Starting phenix.real_space_refine on Sat Jul 20 01:00:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/07_2024/8wp0_37705_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/07_2024/8wp0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/07_2024/8wp0_37705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/07_2024/8wp0_37705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/07_2024/8wp0_37705_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wp0_37705/07_2024/8wp0_37705_neut.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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 5.59, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.7 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: 1.24 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: 3.06 Time building geometry restraints manager: 4.15 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: 80.10 - 92.38: 2 92.38 - 104.67: 116 104.67 - 116.96: 6337 116.96 - 129.25: 6429 129.25 - 141.54: 51 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: 1.38 - 2.08: 3 2.08 - 2.79: 2297 2.79 - 3.49: 11268 3.49 - 4.20: 20705 4.20 - 4.90: 35932 Nonbonded interactions: 70205 Sorted by model distance: nonbonded pdb=" CB ALA A 454 " pdb=" NH1 ARG A 653 " model vdw 1.379 3.540 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 ... (remaining 70200 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: 0.680 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 29.410 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.660 ------------------------------------------------------------------------------- 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 : 0.005 0.096 9547 Z= 0.315 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 : 1.379 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.006 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: 0.3066 time to fit residues: 74.5206 Evaluate side-chains 103 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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: 2.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN A 585 HIS A 602 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 9547 Z= 0.485 Angle : 0.776 8.574 12935 Z= 0.415 Chirality : 0.049 0.168 1486 Planarity : 0.006 0.052 1640 Dihedral : 9.562 80.052 1390 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 1.94 % Allowed : 7.15 % Favored : 90.91 % 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: -5.43 (0.18), residues: 1213 helix: -3.88 (0.12), residues: 692 sheet: -2.39 (0.55), residues: 76 loop : -2.98 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 933 HIS 0.004 0.001 HIS A 749 PHE 0.039 0.003 PHE A 69 TYR 0.017 0.003 TYR A1019 ARG 0.006 0.001 ARG A1161 *********************** 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 126 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.018 Fit side-chains REVERT: A 22 GLN cc_start: 0.7813 (mm110) cc_final: 0.7492 (tp40) REVERT: A 35 LYS cc_start: 0.7926 (mttp) cc_final: 0.7717 (mtmm) REVERT: A 365 ILE cc_start: 0.8556 (mm) cc_final: 0.8352 (mm) REVERT: A 381 MET cc_start: 0.7858 (tpp) cc_final: 0.7469 (mpp) REVERT: A 456 THR cc_start: 0.8859 (p) cc_final: 0.8537 (t) REVERT: A 604 MET cc_start: 0.5205 (ptt) cc_final: 0.4705 (mtp) REVERT: A 711 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7793 (mtm) REVERT: A 961 ASN cc_start: 0.8689 (t0) cc_final: 0.8281 (t0) REVERT: A 975 ARG cc_start: 0.8523 (tmm-80) cc_final: 0.8217 (ttm170) outliers start: 19 outliers final: 8 residues processed: 121 average time/residue: 0.2544 time to fit residues: 41.7618 Evaluate side-chains 107 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 711 MET Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 1111 ASP 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 61 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 GLN A 847 ASN A1080 ASN A1188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9547 Z= 0.156 Angle : 0.582 10.531 12935 Z= 0.311 Chirality : 0.041 0.143 1486 Planarity : 0.004 0.049 1640 Dihedral : 8.810 83.309 1390 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.02 % Allowed : 9.60 % Favored : 89.38 % 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: -3.10 (0.16), residues: 673 sheet: -1.77 (0.64), residues: 66 loop : -2.85 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 684 HIS 0.003 0.000 HIS A1128 PHE 0.017 0.001 PHE A 309 TYR 0.013 0.001 TYR A1019 ARG 0.005 0.000 ARG A1223 *********************** 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 114 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.933 Fit side-chains REVERT: A 22 GLN cc_start: 0.7778 (mm110) cc_final: 0.7472 (tp40) REVERT: A 35 LYS cc_start: 0.8003 (mttp) cc_final: 0.7748 (mtmm) REVERT: A 365 ILE cc_start: 0.8500 (mm) cc_final: 0.8282 (mm) REVERT: A 604 MET cc_start: 0.5165 (ptt) cc_final: 0.4595 (mtp) REVERT: A 653 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7352 (mtm110) REVERT: A 961 ASN cc_start: 0.8639 (t0) cc_final: 0.8221 (t0) REVERT: A 975 ARG cc_start: 0.8430 (tmm-80) cc_final: 0.8139 (ttm170) outliers start: 10 outliers final: 5 residues processed: 111 average time/residue: 0.2486 time to fit residues: 37.4555 Evaluate side-chains 102 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 972 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 9547 Z= 0.530 Angle : 0.747 8.653 12935 Z= 0.394 Chirality : 0.050 0.192 1486 Planarity : 0.005 0.054 1640 Dihedral : 9.036 82.790 1390 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 1.94 % Allowed : 10.83 % Favored : 87.23 % 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: -4.44 (0.20), residues: 1213 helix: -2.99 (0.16), residues: 672 sheet: -2.11 (0.57), residues: 76 loop : -2.77 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 684 HIS 0.004 0.001 HIS A 77 PHE 0.042 0.003 PHE A 69 TYR 0.017 0.002 TYR A 740 ARG 0.007 0.001 ARG A1198 *********************** 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 fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.031 Fit side-chains REVERT: A 22 GLN cc_start: 0.7927 (mm110) cc_final: 0.7726 (mp10) REVERT: A 35 LYS cc_start: 0.8050 (mttp) cc_final: 0.7728 (mtmm) REVERT: A 365 ILE cc_start: 0.8602 (mm) cc_final: 0.8382 (mm) REVERT: A 456 THR cc_start: 0.8895 (p) cc_final: 0.8540 (t) REVERT: A 604 MET cc_start: 0.5530 (ptt) cc_final: 0.4923 (mtp) REVERT: A 653 ARG cc_start: 0.7818 (mtm110) cc_final: 0.7566 (mtm110) REVERT: A 961 ASN cc_start: 0.8695 (t0) cc_final: 0.8221 (t0) REVERT: A 975 ARG cc_start: 0.8603 (tmm-80) cc_final: 0.8223 (ttm170) REVERT: A 1026 MET cc_start: 0.7111 (mmp) cc_final: 0.6902 (mmp) REVERT: A 1094 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6709 (tm-30) REVERT: A 1198 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7484 (mtt-85) outliers start: 19 outliers final: 14 residues processed: 111 average time/residue: 0.2457 time to fit residues: 37.1697 Evaluate side-chains 106 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 141 THR 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 554 THR 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 972 GLU Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1111 ASP 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 66 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9547 Z= 0.158 Angle : 0.550 6.651 12935 Z= 0.296 Chirality : 0.041 0.139 1486 Planarity : 0.003 0.049 1640 Dihedral : 8.414 89.998 1390 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.33 % Allowed : 11.64 % Favored : 87.03 % 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: -3.84 (0.21), residues: 1213 helix: -2.54 (0.17), residues: 672 sheet: -1.73 (0.66), residues: 65 loop : -2.45 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 684 HIS 0.003 0.001 HIS A1128 PHE 0.019 0.001 PHE A 309 TYR 0.013 0.001 TYR A 740 ARG 0.005 0.000 ARG A1198 *********************** 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 112 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.023 Fit side-chains REVERT: A 22 GLN cc_start: 0.7848 (mm110) cc_final: 0.7567 (mm-40) REVERT: A 35 LYS cc_start: 0.8028 (mttp) cc_final: 0.7785 (mtmm) REVERT: A 365 ILE cc_start: 0.8519 (mm) cc_final: 0.8295 (mm) REVERT: A 470 MET cc_start: 0.7364 (tpp) cc_final: 0.7026 (tpt) REVERT: A 604 MET cc_start: 0.5396 (ptt) cc_final: 0.4802 (mtp) REVERT: A 653 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7376 (mtm110) REVERT: A 961 ASN cc_start: 0.8651 (t0) cc_final: 0.8197 (t0) REVERT: A 975 ARG cc_start: 0.8517 (tmm-80) cc_final: 0.8178 (ttm170) REVERT: A 1094 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6642 (tm-30) REVERT: A 1198 ARG cc_start: 0.7890 (mtt-85) cc_final: 0.7381 (mtt-85) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.2524 time to fit residues: 37.7256 Evaluate side-chains 106 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 141 THR 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 972 GLU Chi-restraints excluded: chain A residue 1111 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 117 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9547 Z= 0.268 Angle : 0.587 7.360 12935 Z= 0.312 Chirality : 0.043 0.145 1486 Planarity : 0.003 0.050 1640 Dihedral : 8.364 89.082 1390 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.74 % Allowed : 11.64 % 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: -3.67 (0.22), residues: 1213 helix: -2.38 (0.18), residues: 666 sheet: -1.69 (0.67), residues: 65 loop : -2.42 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 684 HIS 0.003 0.001 HIS A 168 PHE 0.020 0.002 PHE A 69 TYR 0.015 0.001 TYR A 740 ARG 0.004 0.000 ARG A1198 *********************** 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 114 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7914 (mm110) cc_final: 0.7596 (mm-40) REVERT: A 35 LYS cc_start: 0.8055 (mttp) cc_final: 0.7749 (mtmm) REVERT: A 365 ILE cc_start: 0.8590 (mm) cc_final: 0.8367 (mm) REVERT: A 470 MET cc_start: 0.7436 (tpp) cc_final: 0.7213 (tpt) REVERT: A 604 MET cc_start: 0.5474 (ptt) cc_final: 0.4719 (mtp) REVERT: A 622 ARG cc_start: 0.4735 (ptt-90) cc_final: 0.4406 (ptt-90) REVERT: A 653 ARG cc_start: 0.7494 (mtm110) cc_final: 0.7276 (mtm110) REVERT: A 961 ASN cc_start: 0.8666 (t0) cc_final: 0.8215 (t0) REVERT: A 975 ARG cc_start: 0.8505 (tmm-80) cc_final: 0.8250 (ttm170) REVERT: A 1094 GLU cc_start: 0.6922 (tm-30) cc_final: 0.6619 (tm-30) outliers start: 17 outliers final: 15 residues processed: 109 average time/residue: 0.2688 time to fit residues: 39.8881 Evaluate side-chains 108 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 141 THR 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 554 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9547 Z= 0.142 Angle : 0.521 6.418 12935 Z= 0.279 Chirality : 0.041 0.155 1486 Planarity : 0.003 0.046 1640 Dihedral : 7.967 87.306 1390 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 1.74 % Allowed : 11.95 % Favored : 86.31 % 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: -3.28 (0.22), residues: 1213 helix: -2.00 (0.19), residues: 669 sheet: -1.76 (0.62), residues: 76 loop : -2.30 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 684 HIS 0.001 0.000 HIS A 168 PHE 0.018 0.001 PHE A 309 TYR 0.013 0.001 TYR A 740 ARG 0.005 0.000 ARG A1198 *********************** 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 118 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8010 (mttp) cc_final: 0.7727 (mtmm) REVERT: A 365 ILE cc_start: 0.8524 (mm) cc_final: 0.8275 (mm) REVERT: A 653 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7235 (mtm110) REVERT: A 961 ASN cc_start: 0.8625 (t0) cc_final: 0.8230 (t0) REVERT: A 1007 ARG cc_start: 0.6976 (ptt90) cc_final: 0.6499 (ptt90) REVERT: A 1094 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6717 (tm-30) REVERT: A 1191 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6809 (pp) outliers start: 17 outliers final: 9 residues processed: 115 average time/residue: 0.2753 time to fit residues: 42.8364 Evaluate side-chains 104 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 141 THR 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 972 GLU Chi-restraints excluded: chain A residue 1191 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 106 optimal weight: 0.3980 chunk 111 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9547 Z= 0.192 Angle : 0.563 12.910 12935 Z= 0.291 Chirality : 0.042 0.159 1486 Planarity : 0.003 0.047 1640 Dihedral : 7.917 87.877 1390 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.74 % Allowed : 12.16 % Favored : 86.11 % 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: -3.12 (0.23), residues: 1213 helix: -1.84 (0.19), residues: 664 sheet: -1.66 (0.63), residues: 76 loop : -2.29 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 684 HIS 0.003 0.000 HIS A 168 PHE 0.017 0.001 PHE A 309 TYR 0.014 0.001 TYR A 740 ARG 0.004 0.000 ARG A1198 *********************** 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 fitting. rotamer outliers: 17 poor density : 92 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8024 (mttp) cc_final: 0.7743 (mtmm) REVERT: A 365 ILE cc_start: 0.8563 (mm) cc_final: 0.8322 (mm) REVERT: A 961 ASN cc_start: 0.8605 (t0) cc_final: 0.8213 (t0) REVERT: A 1191 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6753 (pp) REVERT: A 1193 ARG cc_start: 0.8026 (ttp-110) cc_final: 0.7825 (mtm-85) outliers start: 17 outliers final: 12 residues processed: 104 average time/residue: 0.2655 time to fit residues: 37.9538 Evaluate side-chains 102 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 141 THR 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 554 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 972 GLU 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 111 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 0.0070 chunk 108 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9547 Z= 0.249 Angle : 0.596 11.399 12935 Z= 0.308 Chirality : 0.043 0.170 1486 Planarity : 0.003 0.047 1640 Dihedral : 7.962 87.763 1390 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.53 % Allowed : 12.77 % Favored : 85.70 % 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: -3.12 (0.23), residues: 1213 helix: -1.83 (0.19), residues: 660 sheet: -1.59 (0.63), residues: 76 loop : -2.33 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 684 HIS 0.003 0.001 HIS A 168 PHE 0.017 0.001 PHE A 69 TYR 0.014 0.001 TYR A 740 ARG 0.007 0.000 ARG A 653 *********************** 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 103 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.096 Fit side-chains REVERT: A 35 LYS cc_start: 0.8013 (mttp) cc_final: 0.7735 (mtmm) REVERT: A 365 ILE cc_start: 0.8561 (mm) cc_final: 0.8338 (mm) REVERT: A 381 MET cc_start: 0.7787 (tpp) cc_final: 0.7562 (mmt) REVERT: A 604 MET cc_start: 0.5581 (ptt) cc_final: 0.4840 (mtp) REVERT: A 961 ASN cc_start: 0.8624 (t0) cc_final: 0.8194 (t0) REVERT: A 1007 ARG cc_start: 0.6965 (ptt90) cc_final: 0.6455 (ptt90) REVERT: A 1191 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6888 (pp) REVERT: A 1193 ARG cc_start: 0.8092 (ttp-110) cc_final: 0.7798 (mtm-85) outliers start: 15 outliers final: 13 residues processed: 99 average time/residue: 0.2515 time to fit residues: 33.9839 Evaluate side-chains 102 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 141 THR 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 350 GLN Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 972 GLU 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 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 120 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 0.0870 chunk 58 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9547 Z= 0.122 Angle : 0.552 11.171 12935 Z= 0.283 Chirality : 0.040 0.146 1486 Planarity : 0.003 0.043 1640 Dihedral : 7.574 84.741 1390 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.23 % Allowed : 13.38 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 1213 helix: -1.49 (0.20), residues: 658 sheet: -1.51 (0.63), residues: 79 loop : -2.32 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 684 HIS 0.001 0.000 HIS A 749 PHE 0.018 0.001 PHE A 36 TYR 0.012 0.001 TYR A 740 ARG 0.004 0.000 ARG A1198 ********************** 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 103 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7999 (mttp) cc_final: 0.7747 (mtmm) REVERT: A 365 ILE cc_start: 0.8517 (mm) cc_final: 0.8280 (mm) REVERT: A 604 MET cc_start: 0.5390 (ptt) cc_final: 0.4844 (mtp) REVERT: A 653 ARG cc_start: 0.7606 (mtm110) cc_final: 0.7225 (mtm180) REVERT: A 961 ASN cc_start: 0.8568 (t0) cc_final: 0.8181 (t0) REVERT: A 1007 ARG cc_start: 0.7023 (ptt90) cc_final: 0.6476 (ptt90) REVERT: A 1191 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6800 (pp) REVERT: A 1193 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7801 (mtm-85) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 0.2470 time to fit residues: 33.6450 Evaluate side-chains 96 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 554 THR Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 972 GLU 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 88 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 0.0570 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.178221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131746 restraints weight = 11146.962| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.24 r_work: 0.3028 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9547 Z= 0.128 Angle : 0.542 11.383 12935 Z= 0.277 Chirality : 0.040 0.151 1486 Planarity : 0.003 0.046 1640 Dihedral : 7.415 84.820 1390 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.23 % Allowed : 13.48 % Favored : 85.29 % 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: -2.51 (0.23), residues: 1213 helix: -1.22 (0.20), residues: 652 sheet: -1.22 (0.64), residues: 77 loop : -2.23 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 684 HIS 0.002 0.000 HIS A 483 PHE 0.021 0.001 PHE A 309 TYR 0.012 0.001 TYR A 740 ARG 0.004 0.000 ARG A1198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.84 seconds wall clock time: 39 minutes 9.95 seconds (2349.95 seconds total)