Starting phenix.real_space_refine on Thu Mar 14 13:20:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/03_2024/6c0v_7325_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/03_2024/6c0v_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_7325/03_2024/6c0v_7325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/03_2024/6c0v_7325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/03_2024/6c0v_7325_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c0v_7325/03_2024/6c0v_7325_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.189 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-dev-5265/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: 5.05, per 1000 atoms: 0.56 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: 3.21 Conformation dependent library (CDL) restraints added in 1.7 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: 2.32 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: 2.66 Time building geometry restraints manager: 3.51 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 - 15.91: 4961 15.91 - 31.83: 383 31.83 - 47.74: 89 47.74 - 63.65: 32 63.65 - 79.57: 12 Dihedral angle restraints: 5477 sinusoidal: 2168 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 5474 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: 2.300 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: 0.000 Extract box with map and model: 11.830 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.260 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.360 ------------------------------------------------------------------------------- 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 : 13.350 79.566 3353 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 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 803 HIS 0.003 0.001 HIS A1007 PHE 0.013 0.001 PHE A 40 TYR 0.011 0.001 TYR A 50 ARG 0.003 0.000 ARG A1138 *********************** 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 : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 PRO cc_start: 0.6566 (Cg_exo) cc_final: 0.6227 (Cg_endo) REVERT: A 105 MET cc_start: 0.6875 (ttm) cc_final: 0.5504 (mmm) REVERT: A 157 ARG cc_start: 0.7792 (ttt180) cc_final: 0.7286 (ttt-90) REVERT: A 184 GLU cc_start: 0.8860 (tp30) cc_final: 0.8640 (tp30) REVERT: A 197 MET cc_start: 0.7677 (mmm) cc_final: 0.7402 (mmm) REVERT: A 275 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7938 (mm-30) REVERT: A 299 ILE cc_start: 0.7955 (mt) cc_final: 0.7655 (mt) REVERT: A 326 TYR cc_start: 0.8409 (m-80) cc_final: 0.7736 (m-80) REVERT: A 353 GLU cc_start: 0.8139 (tt0) cc_final: 0.7868 (tt0) REVERT: A 372 LYS cc_start: 0.8501 (ttmm) cc_final: 0.8013 (ttpt) REVERT: A 376 ASP cc_start: 0.7021 (t0) cc_final: 0.6600 (t0) REVERT: A 392 LEU cc_start: 0.8101 (mt) cc_final: 0.7839 (mm) REVERT: A 450 MET cc_start: 0.6573 (mtt) cc_final: 0.6206 (ptp) REVERT: A 555 ASP cc_start: 0.6528 (t0) cc_final: 0.6240 (t0) REVERT: A 564 GLU cc_start: 0.7958 (tt0) cc_final: 0.7372 (tp30) REVERT: A 566 GLU cc_start: 0.8232 (tt0) cc_final: 0.7994 (tp30) REVERT: A 575 LYS cc_start: 0.8239 (tttt) cc_final: 0.7971 (ttpt) REVERT: A 577 ARG cc_start: 0.6935 (ptt180) cc_final: 0.6582 (ptt180) REVERT: A 603 ASP cc_start: 0.8126 (t0) cc_final: 0.7911 (t0) REVERT: A 609 LYS cc_start: 0.8570 (ptpt) cc_final: 0.8345 (pttm) REVERT: A 703 LEU cc_start: 0.8353 (tp) cc_final: 0.7925 (tt) REVERT: A 771 PHE cc_start: 0.7010 (t80) cc_final: 0.6679 (t80) REVERT: A 787 ARG cc_start: 0.7235 (tpp80) cc_final: 0.6877 (ttt90) REVERT: A 811 THR cc_start: 0.6584 (m) cc_final: 0.6325 (p) REVERT: A 820 ASN cc_start: 0.7352 (t0) cc_final: 0.7058 (t0) REVERT: A 857 LEU cc_start: 0.9118 (mt) cc_final: 0.8902 (mm) REVERT: A 858 THR cc_start: 0.7918 (p) cc_final: 0.7715 (p) REVERT: A 884 LEU cc_start: 0.7402 (tp) cc_final: 0.7195 (tp) REVERT: A 909 SER cc_start: 0.8591 (t) cc_final: 0.8348 (m) REVERT: A 925 GLN cc_start: 0.7411 (tt0) cc_final: 0.7113 (mm-40) REVERT: A 942 PHE cc_start: 0.8144 (t80) cc_final: 0.7835 (t80) REVERT: A 959 PHE cc_start: 0.8226 (t80) cc_final: 0.7564 (t80) REVERT: A 971 PHE cc_start: 0.8187 (p90) cc_final: 0.7860 (p90) REVERT: A 986 MET cc_start: 0.8212 (mtp) cc_final: 0.7832 (ttp) REVERT: A 988 VAL cc_start: 0.8046 (t) cc_final: 0.7788 (m) REVERT: A 990 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7581 (tp-100) REVERT: A 997 ASP cc_start: 0.8172 (m-30) cc_final: 0.7946 (m-30) REVERT: A 1021 TYR cc_start: 0.8112 (m-80) cc_final: 0.7713 (m-80) REVERT: A 1115 ILE cc_start: 0.8945 (pp) cc_final: 0.8459 (pp) REVERT: A 1141 SER cc_start: 0.7746 (t) cc_final: 0.7534 (p) REVERT: A 1159 GLU cc_start: 0.8704 (tp30) cc_final: 0.8370 (mm-30) REVERT: A 1263 GLN cc_start: 0.7773 (mm110) cc_final: 0.7184 (tt0) REVERT: A 1267 TYR cc_start: 0.8333 (t80) cc_final: 0.7950 (t80) REVERT: A 1270 MET cc_start: 0.8927 (tpt) cc_final: 0.8688 (mmm) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.2135 time to fit residues: 104.0464 Evaluate side-chains 234 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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: 0.1980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 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: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3036 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= 0.191 Angle : 0.544 7.808 12365 Z= 0.291 Chirality : 0.039 0.220 1428 Planarity : 0.004 0.039 1555 Dihedral : 7.911 86.834 1306 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.95 % Allowed : 12.07 % Favored : 83.97 % 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: -0.16 (0.23), residues: 1148 helix: 0.72 (0.18), residues: 716 sheet: -0.59 (0.65), residues: 73 loop : -1.61 (0.28), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 708 HIS 0.003 0.001 HIS A1257 PHE 0.017 0.001 PHE A 208 TYR 0.015 0.001 TYR A 130 ARG 0.005 0.000 ARG A 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 291 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASN cc_start: 0.7458 (t0) cc_final: 0.7257 (t0) REVERT: A 105 MET cc_start: 0.6613 (ttm) cc_final: 0.5975 (ppp) REVERT: A 118 TYR cc_start: 0.7250 (m-80) cc_final: 0.6888 (m-80) REVERT: A 157 ARG cc_start: 0.7621 (ttt180) cc_final: 0.7404 (ttt-90) REVERT: A 275 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7934 (mm-30) REVERT: A 372 LYS cc_start: 0.8367 (ttmm) cc_final: 0.7880 (ttpt) REVERT: A 450 MET cc_start: 0.6605 (mtt) cc_final: 0.6214 (ptp) REVERT: A 499 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8131 (mt-10) REVERT: A 555 ASP cc_start: 0.6572 (t0) cc_final: 0.6303 (t0) REVERT: A 609 LYS cc_start: 0.8562 (ptpt) cc_final: 0.8326 (pttm) REVERT: A 703 LEU cc_start: 0.8323 (tp) cc_final: 0.8020 (tt) REVERT: A 707 GLU cc_start: 0.8926 (mp0) cc_final: 0.8721 (mp0) REVERT: A 857 LEU cc_start: 0.9036 (mt) cc_final: 0.8797 (mm) REVERT: A 858 THR cc_start: 0.7897 (p) cc_final: 0.7561 (m) REVERT: A 882 GLN cc_start: 0.7701 (tt0) cc_final: 0.7365 (tt0) REVERT: A 909 SER cc_start: 0.8377 (t) cc_final: 0.8157 (m) REVERT: A 959 PHE cc_start: 0.8082 (t80) cc_final: 0.7338 (t80) REVERT: A 986 MET cc_start: 0.8068 (mtp) cc_final: 0.7529 (ttp) REVERT: A 1084 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: A 1151 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8039 (mm-30) REVERT: A 1166 SER cc_start: 0.8496 (m) cc_final: 0.8190 (p) REVERT: A 1261 LEU cc_start: 0.8815 (mt) cc_final: 0.8569 (mt) outliers start: 37 outliers final: 23 residues processed: 270 average time/residue: 0.1911 time to fit residues: 72.2400 Evaluate side-chains 231 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 870 ILE Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 957 PHE Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1088 ASP Chi-restraints excluded: chain A residue 1203 THR Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 556 GLN A 882 GLN ** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.3832 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= 0.198 Angle : 0.519 6.694 12365 Z= 0.271 Chirality : 0.038 0.148 1428 Planarity : 0.003 0.032 1555 Dihedral : 6.782 77.658 1306 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.63 % Allowed : 16.88 % Favored : 79.49 % 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: 0.36 (0.24), residues: 1148 helix: 1.11 (0.19), residues: 730 sheet: -0.01 (0.66), residues: 70 loop : -1.55 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 708 HIS 0.003 0.001 HIS A1112 PHE 0.020 0.001 PHE A 994 TYR 0.019 0.001 TYR A 962 ARG 0.005 0.000 ARG A 359 *********************** 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 265 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 231 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.5931 (ttm) cc_final: 0.5438 (ppp) REVERT: A 118 TYR cc_start: 0.7414 (m-80) cc_final: 0.7154 (m-80) REVERT: A 275 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7966 (mm-30) REVERT: A 450 MET cc_start: 0.6784 (mtt) cc_final: 0.6360 (ptp) REVERT: A 499 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8080 (mt-10) REVERT: A 555 ASP cc_start: 0.6366 (t0) cc_final: 0.6112 (t0) REVERT: A 582 THR cc_start: 0.7827 (m) cc_final: 0.7560 (p) REVERT: A 609 LYS cc_start: 0.8362 (ptpt) cc_final: 0.8081 (pttm) REVERT: A 703 LEU cc_start: 0.8327 (tp) cc_final: 0.8118 (tt) REVERT: A 858 THR cc_start: 0.7942 (p) cc_final: 0.7732 (m) REVERT: A 882 GLN cc_start: 0.7648 (tt0) cc_final: 0.7282 (tt0) REVERT: A 909 SER cc_start: 0.8412 (t) cc_final: 0.8136 (m) REVERT: A 946 GLN cc_start: 0.8249 (mm110) cc_final: 0.8028 (mm-40) REVERT: A 959 PHE cc_start: 0.8027 (t80) cc_final: 0.7281 (t80) REVERT: A 986 MET cc_start: 0.7966 (mtp) cc_final: 0.7400 (ttp) REVERT: A 1115 ILE cc_start: 0.8842 (pp) cc_final: 0.8586 (pp) REVERT: A 1166 SER cc_start: 0.8577 (m) cc_final: 0.8268 (p) REVERT: A 1216 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8190 (mm-30) REVERT: A 1261 LEU cc_start: 0.8826 (mt) cc_final: 0.8528 (mt) outliers start: 34 outliers final: 22 residues processed: 245 average time/residue: 0.1805 time to fit residues: 63.4550 Evaluate side-chains 228 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 893 SER Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1236 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0670 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 70 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 99 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.2256 ------------------------------------------------------------------------------- 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 611 ASN A 725 GLN A1239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9138 Z= 0.138 Angle : 0.484 7.940 12365 Z= 0.247 Chirality : 0.037 0.160 1428 Planarity : 0.003 0.027 1555 Dihedral : 6.525 89.339 1306 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.31 % Allowed : 19.66 % Favored : 77.03 % 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: 0.74 (0.24), residues: 1148 helix: 1.41 (0.19), residues: 727 sheet: 0.20 (0.64), residues: 70 loop : -1.39 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 708 HIS 0.002 0.000 HIS A 398 PHE 0.014 0.001 PHE A 767 TYR 0.014 0.001 TYR A 962 ARG 0.004 0.000 ARG A 359 *********************** 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 265 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.5670 (ttm) cc_final: 0.5230 (ppp) REVERT: A 275 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7926 (mm-30) REVERT: A 304 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6905 (tp) REVERT: A 326 TYR cc_start: 0.8451 (m-10) cc_final: 0.8161 (m-80) REVERT: A 450 MET cc_start: 0.6896 (mtt) cc_final: 0.6466 (ptp) REVERT: A 499 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 858 THR cc_start: 0.7874 (p) cc_final: 0.7593 (m) REVERT: A 882 GLN cc_start: 0.7597 (tt0) cc_final: 0.7313 (tt0) REVERT: A 909 SER cc_start: 0.8395 (t) cc_final: 0.8136 (m) REVERT: A 946 GLN cc_start: 0.8309 (mm110) cc_final: 0.8108 (mm-40) REVERT: A 959 PHE cc_start: 0.7973 (t80) cc_final: 0.7345 (t80) REVERT: A 986 MET cc_start: 0.7931 (mtp) cc_final: 0.7382 (ttp) REVERT: A 1115 ILE cc_start: 0.8569 (pp) cc_final: 0.8251 (pp) REVERT: A 1159 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8128 (mm-30) REVERT: A 1166 SER cc_start: 0.8614 (m) cc_final: 0.8302 (p) REVERT: A 1216 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8221 (mm-30) REVERT: A 1261 LEU cc_start: 0.8817 (mt) cc_final: 0.8543 (mt) outliers start: 31 outliers final: 20 residues processed: 247 average time/residue: 0.1815 time to fit residues: 64.4100 Evaluate side-chains 224 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1088 ASP Chi-restraints excluded: chain A residue 1236 THR 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: 3.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 914 GLN A 990 GLN A1257 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9138 Z= 0.282 Angle : 0.550 7.452 12365 Z= 0.286 Chirality : 0.039 0.145 1428 Planarity : 0.003 0.031 1555 Dihedral : 6.604 83.362 1306 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.91 % Allowed : 19.66 % Favored : 75.43 % 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: 0.67 (0.24), residues: 1148 helix: 1.24 (0.19), residues: 732 sheet: 0.47 (0.64), residues: 70 loop : -1.24 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 212 HIS 0.008 0.001 HIS A 612 PHE 0.013 0.002 PHE A 366 TYR 0.014 0.001 TYR A 444 ARG 0.003 0.000 ARG A1233 *********************** 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 250 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.5660 (ttm) cc_final: 0.5278 (ppp) REVERT: A 156 MET cc_start: 0.8055 (tpp) cc_final: 0.7743 (mpp) REVERT: A 275 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8001 (mm-30) REVERT: A 450 MET cc_start: 0.6946 (mtt) cc_final: 0.6563 (ptp) REVERT: A 707 GLU cc_start: 0.8792 (mp0) cc_final: 0.8505 (mp0) REVERT: A 858 THR cc_start: 0.7883 (p) cc_final: 0.7604 (m) REVERT: A 909 SER cc_start: 0.8457 (t) cc_final: 0.8160 (m) REVERT: A 917 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8024 (tp30) REVERT: A 946 GLN cc_start: 0.8281 (mm110) cc_final: 0.8042 (mm-40) REVERT: A 959 PHE cc_start: 0.7967 (t80) cc_final: 0.7392 (t80) REVERT: A 986 MET cc_start: 0.8106 (mtp) cc_final: 0.7525 (ttp) REVERT: A 1151 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7994 (mm-30) REVERT: A 1159 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 1166 SER cc_start: 0.8635 (m) cc_final: 0.8335 (p) REVERT: A 1216 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8188 (mm-30) outliers start: 46 outliers final: 38 residues processed: 228 average time/residue: 0.1535 time to fit residues: 51.6268 Evaluate side-chains 229 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 886 ASP Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1236 THR Chi-restraints excluded: chain A residue 1266 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 0.0370 chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.4712 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= 0.168 Angle : 0.497 6.812 12365 Z= 0.254 Chirality : 0.037 0.144 1428 Planarity : 0.003 0.030 1555 Dihedral : 6.460 87.497 1306 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.17 % Allowed : 21.47 % Favored : 74.36 % 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: 0.85 (0.24), residues: 1148 helix: 1.38 (0.19), residues: 735 sheet: 0.37 (0.65), residues: 73 loop : -1.18 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 708 HIS 0.001 0.000 HIS A 383 PHE 0.013 0.001 PHE A 767 TYR 0.012 0.001 TYR A 962 ARG 0.003 0.000 ARG A 359 *********************** 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 249 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.5601 (ttm) cc_final: 0.5192 (ppp) REVERT: A 275 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7904 (mm-30) REVERT: A 450 MET cc_start: 0.6941 (mtt) cc_final: 0.6579 (ptp) REVERT: A 707 GLU cc_start: 0.8736 (mp0) cc_final: 0.8427 (mp0) REVERT: A 858 THR cc_start: 0.7866 (p) cc_final: 0.7619 (m) REVERT: A 909 SER cc_start: 0.8453 (t) cc_final: 0.8157 (m) REVERT: A 946 GLN cc_start: 0.8357 (mm110) cc_final: 0.8146 (mm-40) REVERT: A 959 PHE cc_start: 0.7938 (t80) cc_final: 0.7325 (t80) REVERT: A 986 MET cc_start: 0.8044 (mtp) cc_final: 0.7445 (ttp) REVERT: A 1151 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7998 (mm-30) REVERT: A 1159 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8183 (mm-30) REVERT: A 1166 SER cc_start: 0.8626 (m) cc_final: 0.8312 (p) REVERT: A 1216 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8192 (mm-30) outliers start: 39 outliers final: 34 residues processed: 228 average time/residue: 0.1759 time to fit residues: 58.4658 Evaluate side-chains 227 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 193 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 966 HIS Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1088 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1236 THR 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: 1.9990 chunk 81 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 990 GLN A1258 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9138 Z= 0.233 Angle : 0.529 7.009 12365 Z= 0.275 Chirality : 0.038 0.142 1428 Planarity : 0.003 0.031 1555 Dihedral : 6.452 86.541 1306 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.13 % Allowed : 20.73 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1148 helix: 1.34 (0.19), residues: 733 sheet: 0.40 (0.65), residues: 73 loop : -1.13 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 212 HIS 0.002 0.001 HIS A1112 PHE 0.018 0.001 PHE A 994 TYR 0.009 0.001 TYR A1087 ARG 0.003 0.000 ARG A1233 *********************** 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 243 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 195 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 105 MET cc_start: 0.5396 (ttm) cc_final: 0.5100 (ppp) REVERT: A 450 MET cc_start: 0.6856 (mtt) cc_final: 0.6551 (ptp) REVERT: A 456 GLN cc_start: 0.8865 (mp10) cc_final: 0.8581 (mp10) REVERT: A 522 THR cc_start: 0.7540 (m) cc_final: 0.7188 (p) REVERT: A 707 GLU cc_start: 0.8720 (mp0) cc_final: 0.8421 (mp0) REVERT: A 858 THR cc_start: 0.7876 (p) cc_final: 0.7646 (m) REVERT: A 909 SER cc_start: 0.8451 (t) cc_final: 0.8139 (m) REVERT: A 946 GLN cc_start: 0.8359 (mm110) cc_final: 0.8158 (mm-40) REVERT: A 959 PHE cc_start: 0.7964 (t80) cc_final: 0.7380 (t80) REVERT: A 986 MET cc_start: 0.8120 (mtp) cc_final: 0.7714 (ttp) REVERT: A 1151 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7945 (mm-30) REVERT: A 1159 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 1166 SER cc_start: 0.8647 (m) cc_final: 0.8324 (p) REVERT: A 1216 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8203 (mm-30) outliers start: 48 outliers final: 41 residues processed: 221 average time/residue: 0.1771 time to fit residues: 57.0313 Evaluate side-chains 230 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 993 SER Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1088 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1236 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** A1239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9138 Z= 0.196 Angle : 0.515 6.937 12365 Z= 0.266 Chirality : 0.038 0.144 1428 Planarity : 0.003 0.031 1555 Dihedral : 6.374 89.908 1306 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.02 % Allowed : 21.26 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1148 helix: 1.40 (0.19), residues: 733 sheet: 0.46 (0.65), residues: 73 loop : -1.10 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 708 HIS 0.002 0.001 HIS A 518 PHE 0.019 0.001 PHE A 994 TYR 0.010 0.001 TYR A 962 ARG 0.002 0.000 ARG A1233 *********************** 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 251 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 204 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.5347 (ttm) cc_final: 0.5045 (ppp) REVERT: A 450 MET cc_start: 0.6876 (mtt) cc_final: 0.6562 (ptp) REVERT: A 456 GLN cc_start: 0.8809 (mp10) cc_final: 0.8529 (mp10) REVERT: A 522 THR cc_start: 0.7579 (m) cc_final: 0.7235 (p) REVERT: A 707 GLU cc_start: 0.8708 (mp0) cc_final: 0.8380 (mp0) REVERT: A 858 THR cc_start: 0.7924 (p) cc_final: 0.7692 (m) REVERT: A 909 SER cc_start: 0.8447 (t) cc_final: 0.8137 (m) REVERT: A 946 GLN cc_start: 0.8381 (mm110) cc_final: 0.8168 (mm-40) REVERT: A 959 PHE cc_start: 0.7954 (t80) cc_final: 0.7372 (t80) REVERT: A 986 MET cc_start: 0.8079 (mtp) cc_final: 0.7661 (ttp) REVERT: A 1151 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7960 (mm-30) REVERT: A 1159 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8202 (mm-30) REVERT: A 1166 SER cc_start: 0.8682 (m) cc_final: 0.8350 (p) REVERT: A 1216 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8184 (mm-30) outliers start: 47 outliers final: 39 residues processed: 228 average time/residue: 0.1704 time to fit residues: 56.3180 Evaluate side-chains 231 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1023 THR Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1088 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1236 THR 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: 3.9990 chunk 62 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9138 Z= 0.159 Angle : 0.513 6.741 12365 Z= 0.262 Chirality : 0.037 0.147 1428 Planarity : 0.003 0.031 1555 Dihedral : 6.059 81.524 1306 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.17 % Allowed : 22.12 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1148 helix: 1.55 (0.19), residues: 733 sheet: 0.64 (0.65), residues: 78 loop : -1.11 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 708 HIS 0.001 0.000 HIS A1254 PHE 0.017 0.001 PHE A 994 TYR 0.011 0.001 TYR A 962 ARG 0.002 0.000 ARG A 359 *********************** 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 243 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.5203 (ttm) cc_final: 0.4946 (ppp) REVERT: A 304 LEU cc_start: 0.7487 (tt) cc_final: 0.7059 (tp) REVERT: A 450 MET cc_start: 0.6975 (mtt) cc_final: 0.6660 (ptp) REVERT: A 456 GLN cc_start: 0.8821 (mp10) cc_final: 0.8601 (mp10) REVERT: A 519 LYS cc_start: 0.6579 (mtmt) cc_final: 0.6225 (mttp) REVERT: A 707 GLU cc_start: 0.8680 (mp0) cc_final: 0.8364 (mp0) REVERT: A 858 THR cc_start: 0.7872 (p) cc_final: 0.7644 (m) REVERT: A 909 SER cc_start: 0.8442 (t) cc_final: 0.8132 (m) REVERT: A 959 PHE cc_start: 0.7933 (t80) cc_final: 0.7380 (t80) REVERT: A 986 MET cc_start: 0.8074 (mtp) cc_final: 0.7651 (ttp) REVERT: A 1021 TYR cc_start: 0.8274 (m-80) cc_final: 0.8032 (m-80) REVERT: A 1039 GLU cc_start: 0.7602 (mp0) cc_final: 0.6804 (tt0) REVERT: A 1151 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7959 (mm-30) REVERT: A 1159 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8154 (mm-30) REVERT: A 1216 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8215 (mm-30) outliers start: 39 outliers final: 35 residues processed: 223 average time/residue: 0.1749 time to fit residues: 56.4089 Evaluate side-chains 227 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1088 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1236 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9138 Z= 0.188 Angle : 0.527 6.721 12365 Z= 0.270 Chirality : 0.037 0.151 1428 Planarity : 0.003 0.031 1555 Dihedral : 6.050 81.535 1306 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.74 % Allowed : 22.33 % Favored : 73.93 % 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: 1.50 (0.19), residues: 732 sheet: 0.69 (0.64), residues: 78 loop : -1.08 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 708 HIS 0.001 0.001 HIS A 61 PHE 0.016 0.001 PHE A 994 TYR 0.009 0.001 TYR A 962 ARG 0.002 0.000 ARG A1233 ********************** 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 230 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 195 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.5119 (ttm) cc_final: 0.4877 (ppp) REVERT: A 450 MET cc_start: 0.6949 (mtt) cc_final: 0.6637 (ptp) REVERT: A 456 GLN cc_start: 0.8806 (mp10) cc_final: 0.8604 (mp10) REVERT: A 519 LYS cc_start: 0.6600 (mtmt) cc_final: 0.6232 (mttp) REVERT: A 707 GLU cc_start: 0.8678 (mp0) cc_final: 0.8359 (mp0) REVERT: A 909 SER cc_start: 0.8443 (t) cc_final: 0.8137 (m) REVERT: A 959 PHE cc_start: 0.7934 (t80) cc_final: 0.7378 (t80) REVERT: A 986 MET cc_start: 0.8071 (mtp) cc_final: 0.7668 (ttp) REVERT: A 1039 GLU cc_start: 0.7543 (mp0) cc_final: 0.6732 (tt0) REVERT: A 1151 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7959 (mm-30) REVERT: A 1159 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8202 (mm-30) REVERT: A 1216 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8240 (mm-30) outliers start: 35 outliers final: 35 residues processed: 212 average time/residue: 0.1771 time to fit residues: 55.1647 Evaluate side-chains 224 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 189 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 438 GLN Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 890 LEU Chi-restraints excluded: chain A residue 940 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1035 VAL Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1088 ASP Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1227 CYS Chi-restraints excluded: chain A residue 1236 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 438 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098662 restraints weight = 18280.112| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.21 r_work: 0.3127 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9138 Z= 0.155 Angle : 0.522 7.125 12365 Z= 0.266 Chirality : 0.037 0.163 1428 Planarity : 0.003 0.030 1555 Dihedral : 5.907 78.508 1306 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.21 % Allowed : 22.76 % Favored : 74.04 % 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: 1.11 (0.25), residues: 1148 helix: 1.54 (0.19), residues: 731 sheet: 0.78 (0.65), residues: 78 loop : -1.02 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 708 HIS 0.001 0.000 HIS A 612 PHE 0.016 0.001 PHE A 851 TYR 0.010 0.001 TYR A 962 ARG 0.002 0.000 ARG A1233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2267.48 seconds wall clock time: 41 minutes 10.02 seconds (2470.02 seconds total)