Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 04:05:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/04_2023/6c0v_7325_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/04_2023/6c0v_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_7325/04_2023/6c0v_7325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/04_2023/6c0v_7325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/04_2023/6c0v_7325_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/04_2023/6c0v_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 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. 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-1.21rc1-4938/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: {'peptide': 1154, 'undetermined': 4} 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: 5.46, per 1000 atoms: 0.61 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: 3.76 Conformation dependent library (CDL) restraints added in 1.9 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: 1.62 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: 3.26 Time building geometry restraints manager: 4.01 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 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: 7.710 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: 12.540 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 28.540 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 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 : 0.33 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 : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2299 time to fit residues: 112.8376 Evaluate side-chains 214 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5367 ------------------------------------------------------------------------------- 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: 0.6634 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9138 Z= 0.212 Angle : 0.562 8.228 12365 Z= 0.298 Chirality : 0.040 0.223 1428 Planarity : 0.004 0.032 1555 Dihedral : 4.944 78.659 1244 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 4.38 % 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: -0.20 (0.23), residues: 1148 helix: 0.68 (0.18), residues: 716 sheet: -0.56 (0.65), residues: 73 loop : -1.61 (0.29), residues: 359 *********************** 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 280 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 239 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 27 residues processed: 259 average time/residue: 0.1959 time to fit residues: 71.9920 Evaluate side-chains 216 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 189 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.0872 time to fit residues: 5.8271 ------------------------------------------------------------------------------- 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: 1.9990 chunk 86 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 398 HIS 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.3999 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= 0.179 Angle : 0.521 6.522 12365 Z= 0.271 Chirality : 0.038 0.159 1428 Planarity : 0.003 0.029 1555 Dihedral : 4.685 78.179 1244 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 2.56 % 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: 0.32 (0.24), residues: 1148 helix: 1.10 (0.19), residues: 729 sheet: -0.23 (0.65), residues: 73 loop : -1.55 (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 248 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 224 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 232 average time/residue: 0.1887 time to fit residues: 62.7181 Evaluate side-chains 210 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 198 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0917 time to fit residues: 3.5208 ------------------------------------------------------------------------------- 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: 0.7980 chunk 78 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 chunk 11 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 0.0770 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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: 0.6608 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 9138 Z= 0.152 Angle : 0.487 6.984 12365 Z= 0.251 Chirality : 0.037 0.146 1428 Planarity : 0.003 0.029 1555 Dihedral : 4.412 71.834 1244 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 2.46 % 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: 0.65 (0.24), residues: 1148 helix: 1.36 (0.19), residues: 726 sheet: -0.13 (0.63), residues: 78 loop : -1.43 (0.30), residues: 344 *********************** 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 241 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 1.189 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 226 average time/residue: 0.1854 time to fit residues: 61.0126 Evaluate side-chains 197 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1026 time to fit residues: 3.1065 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 9138 Z= 0.292 Angle : 0.559 7.705 12365 Z= 0.291 Chirality : 0.040 0.179 1428 Planarity : 0.003 0.032 1555 Dihedral : 4.645 67.408 1244 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 3.21 % 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: 0.71 (0.24), residues: 1148 helix: 1.27 (0.19), residues: 720 sheet: 0.17 (0.63), residues: 78 loop : -1.10 (0.31), residues: 350 *********************** 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 221 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 1.171 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 204 average time/residue: 0.1960 time to fit residues: 58.5216 Evaluate side-chains 201 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1001 time to fit residues: 5.7789 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ** A 882 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.4868 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= 0.181 Angle : 0.518 8.098 12365 Z= 0.264 Chirality : 0.037 0.145 1428 Planarity : 0.003 0.031 1555 Dihedral : 4.373 61.923 1244 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 1.50 % 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: 0.87 (0.25), residues: 1148 helix: 1.42 (0.19), residues: 726 sheet: 0.24 (0.63), residues: 78 loop : -1.13 (0.31), residues: 344 *********************** 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 215 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 1.055 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 208 average time/residue: 0.1885 time to fit residues: 56.5923 Evaluate side-chains 192 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 184 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0900 time to fit residues: 2.7448 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN A 990 GLN ** A1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9138 Z= 0.278 Angle : 0.564 7.821 12365 Z= 0.291 Chirality : 0.039 0.143 1428 Planarity : 0.003 0.031 1555 Dihedral : 4.567 61.603 1244 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 2.56 % 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: 0.81 (0.25), residues: 1148 helix: 1.30 (0.19), residues: 718 sheet: 0.28 (0.63), residues: 78 loop : -0.94 (0.32), residues: 352 *********************** 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 219 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 207 average time/residue: 0.1911 time to fit residues: 57.6614 Evaluate side-chains 199 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1049 time to fit residues: 4.9007 ------------------------------------------------------------------------------- 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: 0.5980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.0070 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 HIS A 856 GLN A1239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 9138 Z= 0.158 Angle : 0.522 7.886 12365 Z= 0.264 Chirality : 0.037 0.182 1428 Planarity : 0.003 0.031 1555 Dihedral : 4.331 63.577 1244 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % 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: 0.94 (0.25), residues: 1148 helix: 1.44 (0.19), residues: 729 sheet: 0.46 (0.63), residues: 83 loop : -1.10 (0.31), residues: 336 *********************** 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 222 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 214 time to evaluate : 1.027 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 218 average time/residue: 0.1891 time to fit residues: 59.2246 Evaluate side-chains 192 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0836 time to fit residues: 1.7931 ------------------------------------------------------------------------------- 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: 0.5980 chunk 106 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.1980 chunk 67 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 882 GLN ** A1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9138 Z= 0.175 Angle : 0.542 7.617 12365 Z= 0.273 Chirality : 0.038 0.151 1428 Planarity : 0.003 0.031 1555 Dihedral : 4.260 61.304 1244 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1148 helix: 1.47 (0.19), residues: 720 sheet: 0.54 (0.63), residues: 83 loop : -0.86 (0.32), residues: 345 *********************** 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 208 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 200 average time/residue: 0.1926 time to fit residues: 55.7625 Evaluate side-chains 193 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0936 time to fit residues: 2.5652 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9138 Z= 0.233 Angle : 0.566 8.047 12365 Z= 0.288 Chirality : 0.038 0.163 1428 Planarity : 0.003 0.031 1555 Dihedral : 4.408 62.474 1244 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 0.95 (0.25), residues: 1148 helix: 1.37 (0.19), residues: 726 sheet: 0.49 (0.63), residues: 83 loop : -0.88 (0.32), residues: 339 ********************** 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 199 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 197 average time/residue: 0.1934 time to fit residues: 55.4516 Evaluate side-chains 199 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.110 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1034 time to fit residues: 1.8664 ------------------------------------------------------------------------------- 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: 3.9990 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 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 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.093615 restraints weight = 18896.705| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.35 r_work: 0.3032 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9138 Z= 0.208 Angle : 0.559 7.613 12365 Z= 0.282 Chirality : 0.038 0.152 1428 Planarity : 0.003 0.032 1555 Dihedral : 4.382 63.627 1244 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1148 helix: 1.38 (0.19), residues: 726 sheet: 0.55 (0.63), residues: 83 loop : -0.82 (0.32), residues: 339 =============================================================================== Job complete usr+sys time: 2341.41 seconds wall clock time: 42 minutes 54.41 seconds (2574.41 seconds total)