Starting phenix.real_space_refine (version: dev) on Fri May 13 00:02:05 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/05_2022/6c0v_7325_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/05_2022/6c0v_7325.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/6c0v_7325/05_2022/6c0v_7325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/05_2022/6c0v_7325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/05_2022/6c0v_7325_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/05_2022/6c0v_7325_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.189 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A GLU 393": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A GLU 899": "OE1" <-> "OE2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A GLU 1039": "OE1" <-> "OE2" Residue "A ARG 1047": "NH1" <-> "NH2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A ARG 1103": "NH1" <-> "NH2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A ARG 1222": "NH1" <-> "NH2" Residue "A ARG 1233": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 8976 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 8976 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4, 'peptide': 1154} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 26, 'TRANS': 1127, None: 4} Not linked: pdbres="GLY A1276 " pdbres="ATP A1301 " Not linked: pdbres="ATP A1301 " pdbres="ATP A1302 " Not linked: pdbres="ATP A1302 " pdbres=" MG A1303 " Not linked: pdbres=" MG A1303 " pdbres=" MG A1304 " Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 5.58, per 1000 atoms: 0.62 Number of scatterers: 8976 At special positions: 0 Unit cell: (79.8, 107.52, 141.96, 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 33 16.00 P 6 15.00 Mg 2 11.99 O 1650 8.00 N 1535 7.00 C 5750 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=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 5 sheets defined 64.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 45 through 79 removed outlier: 3.538A pdb=" N ALA A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) Proline residue: A 66 - end of helix removed outlier: 4.378A pdb=" N MET A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 72 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 156 removed outlier: 3.992A pdb=" N THR A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TRP A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 168 through 185 removed outlier: 3.866A pdb=" N ASN A 172 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 175 " --> pdb=" O ASN A 172 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 176 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP A 177 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 179 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 210 removed outlier: 3.574A pdb=" N PHE A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 204 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 259 removed outlier: 4.692A pdb=" N ILE A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER A 222 " --> pdb=" O ILE A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix removed outlier: 3.857A pdb=" N ALA A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 267 Processing helix chain 'A' and resid 270 through 323 removed outlier: 3.845A pdb=" N ASN A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N VAL A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 370 removed outlier: 3.564A pdb=" N THR A 333 " --> pdb=" O GLY A 329 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 3.648A pdb=" N ALA A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 463 through 469 removed outlier: 4.220A pdb=" N ILE A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 491 removed outlier: 4.569A pdb=" N GLY A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 533 through 547 removed outlier: 3.520A pdb=" N GLN A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 590 through 593 No H-bonds generated for 'chain 'A' and resid 590 through 593' Processing helix chain 'A' and resid 612 through 618 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 697 through 704 removed outlier: 3.881A pdb=" N LYS A 702 " --> pdb=" O TRP A 698 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 722 removed outlier: 3.545A pdb=" N ILE A 720 " --> pdb=" O PHE A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 739 removed outlier: 5.204A pdb=" N ALA A 729 " --> pdb=" O GLN A 725 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE A 730 " --> pdb=" O PRO A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 798 removed outlier: 4.035A pdb=" N ASN A 751 " --> pdb=" O LYS A 748 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A 752 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 759 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 762 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 767 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 769 " --> pdb=" O SER A 766 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE A 770 " --> pdb=" O PHE A 767 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A 771 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A 773 " --> pdb=" O PHE A 770 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 776 " --> pdb=" O GLN A 773 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 777 " --> pdb=" O GLY A 774 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 778 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 779 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 781 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 783 " --> pdb=" O ALA A 780 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 785 " --> pdb=" O GLU A 782 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS A 786 " --> pdb=" O ILE A 783 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 790 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 791 " --> pdb=" O LEU A 788 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A 793 " --> pdb=" O TYR A 790 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 796 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 797 " --> pdb=" O ARG A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 811 through 829 removed outlier: 3.560A pdb=" N ALA A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 852 removed outlier: 3.990A pdb=" N VAL A 835 " --> pdb=" O SER A 831 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE A 836 " --> pdb=" O ARG A 832 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 902 removed outlier: 4.172A pdb=" N ILE A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Proline residue: A 866 - end of helix removed outlier: 3.891A pdb=" N LEU A 884 " --> pdb=" O SER A 880 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 885 " --> pdb=" O GLY A 881 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 891 " --> pdb=" O LYS A 887 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 896 " --> pdb=" O GLY A 892 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 910 Processing helix chain 'A' and resid 914 through 966 removed outlier: 3.763A pdb=" N SER A 923 " --> pdb=" O MET A 919 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 924 " --> pdb=" O TYR A 920 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A 925 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.648A pdb=" N ALA A 935 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 949 " --> pdb=" O THR A 945 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 950 " --> pdb=" O GLN A 946 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 957 " --> pdb=" O TYR A 953 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 962 " --> pdb=" O ARG A 958 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA A 965 " --> pdb=" O ALA A 961 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS A 966 " --> pdb=" O TYR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 1013 removed outlier: 3.918A pdb=" N LEU A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 983 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY A 984 " --> pdb=" O ALA A 980 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 985 " --> pdb=" O VAL A 981 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N MET A 986 " --> pdb=" O VAL A 982 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA A 987 " --> pdb=" O PHE A 983 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 989 " --> pdb=" O ALA A 985 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 993 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Proline residue: A 996 - end of helix removed outlier: 3.769A pdb=" N ILE A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1083 Processing helix chain 'A' and resid 1106 through 1112 removed outlier: 3.507A pdb=" N ARG A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS A1112 " --> pdb=" O TRP A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1134 removed outlier: 4.101A pdb=" N GLY A1134 " --> pdb=" O ASN A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1152 removed outlier: 3.536A pdb=" N GLU A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1164 through 1166 No H-bonds generated for 'chain 'A' and resid 1164 through 1166' Processing helix chain 'A' and resid 1178 through 1190 Processing helix chain 'A' and resid 1208 through 1220 removed outlier: 3.724A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A1217 " --> pdb=" O VAL A1213 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A1218 " --> pdb=" O VAL A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 removed outlier: 4.042A pdb=" N ASN A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1262 Processing helix chain 'A' and resid 1266 through 1274 removed outlier: 3.606A pdb=" N VAL A1273 " --> pdb=" O SER A1269 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLN A1274 " --> pdb=" O MET A1270 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 391 through 395 Processing sheet with id= B, first strand: chain 'A' and resid 605 through 610 removed outlier: 6.366A pdb=" N GLY A 600 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 598 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 597 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR A 582 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU A 425 " --> pdb=" O THR A 582 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A 584 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1058 through 1060 removed outlier: 3.648A pdb=" N GLY A1038 " --> pdb=" O LYS A1093 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A1093 " --> pdb=" O GLY A1038 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1250 through 1255 removed outlier: 6.871A pdb=" N VAL A1245 " --> pdb=" O LYS A1252 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS A1254 " --> pdb=" O ILE A1243 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE A1243 " --> pdb=" O HIS A1254 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A1242 " --> pdb=" O THR A1065 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS A1227 " --> pdb=" O LEU A1066 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N LEU A1068 " --> pdb=" O CYS A1227 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A1229 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY A1114 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASP A1200 " --> pdb=" O GLY A1114 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A1116 " --> pdb=" O ASP A1200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1040 through 1042 removed outlier: 7.644A pdb=" N PHE A1042 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN A1054 " --> pdb=" O PHE A1042 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1260 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: 2.72 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2871 1.34 - 1.46: 968 1.46 - 1.58: 5230 1.58 - 1.69: 10 1.69 - 1.81: 59 Bond restraints: 9138 Sorted by residual: bond pdb=" C4 ATP A1301 " pdb=" C5 ATP A1301 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.55e+01 bond pdb=" C4 ATP A1302 " pdb=" C5 ATP A1302 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.53e+01 bond pdb=" C5 ATP A1302 " pdb=" C6 ATP A1302 " ideal model delta sigma weight residual 1.409 1.485 -0.076 1.00e-02 1.00e+04 5.76e+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 5.36e+01 bond pdb=" C8 ATP A1302 " pdb=" N7 ATP A1302 " ideal model delta sigma weight residual 1.310 1.359 -0.049 1.00e-02 1.00e+04 2.36e+01 ... (remaining 9133 not shown) Histogram of bond angle deviations from ideal: 99.98 - 107.34: 221 107.34 - 114.70: 5362 114.70 - 122.06: 4338 122.06 - 129.42: 2396 129.42 - 136.78: 48 Bond angle restraints: 12365 Sorted by residual: angle pdb=" PB ATP A1302 " pdb=" O3B ATP A1302 " pdb=" PG ATP A1302 " ideal model delta sigma weight residual 139.87 123.14 16.73 1.00e+00 1.00e+00 2.80e+02 angle pdb=" PA ATP A1302 " pdb=" O3A ATP A1302 " pdb=" PB ATP A1302 " ideal model delta sigma weight residual 136.83 120.48 16.35 1.00e+00 1.00e+00 2.67e+02 angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 123.74 16.13 1.00e+00 1.00e+00 2.60e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 122.78 14.05 1.00e+00 1.00e+00 1.97e+02 angle pdb=" C5 ATP A1301 " pdb=" C4 ATP A1301 " pdb=" N3 ATP A1301 " ideal model delta sigma weight residual 126.80 118.36 8.44 1.00e+00 1.00e+00 7.13e+01 ... (remaining 12360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.34: 4917 15.34 - 30.67: 364 30.67 - 46.01: 91 46.01 - 61.35: 32 61.35 - 76.68: 11 Dihedral angle restraints: 5415 sinusoidal: 2106 harmonic: 3309 Sorted by residual: dihedral pdb=" CA HIS A 518 " pdb=" C HIS A 518 " pdb=" N LYS A 519 " pdb=" CA LYS A 519 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS A 587 " pdb=" C HIS A 587 " pdb=" N ARG A 588 " pdb=" CA ARG A 588 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" C LYS A 619 " pdb=" N LYS A 619 " pdb=" CA LYS A 619 " pdb=" CB LYS A 619 " ideal model delta harmonic sigma weight residual -122.60 -131.27 8.67 0 2.50e+00 1.60e-01 1.20e+01 ... (remaining 5412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1019 0.059 - 0.119: 318 0.119 - 0.178: 74 0.178 - 0.237: 15 0.237 - 0.296: 2 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA LYS A 619 " pdb=" N LYS A 619 " pdb=" C LYS A 619 " pdb=" CB LYS A 619 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ILE A 585 " pdb=" N ILE A 585 " pdb=" C ILE A 585 " pdb=" CB ILE A 585 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASN A1248 " pdb=" N ASN A1248 " pdb=" C ASN A1248 " pdb=" CB ASN A1248 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1425 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO A 66 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 835 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" C VAL A 835 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL A 835 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 836 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 926 " -0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO A 927 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " -0.020 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 11 2.55 - 3.14: 6391 3.14 - 3.72: 12802 3.72 - 4.31: 17757 4.31 - 4.90: 29171 Nonbonded interactions: 66132 Sorted by model distance: nonbonded pdb=" OG SER A 434 " pdb="MG MG A1304 " model vdw 1.961 2.170 nonbonded pdb=" O2B ATP A1302 " pdb="MG MG A1303 " model vdw 2.004 2.170 nonbonded pdb=" O3G ATP A1301 " pdb="MG MG A1304 " model vdw 2.022 2.170 nonbonded pdb=" OE1 GLN A1118 " pdb="MG MG A1303 " model vdw 2.128 2.170 nonbonded pdb=" O2B ATP A1301 " pdb="MG MG A1304 " model vdw 2.133 2.170 ... (remaining 66127 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 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 33 5.16 5 C 5750 2.51 5 N 1535 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 2.490 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: 12.080 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.060 Process input model: 27.200 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.008 0.081 9138 Z= 0.499 Angle : 1.141 16.734 12365 Z= 0.832 Chirality : 0.061 0.296 1428 Planarity : 0.003 0.057 1555 Dihedral : 12.836 76.684 3291 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.00 % 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: -2.20 (0.20), residues: 1148 helix: -1.08 (0.16), residues: 687 sheet: -1.40 (0.59), residues: 71 loop : -1.90 (0.26), residues: 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2124 time to fit residues: 104.6625 Evaluate side-chains 213 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 441 GLN A 530 GLN A 535 GLN A 570 GLN A 725 GLN ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN A1248 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9138 Z= 0.209 Angle : 0.559 8.384 12365 Z= 0.297 Chirality : 0.040 0.232 1428 Planarity : 0.005 0.092 1555 Dihedral : 4.966 79.465 1244 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 4.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.23), residues: 1148 helix: 0.68 (0.18), residues: 717 sheet: -0.55 (0.65), residues: 73 loop : -1.58 (0.29), residues: 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 260 average time/residue: 0.1867 time to fit residues: 69.4891 Evaluate side-chains 215 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.0886 time to fit residues: 5.2080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 398 HIS A 725 GLN A 882 GLN ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9138 Z= 0.206 Angle : 0.536 7.203 12365 Z= 0.280 Chirality : 0.039 0.195 1428 Planarity : 0.004 0.063 1555 Dihedral : 4.756 79.990 1244 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.24), residues: 1148 helix: 1.05 (0.19), residues: 729 sheet: -0.27 (0.65), residues: 73 loop : -1.53 (0.29), residues: 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 219 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 228 average time/residue: 0.1812 time to fit residues: 59.6980 Evaluate side-chains 205 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 192 time to evaluate : 1.064 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0878 time to fit residues: 3.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.0770 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1238 GLN A1239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9138 Z= 0.166 Angle : 0.505 7.647 12365 Z= 0.259 Chirality : 0.038 0.150 1428 Planarity : 0.003 0.053 1555 Dihedral : 4.508 75.256 1244 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1148 helix: 1.32 (0.19), residues: 727 sheet: -0.14 (0.62), residues: 78 loop : -1.41 (0.30), residues: 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 221 average time/residue: 0.1786 time to fit residues: 58.0052 Evaluate side-chains 207 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 1.086 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.0870 time to fit residues: 2.8064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 GLN A 990 GLN A1175 GLN ** A1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 9138 Z= 0.324 Angle : 0.579 7.577 12365 Z= 0.303 Chirality : 0.040 0.171 1428 Planarity : 0.004 0.046 1555 Dihedral : 4.803 69.363 1244 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 3.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1148 helix: 1.13 (0.19), residues: 721 sheet: -0.03 (0.62), residues: 78 loop : -1.20 (0.31), residues: 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 196 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 27 residues processed: 213 average time/residue: 0.1816 time to fit residues: 55.9658 Evaluate side-chains 210 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0828 time to fit residues: 5.4079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 611 ASN A1258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9138 Z= 0.194 Angle : 0.510 7.599 12365 Z= 0.264 Chirality : 0.038 0.145 1428 Planarity : 0.003 0.043 1555 Dihedral : 4.478 63.463 1244 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1148 helix: 1.34 (0.19), residues: 723 sheet: 0.17 (0.64), residues: 78 loop : -1.20 (0.31), residues: 347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 211 average time/residue: 0.1812 time to fit residues: 56.2301 Evaluate side-chains 194 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0933 time to fit residues: 2.0457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 44 optimal weight: 0.0030 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9138 Z= 0.168 Angle : 0.512 7.377 12365 Z= 0.263 Chirality : 0.037 0.143 1428 Planarity : 0.003 0.041 1555 Dihedral : 4.299 62.913 1244 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 1.82 % 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: 0.89 (0.25), residues: 1148 helix: 1.43 (0.19), residues: 726 sheet: 0.42 (0.64), residues: 83 loop : -1.16 (0.31), residues: 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 204 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 210 average time/residue: 0.1786 time to fit residues: 54.9476 Evaluate side-chains 204 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 194 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0944 time to fit residues: 3.1171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 GLN ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9138 Z= 0.198 Angle : 0.556 8.783 12365 Z= 0.282 Chirality : 0.038 0.162 1428 Planarity : 0.003 0.040 1555 Dihedral : 4.310 61.701 1244 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1148 helix: 1.39 (0.19), residues: 726 sheet: 0.42 (0.63), residues: 83 loop : -1.09 (0.32), residues: 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 205 average time/residue: 0.1838 time to fit residues: 54.9943 Evaluate side-chains 189 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0867 time to fit residues: 2.4923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.6664 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9138 Z= 0.199 Angle : 0.562 8.714 12365 Z= 0.284 Chirality : 0.038 0.163 1428 Planarity : 0.003 0.039 1555 Dihedral : 4.310 62.237 1244 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1148 helix: 1.39 (0.19), residues: 719 sheet: 0.47 (0.63), residues: 83 loop : -0.80 (0.32), residues: 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 194 average time/residue: 0.1795 time to fit residues: 51.1838 Evaluate side-chains 195 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 188 time to evaluate : 1.012 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0910 time to fit residues: 2.5504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.6661 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 9138 Z= 0.202 Angle : 0.563 9.751 12365 Z= 0.287 Chirality : 0.038 0.147 1428 Planarity : 0.003 0.039 1555 Dihedral : 4.304 62.450 1244 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.25), residues: 1148 helix: 1.32 (0.19), residues: 727 sheet: 0.47 (0.63), residues: 83 loop : -0.85 (0.32), residues: 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 199 average time/residue: 0.1859 time to fit residues: 53.8953 Evaluate side-chains 195 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0861 time to fit residues: 2.1138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.0370 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.113538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096078 restraints weight = 18846.478| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.32 r_work: 0.3171 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work: 0.3154 rms_B_bonded: 3.05 restraints_weight: 0.1250 r_work: 0.3146 rms_B_bonded: 3.10 restraints_weight: 0.0625 r_work: 0.3137 rms_B_bonded: 3.17 restraints_weight: 0.0312 r_work: 0.3128 rms_B_bonded: 3.27 restraints_weight: 0.0156 r_work: 0.3118 rms_B_bonded: 3.39 restraints_weight: 0.0078 r_work: 0.3108 rms_B_bonded: 3.52 restraints_weight: 0.0039 r_work: 0.3098 rms_B_bonded: 3.68 restraints_weight: 0.0020 r_work: 0.3088 rms_B_bonded: 3.85 restraints_weight: 0.0010 r_work: 0.3077 rms_B_bonded: 4.04 restraints_weight: 0.0005 r_work: 0.3066 rms_B_bonded: 4.26 restraints_weight: 0.0002 r_work: 0.3055 rms_B_bonded: 4.49 restraints_weight: 0.0001 r_work: 0.3043 rms_B_bonded: 4.75 restraints_weight: 0.0001 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9138 Z= 0.181 Angle : 0.574 12.731 12365 Z= 0.286 Chirality : 0.037 0.162 1428 Planarity : 0.003 0.039 1555 Dihedral : 4.244 62.514 1244 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1148 helix: 1.38 (0.19), residues: 726 sheet: 0.51 (0.64), residues: 83 loop : -0.84 (0.32), residues: 339 =============================================================================== Job complete usr+sys time: 2098.76 seconds wall clock time: 38 minutes 34.96 seconds (2314.96 seconds total)