Starting phenix.real_space_refine on Wed Jul 30 13:22:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8u_42027/07_2025/8u8u_42027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8u_42027/07_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_42027/07_2025/8u8u_42027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8u_42027/07_2025/8u8u_42027.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8u_42027/07_2025/8u8u_42027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8u_42027/07_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-5711/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: 8.86, per 1000 atoms: 0.72 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: 3.64 Conformation dependent library (CDL) restraints added in 1.6 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: 4.68 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: 5.57 Time building geometry restraints manager: 3.90 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: 1.860 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 38.100 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.230 ------------------------------------------------------------------------------- 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 : 1.301 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: 1.3083 time to fit residues: 414.8922 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 : 1.072 ------------------------------------------------------------------------------- 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 = 0.166738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.132338 restraints weight = 16673.213| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.45 r_work: 0.3530 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1642 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 9.478 17575 Z= 0.297 Chirality : 0.038 0.159 1988 Planarity : 0.005 0.056 2028 Dihedral : 19.170 136.314 2259 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.71 % Allowed : 11.43 % Favored : 85.86 % 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 0.05166 ( 616) hydrogen bonds : angle 3.62630 ( 1730) covalent geometry : bond 0.00260 (12756) covalent geometry : angle 0.56803 (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 280 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 1.264 Fit side-chains REVERT: B 276 MET cc_start: 0.6888 (ttm) cc_final: 0.6654 (ppp) REVERT: E 370 THR cc_start: 0.7886 (p) cc_final: 0.7602 (m) REVERT: E 372 LYS cc_start: 0.8637 (tttp) cc_final: 0.8403 (ttpp) REVERT: E 394 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7708 (mmmt) REVERT: E 401 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: E 495 GLU cc_start: 0.7224 (tt0) cc_final: 0.7023 (tt0) REVERT: E 529 HIS cc_start: 0.7811 (m90) cc_final: 0.7590 (t-90) REVERT: E 585 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7980 (tm-30) REVERT: E 636 GLU cc_start: 0.7338 (mp0) cc_final: 0.7005 (mp0) REVERT: E 638 THR cc_start: 0.7901 (p) cc_final: 0.7682 (m) REVERT: E 639 LEU cc_start: 0.8246 (mt) cc_final: 0.7925 (mp) REVERT: E 770 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7414 (mtm-85) REVERT: E 861 LEU cc_start: 0.8529 (tp) cc_final: 0.8188 (tt) REVERT: E 865 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7298 (mp0) REVERT: E 987 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6973 (ttt180) REVERT: E 996 THR cc_start: 0.8514 (p) cc_final: 0.8181 (p) REVERT: E 1016 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6873 (mp0) REVERT: E 1056 GLU cc_start: 0.7928 (tp30) cc_final: 0.7683 (mm-30) outliers start: 32 outliers final: 11 residues processed: 256 average time/residue: 1.2871 time to fit residues: 357.3156 Evaluate side-chains 230 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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: 2.9990 chunk 135 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 138 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 overall best weight: 0.9560 ------------------------------------------------------------------------------- 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 265 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.162307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126891 restraints weight = 16643.683| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.21 r_work: 0.3466 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12756 Z= 0.174 Angle : 0.603 10.906 17575 Z= 0.314 Chirality : 0.040 0.149 1988 Planarity : 0.006 0.056 2028 Dihedral : 18.892 136.351 2256 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.62 % Allowed : 14.31 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.22), residues: 1386 helix: 1.68 (0.19), residues: 732 sheet: -0.05 (0.53), residues: 86 loop : -0.91 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 200 HIS 0.008 0.002 HIS E1150 PHE 0.017 0.002 PHE E 229 TYR 0.022 0.002 TYR E 610 ARG 0.005 0.000 ARG E1003 Details of bonding type rmsd hydrogen bonds : bond 0.05793 ( 616) hydrogen bonds : angle 3.60602 ( 1730) covalent geometry : bond 0.00396 (12756) covalent geometry : angle 0.60298 (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 264 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 1.183 Fit side-chains REVERT: B 256 MET cc_start: 0.8511 (mmt) cc_final: 0.8218 (mmt) REVERT: E 370 THR cc_start: 0.7976 (p) cc_final: 0.7670 (m) REVERT: E 372 LYS cc_start: 0.8660 (tttp) cc_final: 0.8447 (ttpp) REVERT: E 394 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7739 (mmmt) REVERT: E 401 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: E 529 HIS cc_start: 0.7810 (m90) cc_final: 0.7539 (t-90) REVERT: E 585 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7941 (tm-30) REVERT: E 636 GLU cc_start: 0.7442 (mp0) cc_final: 0.7050 (mp0) REVERT: E 638 THR cc_start: 0.7879 (p) cc_final: 0.7679 (m) REVERT: E 770 ARG cc_start: 0.7747 (mtm110) cc_final: 0.7457 (mtm-85) REVERT: E 861 LEU cc_start: 0.8532 (tp) cc_final: 0.8195 (tt) REVERT: E 865 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7408 (mp0) REVERT: E 987 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6884 (ttt180) REVERT: E 996 THR cc_start: 0.8565 (p) cc_final: 0.8244 (p) REVERT: E 1016 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7039 (mp0) REVERT: E 1056 GLU cc_start: 0.7912 (tp30) cc_final: 0.7689 (mm-30) REVERT: E 1117 ASN cc_start: 0.8225 (m-40) cc_final: 0.7999 (m110) outliers start: 31 outliers final: 16 residues processed: 239 average time/residue: 1.4009 time to fit residues: 360.9610 Evaluate side-chains 241 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain 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: 3.9990 chunk 9 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS E 238 GLN ** E 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 HIS ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN E 680 HIS E 847 ASN E1165 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.162524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126898 restraints weight = 16403.405| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.30 r_work: 0.3460 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12756 Z= 0.154 Angle : 0.569 12.894 17575 Z= 0.298 Chirality : 0.039 0.151 1988 Planarity : 0.005 0.049 2028 Dihedral : 18.617 135.923 2256 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.79 % Allowed : 16.43 % Favored : 80.78 % 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: 0.83 (0.22), residues: 1386 helix: 1.75 (0.19), residues: 739 sheet: -0.17 (0.56), residues: 79 loop : -0.97 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 271 HIS 0.007 0.001 HIS E1150 PHE 0.017 0.001 PHE B 265 TYR 0.017 0.001 TYR E 610 ARG 0.008 0.000 ARG E1003 Details of bonding type rmsd hydrogen bonds : bond 0.05245 ( 616) hydrogen bonds : angle 3.48194 ( 1730) covalent geometry : bond 0.00347 (12756) covalent geometry : angle 0.56944 (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 265 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 232 time to evaluate : 1.173 Fit side-chains REVERT: E 370 THR cc_start: 0.8046 (p) cc_final: 0.7720 (m) REVERT: E 372 LYS cc_start: 0.8652 (tttp) cc_final: 0.8445 (ttpp) REVERT: E 394 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7754 (mmmt) REVERT: E 401 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: E 529 HIS cc_start: 0.7786 (m90) cc_final: 0.7508 (t-90) REVERT: E 585 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7960 (tm-30) REVERT: E 636 GLU cc_start: 0.7421 (mp0) cc_final: 0.6981 (mp0) REVERT: E 770 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7459 (mtm-85) REVERT: E 987 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6857 (ttt180) REVERT: E 996 THR cc_start: 0.8590 (p) cc_final: 0.8271 (p) REVERT: E 1013 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.6261 (mpt180) REVERT: E 1016 GLU cc_start: 0.7389 (mm-30) cc_final: 0.7019 (mp0) REVERT: E 1056 GLU cc_start: 0.7980 (tp30) cc_final: 0.7756 (mm-30) outliers start: 33 outliers final: 15 residues processed: 245 average time/residue: 1.3353 time to fit residues: 353.2561 Evaluate side-chains 238 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 238 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 543 VAL Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1072 THR 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: 1.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 91 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 405 HIS E 515 GLN E 680 HIS E 847 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.161529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126023 restraints weight = 16503.552| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.29 r_work: 0.3431 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12756 Z= 0.197 Angle : 0.605 13.286 17575 Z= 0.317 Chirality : 0.040 0.159 1988 Planarity : 0.006 0.049 2028 Dihedral : 18.447 136.324 2256 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.47 % Allowed : 17.36 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1386 helix: 1.68 (0.19), residues: 738 sheet: -0.26 (0.56), residues: 81 loop : -1.09 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 200 HIS 0.007 0.002 HIS E 624 PHE 0.020 0.002 PHE E 229 TYR 0.025 0.002 TYR E 913 ARG 0.007 0.001 ARG E1003 Details of bonding type rmsd hydrogen bonds : bond 0.05881 ( 616) hydrogen bonds : angle 3.59347 ( 1730) covalent geometry : bond 0.00466 (12756) covalent geometry : angle 0.60496 (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 266 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 1.883 Fit side-chains REVERT: B 189 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7923 (mm) REVERT: E 370 THR cc_start: 0.8094 (p) cc_final: 0.7744 (m) REVERT: E 372 LYS cc_start: 0.8658 (tttp) cc_final: 0.8392 (ttpp) REVERT: E 394 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7735 (mmmt) REVERT: E 401 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: E 529 HIS cc_start: 0.7812 (m90) cc_final: 0.7454 (t-170) REVERT: E 585 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7933 (tm-30) REVERT: E 631 LEU cc_start: 0.8213 (mp) cc_final: 0.7990 (mt) REVERT: E 636 GLU cc_start: 0.7518 (mp0) cc_final: 0.7025 (mp0) REVERT: E 770 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7425 (mtt90) REVERT: E 987 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6912 (ttt-90) REVERT: E 996 THR cc_start: 0.8556 (p) cc_final: 0.8244 (p) REVERT: E 1013 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6330 (mpt180) REVERT: E 1016 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7044 (mp0) outliers start: 41 outliers final: 20 residues processed: 241 average time/residue: 1.5580 time to fit residues: 404.7398 Evaluate side-chains 248 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 242 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 189 LEU 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 783 LEU Chi-restraints excluded: chain E residue 818 SER Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1054 LEU 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: 1.9990 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 0.0070 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS E 405 HIS E 680 HIS E 847 ASN E1030 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126919 restraints weight = 16620.120| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.31 r_work: 0.3447 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12756 Z= 0.149 Angle : 0.565 12.187 17575 Z= 0.296 Chirality : 0.038 0.151 1988 Planarity : 0.005 0.047 2028 Dihedral : 18.272 136.545 2256 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.22 % Allowed : 18.54 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.22), residues: 1386 helix: 1.77 (0.19), residues: 741 sheet: -0.07 (0.56), residues: 79 loop : -1.09 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 200 HIS 0.006 0.001 HIS E 405 PHE 0.016 0.001 PHE E 802 TYR 0.014 0.001 TYR E 627 ARG 0.006 0.000 ARG E 511 Details of bonding type rmsd hydrogen bonds : bond 0.05188 ( 616) hydrogen bonds : angle 3.47727 ( 1730) covalent geometry : bond 0.00333 (12756) covalent geometry : angle 0.56464 (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 264 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 1.276 Fit side-chains REVERT: A 352 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7798 (mt-10) REVERT: B 195 GLN cc_start: 0.8398 (pt0) cc_final: 0.8193 (pm20) REVERT: E 370 THR cc_start: 0.8070 (p) cc_final: 0.7713 (m) REVERT: E 372 LYS cc_start: 0.8633 (tttp) cc_final: 0.8367 (ttpp) REVERT: E 394 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7734 (mmmt) REVERT: E 529 HIS cc_start: 0.7769 (m90) cc_final: 0.7455 (t-90) REVERT: E 585 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7922 (tm-30) REVERT: E 636 GLU cc_start: 0.7461 (mp0) cc_final: 0.7005 (mp0) REVERT: E 770 ARG cc_start: 0.7770 (mtm110) cc_final: 0.7453 (mtm-85) REVERT: E 987 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6902 (ttt-90) REVERT: E 996 THR cc_start: 0.8562 (p) cc_final: 0.8246 (p) REVERT: E 1013 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6247 (mpt180) REVERT: E 1016 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6989 (mp0) REVERT: E 1056 GLU cc_start: 0.7965 (tp30) cc_final: 0.7710 (mm-30) outliers start: 38 outliers final: 19 residues processed: 241 average time/residue: 1.3219 time to fit residues: 345.6091 Evaluate side-chains 244 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 214 GLU 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 A residue 352 GLU Chi-restraints excluded: chain E residue 232 CYS 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 818 SER Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 987 ARG Chi-restraints excluded: chain E residue 992 GLN Chi-restraints excluded: chain E residue 999 TYR Chi-restraints excluded: chain E residue 1013 ARG Chi-restraints excluded: chain E residue 1072 THR Chi-restraints excluded: chain E residue 1150 HIS 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: 0.9980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 0.0470 chunk 123 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 E1165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.162856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127462 restraints weight = 16492.329| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.24 r_work: 0.3469 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2727 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= 0.136 Angle : 0.557 13.197 17575 Z= 0.289 Chirality : 0.038 0.148 1988 Planarity : 0.005 0.052 2028 Dihedral : 18.076 136.042 2256 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.47 % Allowed : 18.88 % Favored : 77.65 % 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: 1.89 (0.19), residues: 740 sheet: -0.01 (0.56), residues: 79 loop : -1.06 (0.23), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 200 HIS 0.006 0.001 HIS E 405 PHE 0.016 0.001 PHE E 802 TYR 0.024 0.001 TYR E 913 ARG 0.007 0.000 ARG E 511 Details of bonding type rmsd hydrogen bonds : bond 0.04760 ( 616) hydrogen bonds : angle 3.37971 ( 1730) covalent geometry : bond 0.00299 (12756) covalent geometry : angle 0.55706 (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 273 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 1.187 Fit side-chains REVERT: A 352 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7746 (mm-30) REVERT: E 304 GLN cc_start: 0.7363 (tt0) cc_final: 0.7067 (tp40) REVERT: E 370 THR cc_start: 0.8070 (p) cc_final: 0.7715 (m) REVERT: E 372 LYS cc_start: 0.8623 (tttp) cc_final: 0.8385 (ttpp) REVERT: E 394 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7716 (mmmt) REVERT: E 529 HIS cc_start: 0.7762 (m90) cc_final: 0.7491 (t-90) REVERT: E 585 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7919 (tm-30) REVERT: E 636 GLU cc_start: 0.7399 (mp0) cc_final: 0.6937 (mp0) REVERT: E 770 ARG cc_start: 0.7735 (mtm110) cc_final: 0.7413 (mtm-85) REVERT: E 987 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6850 (ttt-90) REVERT: E 996 THR cc_start: 0.8557 (p) cc_final: 0.8255 (p) REVERT: E 1013 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6290 (mpt180) REVERT: E 1016 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6971 (mp0) outliers start: 41 outliers final: 22 residues processed: 250 average time/residue: 1.3449 time to fit residues: 363.8413 Evaluate side-chains 252 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain 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 328 MET Chi-restraints excluded: chain E residue 232 CYS 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 767 LYS Chi-restraints excluded: chain E residue 783 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 0.0570 chunk 136 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.0040 chunk 132 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 overall best weight: 0.4510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS B 346 GLN E 405 HIS E 493 GLN E 515 GLN E 680 HIS E 847 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.128645 restraints weight = 16528.524| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.14 r_work: 0.3481 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12756 Z= 0.125 Angle : 0.551 13.810 17575 Z= 0.285 Chirality : 0.037 0.154 1988 Planarity : 0.005 0.053 2028 Dihedral : 17.962 135.437 2256 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.98 % Allowed : 18.80 % Favored : 77.22 % 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: 1.02 (0.22), residues: 1386 helix: 1.98 (0.19), residues: 741 sheet: -0.10 (0.56), residues: 79 loop : -1.02 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 200 HIS 0.006 0.001 HIS E 920 PHE 0.015 0.001 PHE E 802 TYR 0.014 0.001 TYR E 627 ARG 0.007 0.000 ARG E 511 Details of bonding type rmsd hydrogen bonds : bond 0.04483 ( 616) hydrogen bonds : angle 3.32262 ( 1730) covalent geometry : bond 0.00266 (12756) covalent geometry : angle 0.55096 (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 275 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 1.272 Fit side-chains REVERT: A 352 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7707 (mt-10) REVERT: E 370 THR cc_start: 0.8055 (p) cc_final: 0.7702 (m) REVERT: E 372 LYS cc_start: 0.8614 (tttp) cc_final: 0.8381 (ttpp) REVERT: E 394 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7711 (mmmt) REVERT: E 478 GLU cc_start: 0.7700 (tp30) cc_final: 0.7446 (mm-30) REVERT: E 529 HIS cc_start: 0.7745 (m90) cc_final: 0.7502 (t-90) REVERT: E 585 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7932 (tm-30) REVERT: E 636 GLU cc_start: 0.7349 (mp0) cc_final: 0.6891 (mp0) REVERT: E 770 ARG cc_start: 0.7691 (mtm110) cc_final: 0.7404 (mtt90) REVERT: E 1013 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.6388 (mpt180) REVERT: E 1016 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6931 (mp0) outliers start: 47 outliers final: 24 residues processed: 249 average time/residue: 1.2710 time to fit residues: 342.9914 Evaluate side-chains 247 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 214 GLU 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 A residue 352 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain E residue 232 CYS 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 678 THR Chi-restraints excluded: chain E residue 767 LYS Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 975 MET 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 1149 VAL 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: 0.5980 chunk 92 optimal weight: 0.0060 chunk 26 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS E 405 HIS E 680 HIS E 847 ASN E1009 GLN E1030 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.164138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128541 restraints weight = 16437.756| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.29 r_work: 0.3460 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12756 Z= 0.135 Angle : 0.566 14.074 17575 Z= 0.291 Chirality : 0.037 0.160 1988 Planarity : 0.005 0.054 2028 Dihedral : 17.896 135.082 2256 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.05 % Allowed : 19.31 % Favored : 77.65 % 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: 1.00 (0.22), residues: 1386 helix: 1.97 (0.19), residues: 740 sheet: -0.15 (0.56), residues: 79 loop : -1.01 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 200 HIS 0.008 0.001 HIS E 920 PHE 0.015 0.001 PHE E 802 TYR 0.025 0.001 TYR E 913 ARG 0.007 0.000 ARG E1190 Details of bonding type rmsd hydrogen bonds : bond 0.04624 ( 616) hydrogen bonds : angle 3.33735 ( 1730) covalent geometry : bond 0.00299 (12756) covalent geometry : angle 0.56560 (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 259 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 1.183 Fit side-chains REVERT: A 352 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: E 304 GLN cc_start: 0.7384 (tt0) cc_final: 0.7097 (tp40) REVERT: E 370 THR cc_start: 0.8082 (p) cc_final: 0.7713 (m) REVERT: E 372 LYS cc_start: 0.8638 (tttp) cc_final: 0.8412 (ttpp) REVERT: E 394 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7740 (mmmt) REVERT: E 401 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: E 529 HIS cc_start: 0.7778 (m90) cc_final: 0.7532 (t-90) REVERT: E 585 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8005 (tm-30) REVERT: E 636 GLU cc_start: 0.7347 (mp0) cc_final: 0.6894 (mp0) REVERT: E 770 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7461 (mtt90) REVERT: E 1013 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.6461 (mpt180) REVERT: E 1016 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7004 (mp0) REVERT: E 1203 GLN cc_start: 0.6628 (pm20) cc_final: 0.6261 (pm20) outliers start: 36 outliers final: 24 residues processed: 240 average time/residue: 1.3000 time to fit residues: 337.7793 Evaluate side-chains 251 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 214 GLU 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 A residue 352 GLU Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 767 LYS Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 975 MET 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 1149 VAL 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: 0.2980 chunk 113 optimal weight: 0.0060 chunk 44 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.163922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.128453 restraints weight = 16337.841| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.30 r_work: 0.3479 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12756 Z= 0.123 Angle : 0.558 14.390 17575 Z= 0.287 Chirality : 0.037 0.160 1988 Planarity : 0.005 0.055 2028 Dihedral : 17.821 134.901 2256 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.05 % Allowed : 19.56 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.22), residues: 1386 helix: 2.03 (0.19), residues: 741 sheet: -0.21 (0.56), residues: 79 loop : -0.99 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 200 HIS 0.008 0.001 HIS E 920 PHE 0.016 0.001 PHE E 802 TYR 0.014 0.001 TYR E 627 ARG 0.008 0.000 ARG E 511 Details of bonding type rmsd hydrogen bonds : bond 0.04355 ( 616) hydrogen bonds : angle 3.29651 ( 1730) covalent geometry : bond 0.00260 (12756) covalent geometry : angle 0.55839 (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 262 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 226 time to evaluate : 1.242 Fit side-chains REVERT: A 352 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: E 304 GLN cc_start: 0.7364 (tt0) cc_final: 0.7075 (tp40) REVERT: E 370 THR cc_start: 0.8058 (p) cc_final: 0.7684 (m) REVERT: E 372 LYS cc_start: 0.8619 (tttp) cc_final: 0.8385 (ttpp) REVERT: E 394 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7722 (mmmt) REVERT: E 401 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7489 (mt-10) REVERT: E 529 HIS cc_start: 0.7733 (m90) cc_final: 0.7491 (t-90) REVERT: E 585 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7966 (tm-30) REVERT: E 636 GLU cc_start: 0.7313 (mp0) cc_final: 0.6832 (mp0) REVERT: E 770 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7400 (mtt90) REVERT: E 924 SER cc_start: 0.8134 (p) cc_final: 0.7500 (m) REVERT: E 987 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7263 (ttt-90) REVERT: E 1013 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.6391 (mpt180) REVERT: E 1016 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6937 (mp0) REVERT: E 1203 GLN cc_start: 0.6556 (pm20) cc_final: 0.6179 (pm20) outliers start: 36 outliers final: 25 residues processed: 242 average time/residue: 1.8422 time to fit residues: 487.7508 Evaluate side-chains 245 residues out of total 1231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 214 GLU 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 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 328 MET Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain E residue 232 CYS Chi-restraints excluded: chain E residue 249 HIS Chi-restraints excluded: chain E residue 401 GLU Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 536 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 678 THR Chi-restraints excluded: chain E residue 783 LEU Chi-restraints excluded: chain E residue 939 VAL Chi-restraints excluded: chain E residue 975 MET 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 1149 VAL 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 81 optimal weight: 2.9990 chunk 56 optimal weight: 0.0010 chunk 79 optimal weight: 0.5980 chunk 122 optimal weight: 0.0020 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 chunk 136 optimal weight: 0.0070 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.1270 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.166558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131373 restraints weight = 16439.039| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.29 r_work: 0.3517 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12756 Z= 0.110 Angle : 0.533 14.800 17575 Z= 0.273 Chirality : 0.036 0.215 1988 Planarity : 0.005 0.053 2028 Dihedral : 17.694 134.669 2256 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.46 % Allowed : 20.66 % Favored : 76.88 % 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: 1.26 (0.22), residues: 1386 helix: 2.21 (0.19), residues: 741 sheet: -0.12 (0.54), residues: 85 loop : -0.94 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 271 HIS 0.006 0.001 HIS E 920 PHE 0.014 0.001 PHE E 802 TYR 0.022 0.001 TYR E 913 ARG 0.007 0.000 ARG E1190 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 616) hydrogen bonds : angle 3.19097 ( 1730) covalent geometry : bond 0.00218 (12756) covalent geometry : angle 0.53340 (17575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11811.49 seconds wall clock time: 206 minutes 14.58 seconds (12374.58 seconds total)