Starting phenix.real_space_refine on Sat Aug 23 03:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wp0_37705/08_2025/8wp0_37705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wp0_37705/08_2025/8wp0_37705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wp0_37705/08_2025/8wp0_37705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wp0_37705/08_2025/8wp0_37705.map" model { file = "/net/cci-nas-00/data/ceres_data/8wp0_37705/08_2025/8wp0_37705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wp0_37705/08_2025/8wp0_37705.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.105 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 5976 2.51 5 N 1595 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9372 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1217, 9308 Classifications: {'peptide': 1217} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 30, 'TRANS': 1186} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.96, per 1000 atoms: 0.21 Number of scatterers: 9372 At special positions: 0 Unit cell: (72.6, 106.7, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 6 15.00 Mg 2 11.99 O 1755 8.00 N 1595 7.00 C 5976 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 290.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 7 sheets defined 48.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 36 through 44 removed outlier: 3.599A pdb=" N LEU A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE A 42 " --> pdb=" O TYR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 54 through 72 removed outlier: 4.111A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 102 removed outlier: 3.627A pdb=" N VAL A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 127 removed outlier: 3.886A pdb=" N VAL A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.754A pdb=" N VAL A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.564A pdb=" N TYR A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 removed outlier: 3.515A pdb=" N SER A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 removed outlier: 4.200A pdb=" N GLY A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 221 removed outlier: 3.682A pdb=" N THR A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 233 removed outlier: 3.639A pdb=" N ALA A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.888A pdb=" N LYS A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 4.037A pdb=" N GLY A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.690A pdb=" N CYS A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 294 removed outlier: 3.860A pdb=" N TRP A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 316 removed outlier: 3.752A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.541A pdb=" N ASN A 324 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 325 " --> pdb=" O PHE A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 325' Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.866A pdb=" N LYS A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 4.377A pdb=" N VAL A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.623A pdb=" N GLY A 464 " --> pdb=" O ILE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.575A pdb=" N GLU A 474 " --> pdb=" O MET A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 512 through 520 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.774A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 3.811A pdb=" N THR A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 605 removed outlier: 3.520A pdb=" N GLU A 603 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 632 removed outlier: 3.922A pdb=" N HIS A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.658A pdb=" N THR A 666 " --> pdb=" O THR A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.583A pdb=" N ARG A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 677 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 689 Processing helix chain 'A' and resid 700 through 715 removed outlier: 3.552A pdb=" N ALA A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 Processing helix chain 'A' and resid 739 through 751 removed outlier: 3.530A pdb=" N GLY A 743 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN A 748 " --> pdb=" O ALA A 744 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 751 " --> pdb=" O ILE A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 758 removed outlier: 3.523A pdb=" N ASN A 758 " --> pdb=" O ILE A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 772 removed outlier: 3.620A pdb=" N ARG A 764 " --> pdb=" O THR A 760 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA A 770 " --> pdb=" O MET A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 4.116A pdb=" N PHE A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 780 " --> pdb=" O VAL A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 780' Processing helix chain 'A' and resid 800 through 805 removed outlier: 3.510A pdb=" N ILE A 804 " --> pdb=" O VAL A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 813 Processing helix chain 'A' and resid 813 through 818 Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.874A pdb=" N GLU A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 853 Proline residue: A 841 - end of helix removed outlier: 3.795A pdb=" N ASN A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLN A 851 " --> pdb=" O ASN A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 865 removed outlier: 4.261A pdb=" N ALA A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 860 through 865' Processing helix chain 'A' and resid 866 through 873 removed outlier: 3.911A pdb=" N ILE A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 872 " --> pdb=" O THR A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 883 Processing helix chain 'A' and resid 884 through 886 No H-bonds generated for 'chain 'A' and resid 884 through 886' Processing helix chain 'A' and resid 887 through 892 removed outlier: 3.811A pdb=" N ILE A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 892' Processing helix chain 'A' and resid 900 through 921 removed outlier: 3.577A pdb=" N TYR A 908 " --> pdb=" O LYS A 904 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER A 910 " --> pdb=" O SER A 906 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 removed outlier: 3.825A pdb=" N TYR A 925 " --> pdb=" O GLN A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 941 removed outlier: 3.656A pdb=" N ILE A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 932 " --> pdb=" O GLU A 928 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 959 Processing helix chain 'A' and resid 959 through 967 removed outlier: 3.746A pdb=" N ALA A 964 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 975 removed outlier: 3.821A pdb=" N ILE A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1059 removed outlier: 3.580A pdb=" N ILE A1058 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A1059 " --> pdb=" O ILE A1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1054 through 1059' Processing helix chain 'A' and resid 1084 through 1086 No H-bonds generated for 'chain 'A' and resid 1084 through 1086' Processing helix chain 'A' and resid 1117 through 1123 Processing helix chain 'A' and resid 1127 through 1133 Processing helix chain 'A' and resid 1150 through 1165 removed outlier: 3.676A pdb=" N GLN A1155 " --> pdb=" O GLY A1151 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG A1156 " --> pdb=" O GLY A1152 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A1157 " --> pdb=" O GLN A1153 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A1160 " --> pdb=" O ARG A1156 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A1162 " --> pdb=" O ALA A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.670A pdb=" N ARG A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1240 through 1247 removed outlier: 4.074A pdb=" N LEU A1244 " --> pdb=" O ALA A1240 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A1247 " --> pdb=" O ARG A1243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 371 removed outlier: 5.828A pdb=" N PHE A 367 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU A 425 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP A 369 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN A 423 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 421 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 558 through 559 removed outlier: 6.983A pdb=" N VAL A 398 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 399 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 574 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 573 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 443 through 445 removed outlier: 6.463A pdb=" N GLY A 444 " --> pdb=" O LEU A 526 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 525 " --> pdb=" O VAL A 556 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 645 through 647 removed outlier: 3.814A pdb=" N GLU A 655 " --> pdb=" O SER A 647 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1028 through 1034 removed outlier: 5.632A pdb=" N ARG A1029 " --> pdb=" O PHE A1017 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE A1017 " --> pdb=" O ARG A1029 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A1015 " --> pdb=" O PHE A1031 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LEU A1033 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ARG A1013 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1042 through 1043 removed outlier: 3.542A pdb=" N GLY A1089 " --> pdb=" O VAL A1169 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A1171 " --> pdb=" O GLY A1089 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1217 through 1220 removed outlier: 7.185A pdb=" N VAL A1218 " --> pdb=" O VAL A1225 " (cutoff:3.500A) 247 hydrogen bonds defined for protein. 708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3036 1.34 - 1.46: 1984 1.46 - 1.58: 4450 1.58 - 1.69: 10 1.69 - 1.81: 67 Bond restraints: 9547 Sorted by residual: bond pdb=" C4 ATP A1303 " pdb=" C5 ATP A1303 " ideal model delta sigma weight residual 1.388 1.484 -0.096 1.00e-02 1.00e+04 9.27e+01 bond pdb=" C5 ATP A1303 " pdb=" C6 ATP A1303 " ideal model delta sigma weight residual 1.409 1.497 -0.088 1.00e-02 1.00e+04 7.72e+01 bond pdb=" C4 ATP A1301 " pdb=" C5 ATP A1301 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C5 ATP A1301 " pdb=" C6 ATP A1301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C8 ATP A1301 " pdb=" N7 ATP A1301 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.19e+01 ... (remaining 9542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.33: 12891 6.33 - 12.65: 36 12.65 - 18.97: 6 18.97 - 25.30: 1 25.30 - 31.62: 1 Bond angle restraints: 12935 Sorted by residual: angle pdb=" C ALA A 858 " pdb=" CA ALA A 858 " pdb=" CB ALA A 858 " ideal model delta sigma weight residual 111.72 80.10 31.62 1.53e+00 4.27e-01 4.27e+02 angle pdb=" PB ATP A1303 " pdb=" O3B ATP A1303 " pdb=" PG ATP A1303 " ideal model delta sigma weight residual 139.87 121.66 18.21 1.00e+00 1.00e+00 3.31e+02 angle pdb=" N GLY A 859 " pdb=" CA GLY A 859 " pdb=" C GLY A 859 " ideal model delta sigma weight residual 111.36 131.39 -20.03 1.17e+00 7.31e-01 2.93e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 121.87 14.96 1.00e+00 1.00e+00 2.24e+02 angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 125.15 14.72 1.00e+00 1.00e+00 2.17e+02 ... (remaining 12930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 5414 16.88 - 33.77: 221 33.77 - 50.65: 44 50.65 - 67.53: 3 67.53 - 84.42: 13 Dihedral angle restraints: 5695 sinusoidal: 2207 harmonic: 3488 Sorted by residual: dihedral pdb=" C ALA A 858 " pdb=" N ALA A 858 " pdb=" CA ALA A 858 " pdb=" CB ALA A 858 " ideal model delta harmonic sigma weight residual -122.60 -84.68 -37.92 0 2.50e+00 1.60e-01 2.30e+02 dihedral pdb=" C SER A 681 " pdb=" N SER A 681 " pdb=" CA SER A 681 " pdb=" CB SER A 681 " ideal model delta harmonic sigma weight residual -122.60 -152.43 29.83 0 2.50e+00 1.60e-01 1.42e+02 dihedral pdb=" N SER A 681 " pdb=" C SER A 681 " pdb=" CA SER A 681 " pdb=" CB SER A 681 " ideal model delta harmonic sigma weight residual 122.80 148.70 -25.90 0 2.50e+00 1.60e-01 1.07e+02 ... (remaining 5692 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 1483 0.249 - 0.498: 1 0.498 - 0.747: 1 0.747 - 0.996: 0 0.996 - 1.245: 1 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CA SER A 681 " pdb=" N SER A 681 " pdb=" C SER A 681 " pdb=" CB SER A 681 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.87e+01 chirality pdb=" CA ALA A 858 " pdb=" N ALA A 858 " pdb=" C ALA A 858 " pdb=" CB ALA A 858 " both_signs ideal model delta sigma weight residual False 2.48 3.06 -0.57 2.00e-01 2.50e+01 8.25e+00 chirality pdb=" CA GLU A 449 " pdb=" N GLU A 449 " pdb=" C GLU A 449 " pdb=" CB GLU A 449 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1483 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP A1303 " 0.009 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" C2 ATP A1303 " 0.003 2.00e-02 2.50e+03 pdb=" C4 ATP A1303 " -0.003 2.00e-02 2.50e+03 pdb=" C5 ATP A1303 " -0.056 2.00e-02 2.50e+03 pdb=" C6 ATP A1303 " 0.007 2.00e-02 2.50e+03 pdb=" C8 ATP A1303 " -0.002 2.00e-02 2.50e+03 pdb=" N1 ATP A1303 " 0.008 2.00e-02 2.50e+03 pdb=" N3 ATP A1303 " 0.000 2.00e-02 2.50e+03 pdb=" N6 ATP A1303 " 0.007 2.00e-02 2.50e+03 pdb=" N7 ATP A1303 " 0.028 2.00e-02 2.50e+03 pdb=" N9 ATP A1303 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 701 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.32e+00 pdb=" N PRO A 702 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 702 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 702 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 449 " -0.043 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO A 450 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 450 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 450 " -0.037 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 38 2.53 - 3.12: 6229 3.12 - 3.71: 13318 3.71 - 4.31: 19260 4.31 - 4.90: 31357 Nonbonded interactions: 70202 Sorted by model distance: nonbonded pdb=" O ALA A 858 " pdb=" CB ALA A 858 " model vdw 1.932 2.768 nonbonded pdb=" CZ TYR A1019 " pdb=" N7 ATP A1303 " model vdw 2.072 2.672 nonbonded pdb=" O1B ATP A1303 " pdb="MG MG A1304 " model vdw 2.141 2.170 nonbonded pdb=" O2G ATP A1303 " pdb="MG MG A1304 " model vdw 2.285 2.170 nonbonded pdb=" O3G ATP A1303 " pdb="MG MG A1304 " model vdw 2.290 2.170 ... (remaining 70197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.010 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.006 0.404 9550 Z= 0.519 Angle : 1.106 31.625 12935 Z= 0.705 Chirality : 0.063 1.245 1486 Planarity : 0.006 0.068 1640 Dihedral : 11.225 84.417 3467 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.50 (0.15), residues: 1213 helix: -4.85 (0.06), residues: 689 sheet: -2.87 (0.51), residues: 87 loop : -3.25 (0.23), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 295 TYR 0.015 0.002 TYR A1019 PHE 0.020 0.002 PHE A 752 TRP 0.022 0.002 TRP A 933 HIS 0.006 0.001 HIS A 937 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9547) covalent geometry : angle 1.10579 (12935) hydrogen bonds : bond 0.35450 ( 247) hydrogen bonds : angle 10.77429 ( 708) Misc. bond : bond 0.23512 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7978 (mttp) cc_final: 0.7585 (mmtt) REVERT: A 251 SER cc_start: 0.8596 (m) cc_final: 0.8368 (p) REVERT: A 365 ILE cc_start: 0.8373 (mm) cc_final: 0.8148 (mm) REVERT: A 961 ASN cc_start: 0.8611 (t0) cc_final: 0.8184 (t0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1039 time to fit residues: 25.5578 Evaluate side-chains 103 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS A 350 GLN A 442 GLN A 585 HIS A 748 GLN A 758 ASN A 784 HIS A 850 GLN A 878 ASN A 921 GLN A1039 HIS A1041 GLN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.178202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129928 restraints weight = 11336.808| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.17 r_work: 0.3029 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9550 Z= 0.143 Angle : 0.637 7.490 12935 Z= 0.348 Chirality : 0.043 0.147 1486 Planarity : 0.005 0.047 1640 Dihedral : 9.252 79.497 1390 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.74 % Allowed : 6.64 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.30 (0.18), residues: 1213 helix: -3.85 (0.12), residues: 677 sheet: -2.41 (0.57), residues: 78 loop : -2.85 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1223 TYR 0.022 0.002 TYR A1019 PHE 0.016 0.002 PHE A 485 TRP 0.012 0.001 TRP A 684 HIS 0.004 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9547) covalent geometry : angle 0.63678 (12935) hydrogen bonds : bond 0.05783 ( 247) hydrogen bonds : angle 5.67033 ( 708) Misc. bond : bond 0.00489 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8457 (mttp) cc_final: 0.8011 (mtmm) REVERT: A 518 MET cc_start: 0.8493 (tpt) cc_final: 0.8284 (tpt) REVERT: A 604 MET cc_start: 0.5737 (ptt) cc_final: 0.4840 (mtp) REVERT: A 961 ASN cc_start: 0.9065 (t0) cc_final: 0.8622 (t0) REVERT: A 975 ARG cc_start: 0.8857 (tmm-80) cc_final: 0.8610 (ttm170) REVERT: A 1120 ASP cc_start: 0.8465 (m-30) cc_final: 0.8214 (m-30) outliers start: 17 outliers final: 8 residues processed: 125 average time/residue: 0.0892 time to fit residues: 15.1229 Evaluate side-chains 102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 43 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 448 GLN A 602 GLN A1128 HIS A1188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.177405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.129997 restraints weight = 11283.965| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.27 r_work: 0.3000 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9550 Z= 0.169 Angle : 0.624 9.515 12935 Z= 0.335 Chirality : 0.044 0.177 1486 Planarity : 0.005 0.146 1640 Dihedral : 8.784 81.003 1390 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.33 % Allowed : 8.27 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.52 (0.20), residues: 1213 helix: -3.10 (0.16), residues: 662 sheet: -2.03 (0.59), residues: 76 loop : -2.76 (0.24), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 653 TYR 0.012 0.002 TYR A1019 PHE 0.023 0.002 PHE A 69 TRP 0.011 0.001 TRP A 684 HIS 0.005 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9547) covalent geometry : angle 0.62396 (12935) hydrogen bonds : bond 0.04966 ( 247) hydrogen bonds : angle 5.06196 ( 708) Misc. bond : bond 0.00311 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.204 Fit side-chains REVERT: A 22 GLN cc_start: 0.8405 (mm110) cc_final: 0.8089 (tp40) REVERT: A 35 LYS cc_start: 0.8491 (mttp) cc_final: 0.8052 (mtmm) REVERT: A 604 MET cc_start: 0.5671 (ptt) cc_final: 0.4861 (mtp) REVERT: A 815 MET cc_start: 0.8425 (mmt) cc_final: 0.8178 (mmp) REVERT: A 961 ASN cc_start: 0.9089 (t0) cc_final: 0.8639 (t0) REVERT: A 975 ARG cc_start: 0.8939 (tmm-80) cc_final: 0.8633 (ttm170) REVERT: A 1007 ARG cc_start: 0.7459 (ptt90) cc_final: 0.7135 (ptt90) REVERT: A 1223 ARG cc_start: 0.8138 (ttt90) cc_final: 0.7728 (ttm110) outliers start: 13 outliers final: 10 residues processed: 109 average time/residue: 0.0859 time to fit residues: 12.5661 Evaluate side-chains 102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.0170 chunk 8 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.177652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124155 restraints weight = 11528.722| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.96 r_work: 0.3060 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9550 Z= 0.116 Angle : 0.556 6.415 12935 Z= 0.300 Chirality : 0.042 0.140 1486 Planarity : 0.011 0.418 1640 Dihedral : 8.625 84.403 1390 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.02 % Allowed : 9.50 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.01 (0.21), residues: 1213 helix: -2.63 (0.17), residues: 660 sheet: -1.95 (0.59), residues: 77 loop : -2.60 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 653 TYR 0.011 0.001 TYR A1019 PHE 0.017 0.001 PHE A 485 TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9547) covalent geometry : angle 0.55592 (12935) hydrogen bonds : bond 0.03756 ( 247) hydrogen bonds : angle 4.66295 ( 708) Misc. bond : bond 0.00463 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8561 (mttp) cc_final: 0.7951 (mtmm) REVERT: A 391 PRO cc_start: 0.7876 (Cg_exo) cc_final: 0.7487 (Cg_endo) REVERT: A 470 MET cc_start: 0.7687 (tpp) cc_final: 0.7245 (tpt) REVERT: A 604 MET cc_start: 0.5984 (ptt) cc_final: 0.5109 (mtp) REVERT: A 961 ASN cc_start: 0.8958 (t0) cc_final: 0.8505 (t0) REVERT: A 975 ARG cc_start: 0.8829 (tmm-80) cc_final: 0.8549 (ttm170) REVERT: A 1007 ARG cc_start: 0.7503 (ptt90) cc_final: 0.7176 (ptt90) REVERT: A 1193 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8430 (mtm-85) REVERT: A 1198 ARG cc_start: 0.8196 (mtt-85) cc_final: 0.7553 (mtt-85) outliers start: 10 outliers final: 6 residues processed: 116 average time/residue: 0.0892 time to fit residues: 13.9516 Evaluate side-chains 103 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 972 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 51 optimal weight: 30.0000 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.172130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118638 restraints weight = 11634.299| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.04 r_work: 0.2997 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9550 Z= 0.221 Angle : 0.635 7.219 12935 Z= 0.337 Chirality : 0.045 0.144 1486 Planarity : 0.004 0.050 1640 Dihedral : 8.494 85.020 1390 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.63 % Allowed : 9.91 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.85 (0.21), residues: 1213 helix: -2.51 (0.18), residues: 658 sheet: -1.89 (0.58), residues: 76 loop : -2.53 (0.25), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 653 TYR 0.013 0.002 TYR A1108 PHE 0.031 0.002 PHE A 69 TRP 0.009 0.002 TRP A 185 HIS 0.003 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 9547) covalent geometry : angle 0.63478 (12935) hydrogen bonds : bond 0.05072 ( 247) hydrogen bonds : angle 4.83891 ( 708) Misc. bond : bond 0.00343 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.321 Fit side-chains REVERT: A 22 GLN cc_start: 0.8449 (mm110) cc_final: 0.8041 (tp40) REVERT: A 35 LYS cc_start: 0.8573 (mttp) cc_final: 0.8019 (mtmm) REVERT: A 604 MET cc_start: 0.6108 (ptt) cc_final: 0.5209 (mtp) REVERT: A 815 MET cc_start: 0.8460 (mmt) cc_final: 0.8225 (mmp) REVERT: A 874 GLU cc_start: 0.8171 (pt0) cc_final: 0.7897 (pt0) REVERT: A 961 ASN cc_start: 0.8983 (t0) cc_final: 0.8539 (t0) REVERT: A 975 ARG cc_start: 0.8952 (tmm-80) cc_final: 0.8618 (ttm170) REVERT: A 1007 ARG cc_start: 0.7561 (ptt90) cc_final: 0.7242 (ptt90) REVERT: A 1193 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.8458 (mtm-85) REVERT: A 1198 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7711 (mtt-85) outliers start: 16 outliers final: 14 residues processed: 109 average time/residue: 0.0957 time to fit residues: 14.0139 Evaluate side-chains 108 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.175645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121588 restraints weight = 11545.092| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.89 r_work: 0.3032 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9550 Z= 0.123 Angle : 0.557 7.548 12935 Z= 0.297 Chirality : 0.042 0.142 1486 Planarity : 0.003 0.048 1640 Dihedral : 8.188 89.046 1390 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.63 % Allowed : 10.11 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.22), residues: 1213 helix: -2.23 (0.18), residues: 667 sheet: -1.93 (0.55), residues: 86 loop : -2.36 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 653 TYR 0.012 0.001 TYR A 740 PHE 0.018 0.001 PHE A 309 TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9547) covalent geometry : angle 0.55671 (12935) hydrogen bonds : bond 0.03788 ( 247) hydrogen bonds : angle 4.56995 ( 708) Misc. bond : bond 0.00252 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.242 Fit side-chains REVERT: A 35 LYS cc_start: 0.8528 (mttp) cc_final: 0.7994 (mtmm) REVERT: A 65 MET cc_start: 0.8439 (ttm) cc_final: 0.7993 (ttt) REVERT: A 430 GLU cc_start: 0.8507 (tt0) cc_final: 0.7984 (tp30) REVERT: A 470 MET cc_start: 0.7655 (tpp) cc_final: 0.7351 (tpt) REVERT: A 604 MET cc_start: 0.6110 (ptt) cc_final: 0.5205 (mtp) REVERT: A 622 ARG cc_start: 0.5054 (ptt-90) cc_final: 0.4763 (ptt-90) REVERT: A 961 ASN cc_start: 0.8954 (t0) cc_final: 0.8506 (t0) REVERT: A 975 ARG cc_start: 0.8886 (tmm-80) cc_final: 0.8595 (ttm170) REVERT: A 1007 ARG cc_start: 0.7470 (ptt90) cc_final: 0.7193 (ptt90) REVERT: A 1161 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.6363 (mtt90) REVERT: A 1193 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8544 (mtm-85) REVERT: A 1198 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7663 (mtt-85) outliers start: 16 outliers final: 10 residues processed: 105 average time/residue: 0.0991 time to fit residues: 13.8519 Evaluate side-chains 102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1170 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 23 optimal weight: 0.4980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 119 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.176737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123347 restraints weight = 11503.778| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.00 r_work: 0.3036 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9550 Z= 0.103 Angle : 0.551 15.969 12935 Z= 0.286 Chirality : 0.041 0.143 1486 Planarity : 0.003 0.044 1640 Dihedral : 7.920 89.156 1390 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.94 % Allowed : 10.42 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.22), residues: 1213 helix: -1.89 (0.19), residues: 664 sheet: -1.60 (0.56), residues: 86 loop : -2.30 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 217 TYR 0.011 0.001 TYR A 740 PHE 0.017 0.001 PHE A 309 TRP 0.009 0.001 TRP A 684 HIS 0.001 0.000 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 9547) covalent geometry : angle 0.55121 (12935) hydrogen bonds : bond 0.03341 ( 247) hydrogen bonds : angle 4.37313 ( 708) Misc. bond : bond 0.00262 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8560 (mttp) cc_final: 0.8005 (mtmm) REVERT: A 65 MET cc_start: 0.8458 (ttm) cc_final: 0.7946 (ttt) REVERT: A 351 ASP cc_start: 0.8220 (m-30) cc_final: 0.7997 (t0) REVERT: A 430 GLU cc_start: 0.8536 (tt0) cc_final: 0.8017 (tp30) REVERT: A 470 MET cc_start: 0.7605 (tpp) cc_final: 0.7230 (tpt) REVERT: A 604 MET cc_start: 0.5864 (ptt) cc_final: 0.4938 (mtp) REVERT: A 622 ARG cc_start: 0.5016 (ptt-90) cc_final: 0.4730 (ptt-90) REVERT: A 961 ASN cc_start: 0.8970 (t0) cc_final: 0.8530 (t0) REVERT: A 975 ARG cc_start: 0.8984 (tmm-80) cc_final: 0.8770 (ttm170) REVERT: A 1007 ARG cc_start: 0.7478 (ptt90) cc_final: 0.7262 (ptt90) REVERT: A 1070 MET cc_start: 0.7604 (tpp) cc_final: 0.7393 (tpp) REVERT: A 1161 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7552 (mtm-85) REVERT: A 1193 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8507 (mtm-85) REVERT: A 1198 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7632 (mtt-85) outliers start: 19 outliers final: 9 residues processed: 108 average time/residue: 0.0906 time to fit residues: 12.8605 Evaluate side-chains 99 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1161 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.173890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.119543 restraints weight = 11441.215| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.88 r_work: 0.3015 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9550 Z= 0.157 Angle : 0.597 14.864 12935 Z= 0.307 Chirality : 0.043 0.143 1486 Planarity : 0.003 0.047 1640 Dihedral : 7.948 84.730 1390 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.74 % Allowed : 10.52 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.23), residues: 1213 helix: -1.84 (0.19), residues: 666 sheet: -1.57 (0.57), residues: 86 loop : -2.24 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1223 TYR 0.013 0.001 TYR A 740 PHE 0.022 0.001 PHE A 309 TRP 0.008 0.001 TRP A 684 HIS 0.002 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9547) covalent geometry : angle 0.59733 (12935) hydrogen bonds : bond 0.04181 ( 247) hydrogen bonds : angle 4.50026 ( 708) Misc. bond : bond 0.00243 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.206 Fit side-chains REVERT: A 35 LYS cc_start: 0.8578 (mttp) cc_final: 0.8025 (mtmm) REVERT: A 65 MET cc_start: 0.8471 (ttm) cc_final: 0.8009 (ttt) REVERT: A 430 GLU cc_start: 0.8514 (tt0) cc_final: 0.7976 (tp30) REVERT: A 470 MET cc_start: 0.7664 (tpp) cc_final: 0.7306 (tpt) REVERT: A 604 MET cc_start: 0.5909 (ptt) cc_final: 0.4936 (mtp) REVERT: A 622 ARG cc_start: 0.5045 (ptt-90) cc_final: 0.4723 (ptt-90) REVERT: A 874 GLU cc_start: 0.8183 (pt0) cc_final: 0.7755 (pt0) REVERT: A 961 ASN cc_start: 0.8986 (t0) cc_final: 0.8551 (t0) REVERT: A 975 ARG cc_start: 0.8992 (tmm-80) cc_final: 0.8788 (ttm170) REVERT: A 1007 ARG cc_start: 0.7703 (ptt90) cc_final: 0.7393 (ptt90) REVERT: A 1161 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.6484 (mtt90) REVERT: A 1191 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7116 (pp) REVERT: A 1193 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8564 (mtm-85) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 0.0872 time to fit residues: 12.6733 Evaluate side-chains 104 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1071 ILE Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1195 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 51 optimal weight: 20.0000 chunk 5 optimal weight: 0.0040 chunk 115 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 102 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.173150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119264 restraints weight = 11449.186| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.88 r_work: 0.2995 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9550 Z= 0.169 Angle : 0.605 14.466 12935 Z= 0.310 Chirality : 0.043 0.177 1486 Planarity : 0.003 0.047 1640 Dihedral : 7.929 86.372 1390 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.63 % Allowed : 10.83 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.05 (0.23), residues: 1213 helix: -1.82 (0.19), residues: 666 sheet: -1.64 (0.57), residues: 88 loop : -2.18 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1223 TYR 0.013 0.001 TYR A 740 PHE 0.021 0.002 PHE A 69 TRP 0.008 0.001 TRP A 684 HIS 0.002 0.001 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9547) covalent geometry : angle 0.60548 (12935) hydrogen bonds : bond 0.04232 ( 247) hydrogen bonds : angle 4.53759 ( 708) Misc. bond : bond 0.00226 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.284 Fit side-chains REVERT: A 35 LYS cc_start: 0.8580 (mttp) cc_final: 0.8024 (mtmm) REVERT: A 65 MET cc_start: 0.8416 (ttm) cc_final: 0.7937 (ttt) REVERT: A 430 GLU cc_start: 0.8512 (tt0) cc_final: 0.7971 (tp30) REVERT: A 470 MET cc_start: 0.7709 (tpp) cc_final: 0.7393 (tpt) REVERT: A 604 MET cc_start: 0.5907 (ptt) cc_final: 0.4981 (mtp) REVERT: A 622 ARG cc_start: 0.5006 (ptt-90) cc_final: 0.4715 (ptt-90) REVERT: A 815 MET cc_start: 0.8562 (mmt) cc_final: 0.8356 (mmp) REVERT: A 874 GLU cc_start: 0.8141 (pt0) cc_final: 0.7719 (pt0) REVERT: A 961 ASN cc_start: 0.8980 (t0) cc_final: 0.8547 (t0) REVERT: A 975 ARG cc_start: 0.9016 (tmm-80) cc_final: 0.8804 (ttm170) REVERT: A 1007 ARG cc_start: 0.7608 (ptt90) cc_final: 0.7403 (ptt90) REVERT: A 1161 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6466 (mtt90) REVERT: A 1191 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6959 (pp) outliers start: 16 outliers final: 14 residues processed: 106 average time/residue: 0.0998 time to fit residues: 14.0730 Evaluate side-chains 107 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1111 ASP Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1195 MET Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 79 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 GLN ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.176082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122274 restraints weight = 11473.406| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.96 r_work: 0.3038 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9550 Z= 0.112 Angle : 0.570 14.476 12935 Z= 0.292 Chirality : 0.042 0.164 1486 Planarity : 0.003 0.045 1640 Dihedral : 7.703 88.178 1390 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.43 % Allowed : 11.03 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.23), residues: 1213 helix: -1.66 (0.20), residues: 664 sheet: -1.50 (0.58), residues: 88 loop : -2.15 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 217 TYR 0.012 0.001 TYR A 740 PHE 0.025 0.001 PHE A 372 TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A 784 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9547) covalent geometry : angle 0.57029 (12935) hydrogen bonds : bond 0.03523 ( 247) hydrogen bonds : angle 4.43467 ( 708) Misc. bond : bond 0.00203 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.234 Fit side-chains REVERT: A 35 LYS cc_start: 0.8575 (mttp) cc_final: 0.8025 (mtmm) REVERT: A 65 MET cc_start: 0.8472 (ttm) cc_final: 0.8185 (ttt) REVERT: A 418 ASP cc_start: 0.8339 (m-30) cc_final: 0.8055 (t0) REVERT: A 430 GLU cc_start: 0.8542 (tt0) cc_final: 0.8037 (tp30) REVERT: A 470 MET cc_start: 0.7695 (tpp) cc_final: 0.7374 (tpt) REVERT: A 604 MET cc_start: 0.5908 (ptt) cc_final: 0.4983 (mtp) REVERT: A 622 ARG cc_start: 0.4971 (ptt-90) cc_final: 0.4667 (ptt-90) REVERT: A 874 GLU cc_start: 0.8118 (pt0) cc_final: 0.7763 (pt0) REVERT: A 961 ASN cc_start: 0.8989 (t0) cc_final: 0.8548 (t0) REVERT: A 1001 ASP cc_start: 0.8331 (t70) cc_final: 0.7900 (t0) REVERT: A 1007 ARG cc_start: 0.7716 (ptt90) cc_final: 0.7459 (ptt90) REVERT: A 1161 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7523 (mtm-85) REVERT: A 1191 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7048 (pp) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.0905 time to fit residues: 13.0756 Evaluate side-chains 105 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1191 LEU Chi-restraints excluded: chain A residue 1195 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 70 optimal weight: 0.0670 chunk 45 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123231 restraints weight = 11347.675| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.99 r_work: 0.3006 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9550 Z= 0.122 Angle : 0.575 14.266 12935 Z= 0.294 Chirality : 0.042 0.162 1486 Planarity : 0.003 0.044 1640 Dihedral : 7.611 88.527 1390 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.53 % Allowed : 10.83 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.23), residues: 1213 helix: -1.59 (0.20), residues: 664 sheet: -1.39 (0.59), residues: 88 loop : -2.17 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1223 TYR 0.012 0.001 TYR A 740 PHE 0.018 0.001 PHE A 309 TRP 0.009 0.001 TRP A 684 HIS 0.001 0.000 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9547) covalent geometry : angle 0.57512 (12935) hydrogen bonds : bond 0.03700 ( 247) hydrogen bonds : angle 4.46108 ( 708) Misc. bond : bond 0.00204 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1993.81 seconds wall clock time: 34 minutes 39.66 seconds (2079.66 seconds total)