_final: 0.8019 (mt) REVERT: E 770 ARG cc_start: 0.7645 (mtm110) cc_final: 0.7387 (mtt90) REVERT: E 1013 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6352 (mpt180) outliers start: 33 outliers final: 14 residues processed: 237 average time/residue: 1.3226 time to fit residues: 339.5776 Evaluate side-chains 230 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 214 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 858 ARG Chi-restraints excluded: chain E residue 943 SER Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1072 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.0030 chunk 79 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 overall best weight: 0.3106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 238 GLN E 405 HIS E 493 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 680 HIS E 847 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.165945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131086 restraints weight = 16398.763| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.21 r_work: 0.3506 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12756 Z= 0.115 Angle : 0.550 14.183 17575 Z= 0.281 Chirality : 0.037 0.213 1988 Planarity : 0.005 0.053 2028 Dihedral : 17.515 134.157 2256 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.95 % Allowed : 22.44 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1386 helix: 2.18 (0.19), residues: 741 sheet: -0.12 (0.54), residues: 85 loop : -0.95 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 271 HIS 0.006 0.001 HIS E 405 PHE 0.016 0.001 PHE E 802 TYR 0.015 0.001 TYR E 627 ARG 0.010 0.000 ARG E 511 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 616) hydrogen bonds : angle 3.18967 ( 1730) covalent geometry : bond 0.00240 (12756) covalent geometry : angle 0.55024 (17575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10982.16 seconds wall clock time: 189 minutes 5.65 seconds (11345.65 seconds total)