Starting phenix.real_space_refine on Mon May 12 22:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wp0_37705/05_2025/8wp0_37705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wp0_37705/05_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_37705/05_2025/8wp0_37705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wp0_37705/05_2025/8wp0_37705.map" model { file = "/net/cci-nas-00/data/ceres_data/8wp0_37705/05_2025/8wp0_37705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wp0_37705/05_2025/8wp0_37705.cif" } resolution = 3.4 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= 0.005 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.54, per 1000 atoms: 0.59 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: 2.42 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.16 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: 2.84 Time building geometry restraints manager: 2.79 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.430 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.490 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.022 0.002 TRP A 933 HIS 0.006 0.001 HIS A 937 PHE 0.020 0.002 PHE A 752 TYR 0.015 0.002 TYR A1019 ARG 0.007 0.001 ARG A 295 Details of bonding type rmsd hydrogen bonds : bond 0.35450 ( 247) hydrogen bonds : angle 10.77429 ( 708) covalent geometry : bond 0.00474 ( 9547) covalent geometry : angle 1.10579 (12935) 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 : 1.026 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: 0.8149 (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: 0.2965 time to fit residues: 72.1353 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 : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 57 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- 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 602 GLN A 748 GLN A 758 ASN A 784 HIS A 850 GLN A 878 ASN A 921 GLN A1039 HIS A1041 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.178366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.130462 restraints weight = 11301.864| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.14 r_work: 0.3037 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9550 Z= 0.139 Angle : 0.632 7.361 12935 Z= 0.346 Chirality : 0.043 0.146 1486 Planarity : 0.005 0.047 1640 Dihedral : 9.247 79.569 1390 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.63 % Allowed : 6.54 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -5.25 (0.18), residues: 1213 helix: -3.82 (0.13), residues: 668 sheet: -2.42 (0.57), residues: 78 loop : -2.85 (0.24), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 684 HIS 0.004 0.001 HIS A1128 PHE 0.016 0.002 PHE A 752 TYR 0.020 0.001 TYR A1019 ARG 0.006 0.000 ARG A1223 Details of bonding type rmsd hydrogen bonds : bond 0.05895 ( 247) hydrogen bonds : angle 5.64281 ( 708) covalent geometry : bond 0.00302 ( 9547) covalent geometry : angle 0.63250 (12935) Misc. bond : bond 0.00364 ( 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 125 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8470 (mttp) cc_final: 0.8021 (mtmm) REVERT: A 518 MET cc_start: 0.8475 (tpt) cc_final: 0.8267 (tpt) REVERT: A 604 MET cc_start: 0.5683 (ptt) cc_final: 0.4816 (mtp) REVERT: A 961 ASN cc_start: 0.9060 (t0) cc_final: 0.8609 (t0) REVERT: A 975 ARG cc_start: 0.8823 (tmm-80) cc_final: 0.8575 (ttm170) REVERT: A 1120 ASP cc_start: 0.8460 (m-30) cc_final: 0.8205 (m-30) outliers start: 16 outliers final: 7 residues processed: 123 average time/residue: 0.2529 time to fit residues: 42.0975 Evaluate side-chains 98 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 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 105 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 52 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 A1128 HIS A1188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.176992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128609 restraints weight = 11295.068| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.25 r_work: 0.2979 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9550 Z= 0.161 Angle : 0.618 10.022 12935 Z= 0.331 Chirality : 0.043 0.182 1486 Planarity : 0.005 0.161 1640 Dihedral : 8.789 80.985 1390 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 1.12 % Allowed : 8.38 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.55 (0.20), residues: 1213 helix: -3.13 (0.16), residues: 661 sheet: -2.03 (0.58), residues: 76 loop : -2.78 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 684 HIS 0.005 0.001 HIS A1128 PHE 0.020 0.002 PHE A 69 TYR 0.013 0.002 TYR A1019 ARG 0.032 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 247) hydrogen bonds : angle 5.07796 ( 708) covalent geometry : bond 0.00371 ( 9547) covalent geometry : angle 0.61763 (12935) Misc. bond : bond 0.00344 ( 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 108 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8509 (mttp) cc_final: 0.8061 (mtmm) REVERT: A 604 MET cc_start: 0.5739 (ptt) cc_final: 0.4940 (mtp) REVERT: A 815 MET cc_start: 0.8514 (mmt) cc_final: 0.8253 (mmp) REVERT: A 961 ASN cc_start: 0.9102 (t0) cc_final: 0.8656 (t0) REVERT: A 975 ARG cc_start: 0.8937 (tmm-80) cc_final: 0.8630 (ttm170) REVERT: A 1007 ARG cc_start: 0.7412 (ptt90) cc_final: 0.6796 (ptt90) REVERT: A 1223 ARG cc_start: 0.8143 (ttt90) cc_final: 0.7739 (ttm110) outliers start: 11 outliers final: 7 residues processed: 105 average time/residue: 0.2669 time to fit residues: 37.9646 Evaluate side-chains 96 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 795 THR 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 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.0010 chunk 80 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.176519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127969 restraints weight = 11226.079| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.18 r_work: 0.2961 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9550 Z= 0.169 Angle : 0.592 6.355 12935 Z= 0.319 Chirality : 0.043 0.142 1486 Planarity : 0.004 0.048 1640 Dihedral : 8.563 83.115 1390 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.43 % Allowed : 9.30 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.11 (0.21), residues: 1213 helix: -2.73 (0.17), residues: 661 sheet: -1.91 (0.59), residues: 75 loop : -2.63 (0.24), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A 784 PHE 0.023 0.002 PHE A 69 TYR 0.011 0.002 TYR A 740 ARG 0.004 0.000 ARG A1198 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 247) hydrogen bonds : angle 4.82161 ( 708) covalent geometry : bond 0.00393 ( 9547) covalent geometry : angle 0.59222 (12935) Misc. bond : bond 0.00419 ( 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 112 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.034 Fit side-chains REVERT: A 35 LYS cc_start: 0.8570 (mttp) cc_final: 0.8043 (mtmm) REVERT: A 604 MET cc_start: 0.6025 (ptt) cc_final: 0.5127 (mtp) REVERT: A 653 ARG cc_start: 0.6519 (mtm-85) cc_final: 0.5921 (mtm-85) REVERT: A 961 ASN cc_start: 0.9093 (t0) cc_final: 0.8646 (t0) REVERT: A 975 ARG cc_start: 0.8903 (tmm-80) cc_final: 0.8598 (ttm170) REVERT: A 1007 ARG cc_start: 0.7560 (ptt90) cc_final: 0.7231 (ptt90) REVERT: A 1198 ARG cc_start: 0.8191 (mtt-85) cc_final: 0.7556 (mtt-85) outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 0.2545 time to fit residues: 37.4361 Evaluate side-chains 101 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 462 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1200 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 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 = 0.3976 r_free = 0.3976 target = 0.176126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.128543 restraints weight = 11202.966| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.20 r_work: 0.2973 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9550 Z= 0.177 Angle : 0.599 7.918 12935 Z= 0.320 Chirality : 0.044 0.159 1486 Planarity : 0.004 0.050 1640 Dihedral : 8.422 86.471 1390 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.43 % Allowed : 10.62 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.86 (0.21), residues: 1213 helix: -2.47 (0.18), residues: 662 sheet: -1.91 (0.59), residues: 76 loop : -2.59 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 185 HIS 0.002 0.001 HIS A 784 PHE 0.024 0.002 PHE A 69 TYR 0.012 0.002 TYR A 740 ARG 0.005 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 247) hydrogen bonds : angle 4.73772 ( 708) covalent geometry : bond 0.00419 ( 9547) covalent geometry : angle 0.59931 (12935) Misc. bond : bond 0.00277 ( 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 113 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.931 Fit side-chains REVERT: A 22 GLN cc_start: 0.8510 (mm110) cc_final: 0.8126 (tp40) REVERT: A 35 LYS cc_start: 0.8571 (mttp) cc_final: 0.7889 (pptt) REVERT: A 470 MET cc_start: 0.7611 (tpp) cc_final: 0.7161 (tpt) REVERT: A 604 MET cc_start: 0.6095 (ptt) cc_final: 0.5191 (mtp) REVERT: A 815 MET cc_start: 0.8483 (mmt) cc_final: 0.8219 (mmp) REVERT: A 961 ASN cc_start: 0.9105 (t0) cc_final: 0.8660 (t0) REVERT: A 975 ARG cc_start: 0.8989 (tmm-80) cc_final: 0.8663 (ttm170) REVERT: A 1007 ARG cc_start: 0.7524 (ptt90) cc_final: 0.7239 (ptt90) REVERT: A 1193 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8322 (mtm-85) REVERT: A 1198 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7581 (mtt-85) outliers start: 14 outliers final: 12 residues processed: 108 average time/residue: 0.2436 time to fit residues: 35.8041 Evaluate side-chains 103 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 795 THR Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1111 ASP 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 12 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 51 optimal weight: 30.0000 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 93 optimal weight: 0.0000 chunk 73 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 115 optimal weight: 0.0040 chunk 111 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.176896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122824 restraints weight = 11324.586| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.92 r_work: 0.3067 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9550 Z= 0.097 Angle : 0.543 12.460 12935 Z= 0.290 Chirality : 0.041 0.148 1486 Planarity : 0.005 0.156 1640 Dihedral : 8.097 89.810 1390 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.43 % Allowed : 10.42 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.40 (0.22), residues: 1213 helix: -2.07 (0.19), residues: 661 sheet: -1.97 (0.57), residues: 85 loop : -2.35 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 684 HIS 0.001 0.000 HIS A 784 PHE 0.017 0.001 PHE A 309 TYR 0.011 0.001 TYR A 169 ARG 0.013 0.000 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 247) hydrogen bonds : angle 4.43903 ( 708) covalent geometry : bond 0.00214 ( 9547) covalent geometry : angle 0.54268 (12935) Misc. bond : bond 0.00444 ( 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 115 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8318 (mm110) cc_final: 0.7975 (tp40) REVERT: A 35 LYS cc_start: 0.8525 (mttp) cc_final: 0.7726 (pptt) REVERT: A 65 MET cc_start: 0.8421 (ttm) cc_final: 0.7924 (ttt) REVERT: A 391 PRO cc_start: 0.7890 (Cg_exo) cc_final: 0.7516 (Cg_endo) REVERT: A 604 MET cc_start: 0.6012 (ptt) cc_final: 0.5079 (mtp) REVERT: A 961 ASN cc_start: 0.8935 (t0) cc_final: 0.8480 (t0) REVERT: A 975 ARG cc_start: 0.8897 (tmm-80) cc_final: 0.8652 (ttm170) REVERT: A 1007 ARG cc_start: 0.7461 (ptt90) cc_final: 0.7128 (ptt90) REVERT: A 1161 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7479 (mtm-85) REVERT: A 1193 ARG cc_start: 0.8642 (mmm-85) cc_final: 0.8365 (mtm-85) outliers start: 14 outliers final: 7 residues processed: 113 average time/residue: 0.2663 time to fit residues: 40.1492 Evaluate side-chains 104 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 380 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 1161 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 70 optimal weight: 0.0870 chunk 65 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.177070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.124297 restraints weight = 11480.861| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.03 r_work: 0.3063 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9550 Z= 0.104 Angle : 0.557 14.420 12935 Z= 0.292 Chirality : 0.041 0.130 1486 Planarity : 0.011 0.428 1640 Dihedral : 8.310 96.175 1390 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.63 % Allowed : 10.93 % Favored : 87.44 % 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: -3.10 (0.22), residues: 1213 helix: -1.79 (0.19), residues: 659 sheet: -1.78 (0.57), residues: 88 loop : -2.31 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 684 HIS 0.001 0.000 HIS A 784 PHE 0.016 0.001 PHE A 309 TYR 0.011 0.001 TYR A 740 ARG 0.037 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 247) hydrogen bonds : angle 4.32220 ( 708) covalent geometry : bond 0.00227 ( 9547) covalent geometry : angle 0.55743 (12935) Misc. bond : bond 0.00453 ( 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: 16 poor density : 96 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8561 (mttp) cc_final: 0.8003 (mtmm) REVERT: A 65 MET cc_start: 0.8462 (ttm) cc_final: 0.8152 (ttt) REVERT: A 351 ASP cc_start: 0.8211 (m-30) cc_final: 0.7984 (t0) REVERT: A 470 MET cc_start: 0.7430 (tpt) cc_final: 0.7209 (tpp) REVERT: A 604 MET cc_start: 0.5910 (ptt) cc_final: 0.4887 (mtp) REVERT: A 961 ASN cc_start: 0.8945 (t0) cc_final: 0.8504 (t0) REVERT: A 975 ARG cc_start: 0.8910 (tmm-80) cc_final: 0.8707 (ttm170) REVERT: A 1007 ARG cc_start: 0.7465 (ptt90) cc_final: 0.7233 (ptt90) REVERT: A 1070 MET cc_start: 0.7536 (tpp) cc_final: 0.7320 (tpp) REVERT: A 1161 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7562 (mtm-85) REVERT: A 1193 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8369 (mtm-85) REVERT: A 1198 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7721 (mtt-85) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 0.2935 time to fit residues: 43.3355 Evaluate side-chains 103 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 380 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 967 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.173801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.120706 restraints weight = 11534.176| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.11 r_work: 0.3004 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3578 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= 0.168 Angle : 0.623 14.810 12935 Z= 0.317 Chirality : 0.043 0.163 1486 Planarity : 0.006 0.194 1640 Dihedral : 8.050 89.860 1390 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.53 % Allowed : 11.75 % Favored : 86.72 % 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: -3.07 (0.23), residues: 1213 helix: -1.77 (0.19), residues: 659 sheet: -1.70 (0.56), residues: 89 loop : -2.30 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 684 HIS 0.002 0.001 HIS A 784 PHE 0.022 0.002 PHE A 69 TYR 0.012 0.001 TYR A 740 ARG 0.051 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 247) hydrogen bonds : angle 4.48299 ( 708) covalent geometry : bond 0.00394 ( 9547) covalent geometry : angle 0.62262 (12935) Misc. bond : bond 0.00455 ( 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 109 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.987 Fit side-chains REVERT: A 22 GLN cc_start: 0.8345 (mm110) cc_final: 0.7922 (tp40) REVERT: A 35 LYS cc_start: 0.8569 (mttp) cc_final: 0.7996 (mtmm) REVERT: A 65 MET cc_start: 0.8459 (ttm) cc_final: 0.8185 (ttt) REVERT: A 470 MET cc_start: 0.7443 (tpt) cc_final: 0.7235 (tpp) REVERT: A 604 MET cc_start: 0.5907 (ptt) cc_final: 0.4883 (mtp) REVERT: A 961 ASN cc_start: 0.8975 (t0) cc_final: 0.8549 (t0) REVERT: A 1007 ARG cc_start: 0.7701 (ptt90) cc_final: 0.7368 (ptt90) REVERT: A 1161 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.6418 (mtt90) REVERT: A 1191 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7148 (pp) REVERT: A 1193 ARG cc_start: 0.8667 (mmm-85) cc_final: 0.8445 (mtm-85) outliers start: 15 outliers final: 11 residues processed: 108 average time/residue: 0.2879 time to fit residues: 41.5594 Evaluate side-chains 102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 967 VAL 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 1111 ASP Chi-restraints excluded: chain A residue 1161 ARG Chi-restraints excluded: chain A residue 1191 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.174399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.120860 restraints weight = 11465.917| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.12 r_work: 0.2989 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3665 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 : 0.604 10.960 12935 Z= 0.312 Chirality : 0.043 0.172 1486 Planarity : 0.011 0.441 1640 Dihedral : 8.400 103.620 1390 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.63 % Allowed : 11.54 % Favored : 86.82 % 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: -2.98 (0.23), residues: 1213 helix: -1.72 (0.20), residues: 650 sheet: -1.58 (0.57), residues: 89 loop : -2.23 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.002 0.001 HIS A 784 PHE 0.021 0.002 PHE A 69 TYR 0.012 0.001 TYR A 740 ARG 0.020 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 247) hydrogen bonds : angle 4.52453 ( 708) covalent geometry : bond 0.00400 ( 9547) covalent geometry : angle 0.60406 (12935) Misc. bond : bond 0.00260 ( 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 105 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.024 Fit side-chains REVERT: A 35 LYS cc_start: 0.8599 (mttp) cc_final: 0.8029 (mtmm) REVERT: A 65 MET cc_start: 0.8529 (ttm) cc_final: 0.8056 (ttt) REVERT: A 470 MET cc_start: 0.7431 (tpt) cc_final: 0.7222 (tpp) REVERT: A 604 MET cc_start: 0.5901 (ptt) cc_final: 0.4931 (mtp) REVERT: A 961 ASN cc_start: 0.8999 (t0) cc_final: 0.8566 (t0) REVERT: A 1161 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6463 (mtt90) REVERT: A 1191 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7014 (pp) outliers start: 16 outliers final: 12 residues processed: 101 average time/residue: 0.2715 time to fit residues: 37.1010 Evaluate side-chains 98 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 795 THR Chi-restraints excluded: chain A residue 967 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 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 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.172678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.119148 restraints weight = 11564.251| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.01 r_work: 0.2974 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3712 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= 0.186 Angle : 0.629 10.456 12935 Z= 0.324 Chirality : 0.044 0.164 1486 Planarity : 0.011 0.440 1640 Dihedral : 8.352 95.477 1390 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.33 % Allowed : 11.85 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.99 (0.23), residues: 1213 helix: -1.75 (0.19), residues: 657 sheet: -1.54 (0.57), residues: 89 loop : -2.22 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.002 0.001 HIS A 784 PHE 0.024 0.002 PHE A 69 TYR 0.013 0.002 TYR A 740 ARG 0.029 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 247) hydrogen bonds : angle 4.61627 ( 708) covalent geometry : bond 0.00441 ( 9547) covalent geometry : angle 0.62916 (12935) Misc. bond : bond 0.00295 ( 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 101 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.448 Fit side-chains REVERT: A 35 LYS cc_start: 0.8560 (mttp) cc_final: 0.8009 (mtmm) REVERT: A 65 MET cc_start: 0.8400 (ttm) cc_final: 0.7914 (ttt) REVERT: A 470 MET cc_start: 0.7449 (tpt) cc_final: 0.7240 (tpp) REVERT: A 604 MET cc_start: 0.5861 (ptt) cc_final: 0.4967 (mtp) REVERT: A 815 MET cc_start: 0.8646 (mmt) cc_final: 0.8438 (mmp) REVERT: A 961 ASN cc_start: 0.8970 (t0) cc_final: 0.8538 (t0) REVERT: A 1161 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6424 (mtt90) REVERT: A 1191 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7140 (pp) outliers start: 13 outliers final: 11 residues processed: 98 average time/residue: 0.2660 time to fit residues: 35.7937 Evaluate side-chains 99 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 795 THR Chi-restraints excluded: chain A residue 967 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 1191 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 0.0060 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 878 ASN ** 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 = 0.3950 r_free = 0.3950 target = 0.173199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119826 restraints weight = 11495.636| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.19 r_work: 0.2966 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9550 Z= 0.163 Angle : 0.615 10.015 12935 Z= 0.317 Chirality : 0.043 0.157 1486 Planarity : 0.011 0.431 1640 Dihedral : 8.122 88.338 1390 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.43 % Allowed : 11.95 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (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: -2.92 (0.23), residues: 1213 helix: -1.69 (0.20), residues: 657 sheet: -1.44 (0.58), residues: 89 loop : -2.21 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 185 HIS 0.002 0.001 HIS A 784 PHE 0.020 0.002 PHE A 69 TYR 0.012 0.001 TYR A 740 ARG 0.027 0.001 ARG A 653 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 247) hydrogen bonds : angle 4.63782 ( 708) covalent geometry : bond 0.00384 ( 9547) covalent geometry : angle 0.61517 (12935) Misc. bond : bond 0.00326 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5324.97 seconds wall clock time: 92 minutes 43.64 seconds (5563.64 seconds total)